From nih-image-request@io.ece.drexel.edu Wed Sep 9 10:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id KAA20626; Wed, 9 Sep 1998 10:21:21 -0400 (EDT) Resent-Date: Wed, 9 Sep 1998 10:21:21 -0400 (EDT) Message-Id: In-Reply-To: <81DAE9E2114@rna.bio.mq.edu.au> Mime-Version: 1.0 Date: Wed, 9 Sep 1998 09:04:13 -0500 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: Transferring ROIs to a new image Resent-Message-ID: <"aikOt3.0.rY4.Uhezr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/324 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3296 Status: RO >>Date: Tue, 8 Sep 1998 09:06:15 -0400 >>To: nih-image@io.ece.drexel.edu >>From: Laird Bloom >> I'd like to write a macro that allows me to draw a freehand ROI in >>an image (e.g., the outline of rhodamine-stained cells), open another image >>(e.g., the FITC channel image of the same cells), and count particles >>within the same ROI in the second image. I'd like it to be able to analyze >>multiple ROIs within the same image, but also to keep the data for each ROI >>separate. In the NIH Image archives, I saw a suggestion for copying the >>two images to a stack, then toggling back and forth between slices to do >>this analysis. Has anyone written such a macro using this or another >>algorithm? >>Thanks, >>Laird Bloom >>MIT Center for Cancer Research > >There are a number of approachs available to this including >the stack method you mention, >the mapping method suggested by Jonathan Nissanov, >particular applications as in Doug Morris's site, etc but >the simplest most useful method is often overlooked, >probably because this specific application is not explicitly mentioned in the >manual. > >The macro restoreRoi or the restore selection (analyse Menu) will >restore the previously active selection to the current image >(even if a compound ROI selection made using control/option keys). >The trick is that the restoration takes effect on the current image even >if the >ROI was active on a different but previously active image >regardless of whether the previous image associated with the ROI was of the >same dimensions or not. >It is located in the same position relative to 0,0 ie topleft. >Thus a ROI established on an image >(a roi can be associated with any/each open window) >can be transferred from that image to another, simply by: > > activating the image carrying the ROI; > activate the image to receive the ROI; > invoke restore selection (analyse Menu) > >or > >selectPic(pid2);killRoi; >selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2} > >In addition, you can >selectPic(pid1); >SetSaveAs('Outline');saveas('aParticularROI'); >selectPic(pid2);open('aParticularROI'); >if you want to have a disk record of the ROI. > I agree that the restoreRoi is the simplest approach. For it to work, though, you must delineate one ROI, analyze then delineate the next one and analyze and so forth. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Wed Sep 9 11:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA28554; Wed, 9 Sep 1998 11:43:21 -0400 (EDT) Resent-Date: Wed, 9 Sep 1998 11:43:21 -0400 (EDT) Message-ID: <35F6A787.EAB1C51D@netmatters.co.uk> Date: Wed, 09 Sep 1998 16:06:35 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"H_MXh2.0.6T6.cqfzr"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/325 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1451 Status: O To save and recall multiple ROI of any form you could try the following. Drop a folder called 'ROI Folder' into you preference folder (or anywhere else as long as you modify the path name appropriately) and use as many repeats of the following you require ROI1, ROI2 etc. To apply the ROI in your macro call the procedures ApplyROI1, ApplyROI2 etc....... procedure ApplyROI1; begin Open(GetPath('pref'),'ROI Folder:ROI1'); end; macro '[1] Set Region of Interest 1'; begin SetSaveAs('Outline'); SaveAs(GetPath('pref'),'ROI Folder:ROI'); end; Jeremy Laird Bloom wrote: > Hi, > I'd like to write a macro that allows me to draw a freehand ROI in > an image (e.g., the outline of rhodamine-stained cells), open another image > (e.g., the FITC channel image of the same cells), and count particles > within the same ROI in the second image. I'd like it to be able to analyze > multiple ROIs within the same image, but also to keep the data for each ROI > separate. In the NIH Image archives, I saw a suggestion for copying the > two images to a stack, then toggling back and forth between slices to do > this analysis. Has anyone written such a macro using this or another > algorithm? > Thanks, > Laird Bloom > MIT Center for Cancer Research -- *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-request@io.ece.drexel.edu Thu Sep 10 03:25 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA21179; Thu, 10 Sep 1998 03:25:51 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 03:25:51 -0400 (EDT) Message-Id: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr> X-Sender: leguer@messv2.univ-pau.fr X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Date: Thu, 10 Sep 1998 09:18:06 +0100 To: nih-image@io.ece.drexel.edu From: Yves LE GUER Subject: spatio-temporal image Resent-Message-ID: <"U6w7Y2.0.ir4.Lntzr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/326 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 778 Status: O Hi all, I'm started to use image PC with the Scion CG-7 frame grabber and a Sony color video camera. I'd like to write a macro that allows me to make a spatio-temporal image by recording the same successive selected vertical (or horizontal) line and choosing time step beetwen the capture of two lines and the number of lines in order to reconstruct another image. Has anyone written such a macro for this ? Thanks, _________________________________________________________________________ Yves Le Guer Laboratoire de Transferts Thermiques - UPPA Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 E-mail : leguer@univ-pau.fr From nih-image-d-request@io.ece.drexel.edu Thu Sep 10 03:47 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id DAA23408; Thu, 10 Sep 1998 03:47:22 -0400 (EDT) Date: Thu, 10 Sep 1998 03:47:22 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809100747.DAA23408@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #58 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/58 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6949 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 58 Today's Topics: Re: Transferring ROIs to a new image [ Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image Message-Id: Content-Type: text/plain; charset="us-ascii" >>Date: Tue, 8 Sep 1998 09:06:15 -0400 >>To: nih-image@io.ece.drexel.edu >>From: Laird Bloom >> I'd like to write a macro that allows me to draw a freehand ROI in >>an image (e.g., the outline of rhodamine-stained cells), open another image >>(e.g., the FITC channel image of the same cells), and count particles >>within the same ROI in the second image. I'd like it to be able to analyze >>multiple ROIs within the same image, but also to keep the data for each ROI >>separate. In the NIH Image archives, I saw a suggestion for copying the >>two images to a stack, then toggling back and forth between slices to do >>this analysis. Has anyone written such a macro using this or another >>algorithm? >>Thanks, >>Laird Bloom >>MIT Center for Cancer Research > >There are a number of approachs available to this including >the stack method you mention, >the mapping method suggested by Jonathan Nissanov, >particular applications as in Doug Morris's site, etc but >the simplest most useful method is often overlooked, >probably because this specific application is not explicitly mentioned in the >manual. > >The macro restoreRoi or the restore selection (analyse Menu) will >restore the previously active selection to the current image >(even if a compound ROI selection made using control/option keys). >The trick is that the restoration takes effect on the current image even >if the >ROI was active on a different but previously active image >regardless of whether the previous image associated with the ROI was of the >same dimensions or not. >It is located in the same position relative to 0,0 ie topleft. >Thus a ROI established on an image >(a roi can be associated with any/each open window) >can be transferred from that image to another, simply by: > > activating the image carrying the ROI; > activate the image to receive the ROI; > invoke restore selection (analyse Menu) > >or > >selectPic(pid2);killRoi; >selectPic(pid1);selectPic(pid2);restoreRoi;{transfers ROI from pid1 to 2} > >In addition, you can >selectPic(pid1); >SetSaveAs('Outline');saveas('aParticularROI'); >selectPic(pid2);open('aParticularROI'); >if you want to have a disk record of the ROI. > I agree that the restoreRoi is the simplest approach. For it to work, though, you must delineate one ROI, analyze then delineate the next one and analyze and so forth. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Wed, 09 Sep 1998 16:06:35 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Transferring ROIs to a new image Message-ID: <35F6A787.EAB1C51D@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit To save and recall multiple ROI of any form you could try the following. Drop a folder called 'ROI Folder' into you preference folder (or anywhere else as long as you modify the path name appropriately) and use as many repeats of the following you require ROI1, ROI2 etc. To apply the ROI in your macro call the procedures ApplyROI1, ApplyROI2 etc....... procedure ApplyROI1; begin Open(GetPath('pref'),'ROI Folder:ROI1'); end; macro '[1] Set Region of Interest 1'; begin SetSaveAs('Outline'); SaveAs(GetPath('pref'),'ROI Folder:ROI'); end; Jeremy Laird Bloom wrote: > Hi, > I'd like to write a macro that allows me to draw a freehand ROI in > an image (e.g., the outline of rhodamine-stained cells), open another image > (e.g., the FITC channel image of the same cells), and count particles > within the same ROI in the second image. I'd like it to be able to analyze > multiple ROIs within the same image, but also to keep the data for each ROI > separate. In the NIH Image archives, I saw a suggestion for copying the > two images to a stack, then toggling back and forth between slices to do > this analysis. Has anyone written such a macro using this or another > algorithm? > Thanks, > Laird Bloom > MIT Center for Cancer Research -- *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html ------------------------------ Date: Thu, 10 Sep 1998 09:18:06 +0100 From: Yves LE GUER To: nih-image@io.ece.drexel.edu Subject: spatio-temporal image Message-Id: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr> Content-Type: text/plain; charset="us-ascii" Hi all, I'm started to use image PC with the Scion CG-7 frame grabber and a Sony color video camera. I'd like to write a macro that allows me to make a spatio-temporal image by recording the same successive selected vertical (or horizontal) line and choosing time step beetwen the capture of two lines and the number of lines in order to reconstruct another image. Has anyone written such a macro for this ? Thanks, _________________________________________________________________________ Yves Le Guer Laboratoire de Transferts Thermiques - UPPA Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 E-mail : leguer@univ-pau.fr -------------------------------- End of nih-image-d Digest V98 Issue #58 *************************************** From nih-image-request@io.ece.drexel.edu Thu Sep 10 12:41 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA10857; Thu, 10 Sep 1998 12:40:27 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 12:40:27 -0400 (EDT) X-Sender: cozturk@tempest.bme-mri.jhu.edu Message-Id: In-Reply-To: <1.5.4.32.19980910081806.008f1ff0@messv2.univ-pau.fr> Mime-Version: 1.0 Date: Thu, 10 Sep 1998 12:27:10 -0400 To: nih-image@io.ece.drexel.edu From: Cengizhan Ozturk Subject: Re: spatio-temporal image Resent-Message-ID: <"wwRt12.0.vL2.5t_zr"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/327 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1195 Status: O >Hi all, > >I'm started to use image PC with the Scion CG-7 frame grabber and a Sony >color video camera. >I'd like to write a macro that allows me to make a spatio-temporal image by >recording the same successive selected vertical (or horizontal) line and >choosing time step beetwen the capture of two lines and the number of lines >in order to reconstruct another image. >Has anyone written such a macro for this ? > >Thanks, >_________________________________________________________________________ > >Yves Le Guer >Laboratoire de Transferts Thermiques - UPPA >Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE >Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) >Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 >E-mail : leguer@univ-pau.fr Just capture as usual. (as big fat images!) Put them in a stack. Reslice them along vertical and horizontal lines. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= From nih-image-request@io.ece.drexel.edu Thu Sep 10 13:28 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA14138; Thu, 10 Sep 1998 13:27:39 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 13:27:39 -0400 (EDT) X-Sender: mathias@ruby.unibe.ch Message-Id: Mime-Version: 1.0 Date: Thu, 10 Sep 1998 19:20:16 +0100 To: nih-image@io.ece.drexel.edu From: mathias@mpi.unibe.ch (mathias rickli) Subject: adjacent image alignment Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id NAA13213 Resent-Message-ID: <"VqjvR2.0.iE3.zb0-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/328 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 830 Status: O I am rather new to the image analysis world and I have two questions. 1) does anyone work on microstructure analysis of heavy clay ceramics? 2) has anyone written a macro to join adjacent, slightly overlapping images automatically? My idea is to transform 16 (4x4) or more grayscale SEM images from polished sections of ceramics into binary Tiff files and then to merge them together in one file in order to apply object (pore) size measurements. I wonder if this way of image treatment exeeds the capacity of even high performance Mac plattforms. thanks for answering cheers mathias Mathias Rickli [dipl. Min.] Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 home: Freiestrasse 35 CH-3012 Bern Switzerland Tel: +41-31-302-9564 From nih-image-request@io.ece.drexel.edu Thu Sep 10 16:25 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id QAA13515; Thu, 10 Sep 1998 16:25:06 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 16:25:06 -0400 (EDT) X-Sender: cozturk@tempest.bme-mri.jhu.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 10 Sep 1998 16:03:34 -0400 To: nih-image@io.ece.drexel.edu From: Cengizhan Ozturk Subject: Re: adjacent image alignment Resent-Message-ID: <"t_U0a3.0.r36.-13-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/329 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 6645 Status: O >I am rather new to the image analysis world and I have two questions. >1) does anyone work on microstructure analysis of heavy clay ceramics? >2) has anyone written a macro to join adjacent, slightly overlapping images >automatically? >My idea is to transform 16 (4x4) or more grayscale SEM images from polished >sections of ceramics into binary Tiff files and then to merge them together >in one file in order to apply object (pore) size measurements. I wonder if >this way of image treatment exeeds the capacity of even high performance >Mac plattforms. >thanks for answering > >cheers >mathias ----------------------------------------------------------------- Hi, A little search on mosaic and image puzzle dig up this from my humble "the-best-of-NIH-Image" database. Have fun with it. Cengizhan P.S. My Align will be a bad choice for partial to partial alignment. ____________________ included text below ____________________ On Thu, 25 Jul 1996 magyar@cell.biol.ethz.ch wrote: > Dear Imagers > > In our group, we are working among others with the morphological analysis > of peripheral nerve cross sections. Now, since we want to analyse the > different parameters of single axons (a more or less regular round shape) > and their surrounding myelin sheats (looks like a dark ring around the > axon), I wrote a macro to measure everything as efficient as possible. > The point is, that we collect the pictures with a CCD camera at a certain > magnification. If we take a magnification good enought to have a resolution > of also small axons (63x), then only few (appr. 20) axons are within the > field of view. If we lower the magnification (20x or 40x), then the > resolution of the collected picts is not good enought to make reliable > analysis of all axonal and myelin parameters. > Now I wrote an other macro, which enables one to fit a new overlapping view > into an other allready existing pict. This works astounishingly good, so > that you can nearby not see any transitions. This works by selecting > certain structures while thresholding in one of the pict and then selecting > the same stucture at the same threshold level in the other pict (all picts > are taken in the same angle of view). Using this, you can puzzle together a > pict of originally e.g. 20 or even more CCD camera gained pictures (only > limitation is your RAM). > I am wondering now, whether there are any macros or algorhytms doing the > same job automaticaly e.g. by pattern recognition or so. Could this work > perhaps also by comparison of histogramm values, since the picts are > oriented the same way? > > Thanks for thinking... > > Josef Peter Magyar > > >******************************************************************************* >> * _/_/_/_/_/_/_/_/_/ _/ Eidgenoessische Technische Hochschule >Zuerich * > * _/ _/ _/ _/ Swiss Federal Institute of Technology >Zurich * > * _/_/_/ _/ _/_/_/_/ Ecole polytechnique federale de Zurich >* > * _/ _/ _/ _/ Politecnico federale di Zurigo >* > * _/_/_/_/ _/ _/ _/ >* > * >* > >*-----------------------------------------------------------------------------* >> * Josef Peter Magyar, Ph.D. | Tel: +41/1/633 34 91 >* > * Institute of Cell Biology | +41/1/633 34 92 >* > * Swiss Federal Institute of Technology | Fax: +41/1/633 10 69 >* > * ETH-Hoenggerberg HPM E25 | >* > * CH-8093 Zurich, Switzerland | eMail: >magyar@cell.biol.ethz.ch * > * | >* > >******************************************************************************* >> There are at least two other programs available to accomplish this task -- S. Ott wrote one, which has its own webpage and everything, and I have one at a beta-test stage. Re the first: QUOTE: You might be interested to know that I have released "AutoMatch" a couple of weeks ago which does exactly the same job in NIH Image. Well it doesn't give you a scaled-down map which seems very useful to me. On the other hand, it gives you a full "postview" of the previously captured frame. This 1:1 view is very useful for moving the stage during live acquisition. The algorithm can handle frames of any size, by trading accurracy of alignment versus frame size (of course it does not handle 3000x2000 frames too well...). AutoMatch has a full-featured graphical user interface (not just those basic dialogs the macro language provides) and is written entirely in NIH macro code (yes, you can do that...). Full documentation is included with the package, and a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a Desktop Microcomputer) For more information see: http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html ----------------------------------------------------- Swidbert R. OTT, MSc Department of Neurobiology Institute of Zoology University of Graz, Austria/Europe voice: +43 316 380 5602, 5702, 5282 fax: 380 9875 email: ott@balu.kfunigraz.ac.at WWW: http://wwwzoo.kfunigraz.ac.at/~swidi/home.html ----------------------------------------------------- ENDQUOTE The other approach is mine, which isn't as mature but functions well enough to try out. I call it "Pan-and-Paint", as the goal is to be able to just pan the microscopy stage and paint an image as you go on a video monitor. Pros: 10 seconds per image, builds a real-time montage as you go, works up to a composite of 4x4 times 640x480 greyscale, does the time-consuming work in batch mode after the operator is done collecting the images -- manual override for manual aligning a tricky image is nifty (IMHO) Cons: beta-stage so it changes (improves) more or less weekly. Batch mode is pretty verbose (but ignorable). No web page (yet). The current shareware executable, documentation, and a worked example with stack of actual biomedical images (eg, immunohistochemically stained tissue) can be obtained by anonymous ftp from host "141.214.135.241", in directory "/pub/programs/" which has three equivalent versions -- a macbinary folder, a stuffed version, and a stuffed and binhexed version. Wade Schuette University of Michigan schuette@umich.edu -------------------- Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= From nih-image-request@io.ece.drexel.edu Thu Sep 10 17:19 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA17573; Thu, 10 Sep 1998 17:18:31 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 17:18:31 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Thu, 10 Sep 1998 14:03:00 -0700 To: nih-image@io.ece.drexel.edu From: Geno Pawlak Subject: Image Capture for PC Resent-Message-ID: <"6elpQ3.0.n04.yx3-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/330 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 924 Status: O Hello, I'm new to the list so forgive me if this has already been discussed - I'm interested in capturing grayscale images realtime (30fps) to RAM on a PC, most likely from a Hi 8 VCR. I've worked with a Scion LG-3 card on a Mac before and it worked wonderfully, however, I've moved to a new job and have to work with a PC now. Does anyone have any experience with this card on a PC? Capturing from a VCR? On the Mac, the LG-3 would occassionally miss a frame, but this wasn't a problem. In addition I would like to use my NIH Image macros on the PC, with Scion's program - will this work ok? Any other suggestions for framegrabbing hardware are welcome. Thanks, Geno ------------------------------------------- Geno Pawlak University of Washington School of Oceanography Box 357940 Seattle, WA 98195-7940 phone: (206) 543-8543 e-mail: gpawlak@ocean.washington.edu ------------------------------------------- From nih-image-request@io.ece.drexel.edu Thu Sep 10 19:41 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id TAA27663; Thu, 10 Sep 1998 19:41:22 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 19:41:22 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Fri, 11 Sep 1998 9:34:07 GMT+1000 Subject: Re: spatio-temporal image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <84CB54A52E0@rna.bio.mq.edu.au> Resent-Message-ID: <"Gj0cm1.0.IZ6.l56-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/331 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1962 Status: O >Date: Thu, 10 Sep 1998 12:27:10 -0400 >To: nih-image@io.ece.drexel.edu >From: Cengizhan Ozturk >Subject: Re: spatio-temporal image >> >>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony >>color video camera. >>I'd like to write a macro that allows me to make a spatio-temporal image by >>recording the same successive selected vertical (or horizontal) line and >>choosing time step beetwen the capture of two lines and the number of lines >>in order to reconstruct another image. >>Has anyone written such a macro for this ? >> >>Thanks, >>_________________________________________________________________________ >> >>Yves Le Guer >>Laboratoire de Transferts Thermiques - UPPA >>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE >>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) >>Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 >>E-mail : leguer@univ-pau.fr > >Just capture as usual. (as big fat images!) >Put them in a stack. >Reslice them along vertical and horizontal lines. > >Dr. Cengizhan Ozturk >======================= >Johns Hopkins University - Medical Imaging Lab >407 Traylor Building / 720 Rutland Av. >Baltimore, MD 21205-2196 >Phone: (410) 614 5292 >Fax: (410) 502 6915 >E-mail: cozturk@mri.jhu.edu >http://www.mri.jhu.edu/~cozturk/ >======================= Cengizhan, your reply "Just capture as usual. (as big fat images!)" etc is right on the mark but does also suggest that Yves Le Guer may have missed the obvious ie: "capture" & "make movie" will operate on selections (including long thin rectangular selections either horizontal or vertical) which will allow much faster operation and avoid RAM shortages. Stacks can now be 5000 frames in lastest Image versions. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Sep 10 20:23 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA00781; Thu, 10 Sep 1998 20:23:09 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 20:23:09 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Fri, 11 Sep 1998 10:15:28 GMT+1000 Subject: Re: adjacent image alignment Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <84D65615701@rna.bio.mq.edu.au> Resent-Message-ID: <"an15n1.0.CI7.qh6-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/332 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2462 Status: O >Date: Thu, 10 Sep 1998 16:03:34 -0400 > >>I am rather new to the image analysis world and I have two questions. >>1) does anyone work on microstructure analysis of heavy clay ceramics? >>2) has anyone written a macro to join adjacent, slightly overlapping images >>automatically? >>My idea is to transform 16 (4x4) or more grayscale SEM images from polished >>sections of ceramics into binary Tiff files and then to merge them together >>in one file in order to apply object (pore) size measurements. I wonder if >>this way of image treatment exeeds the capacity of even high performance >>Mac plattforms. >>thanks for answering >> >>cheers >>mathias >----------------------------------------------------------------- Cengizhan's very comprehensive reply to this question didn't make direct reference to an extremely useful mechanism in NIH-Image which is applicable in this context, particularly for those new to Image and not everyone would followup the web and macro refererence detail. (I have been unable to raise 141.214.135.241. It may be off "overnight" :-) "Manual" procedures are commonly sufficient particularly for tiled montages where orientation is maintained (eg by microscope stage). The "paste" with "XOR" option is a very powerful tool in this context. Make a new image large enough to accomodate the montage (The old restriction on maximum image width of 4096 has been removed). copy and paste the topleft or some other starting component activate "Show Paste Control(Windows menu" pan (if necessary) so that next paste will be roughly central in the window. copy and paste next component with an overlap. choose "XOR" option in Paste Control Window. pasted ROI can be moved by mouse or, more importantly, by arrow keys till it is accurately placed. "XOR" will make overlapping alignment very apparent as both layers can be readily seen until overlap is accurate. If overlap is identical then the overlap will suddenly go to white (all zeros). The paste option can then be switched to "Replace" or (else the paste "Undo"ne so that the ROI can then be restoreRoi'd, giving accurate position of montage component) This manual procedure can be quite quick and is accurate to the pixel (if the overlaps are properly oriented and undistorted). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Sep 10 21:09 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id VAA04174; Thu, 10 Sep 1998 21:09:22 -0400 (EDT) Resent-Date: Thu, 10 Sep 1998 21:09:22 -0400 (EDT) From: DrJohnRuss@aol.com Message-ID: <5bf7dced.35f8745f@aol.com> Date: Thu, 10 Sep 1998 20:52:47 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: adjacent image alignment Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"j6VhX.0.Aj.5I7-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/333 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1238 Status: O In a message dated 9/10/98 5:22:01 PM, Mathias Rickli [dipl. Min.] wrote: >2) has anyone written a macro to join adjacent, slightly overlapping images >automatically? > >My idea is to transform 16 (4x4) or more grayscale SEM images from polished >sections of ceramics into binary Tiff files and then to merge them together >in one file in order to apply object (pore) size measurements. I wonder if >this way of image treatment exeeds the capacity of even high performance >Mac plattforms. We have a program (Windows NT, not Mac, although it could be recompiled fairly easily) that will take any array of tiffs - mine are usually 1000x1000 pixels or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on each side and seamlessly stitch them together using cross-correlation in the overlap regions to determine the best alignment (including rotation). It isn't fast - a job like the one above takes several hours - but the results are spectacular. We primarily use it on AFM images, occasionally on SEM, and it has also been used on aerial reconnaissance photos. The program is not presently available to others but if there is enough demand we might consider working out some arrangement for its use. John Russ From nih-image-request@io.ece.drexel.edu Fri Sep 11 05:40 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA15389; Fri, 11 Sep 1998 05:40:13 -0400 (EDT) Resent-Date: Fri, 11 Sep 1998 05:40:13 -0400 (EDT) Message-ID: <35F8FA9A.A3B8EC5B@netmatters.co.uk> Date: Fri, 11 Sep 1998 10:25:34 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"AF8YY2.0.TO3.rnE-r"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/334 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 3423 Status: O Cengizhan Ozturk wrote: > >I am rather new to the image analysis world and I have two questions. > >1) does anyone work on microstructure analysis of heavy clay ceramics? > >2) has anyone written a macro to join adjacent, slightly overlapping images > >automatically? > >My idea is to transform 16 (4x4) or more grayscale SEM images from polished > >sections of ceramics into binary Tiff files and then to merge them together > >in one file in order to apply object (pore) size measurements. I wonder if > >this way of image treatment exeeds the capacity of even high performance > >Mac plattforms. > >thanks for answering > > > >cheers > >mathias > ----------------------------------------------------------------- > Hi, > > A little search on mosaic and image puzzle dig up this from my humble > "the-best-of-NIH-Image" database. > Have fun with it. > > Cengizhan > > AutoMatch has a full-featured graphical user interface (not just those basic > dialogs the macro language provides) and is written entirely in NIH macro code > (yes, you can do that...). Full documentation is included with the package, > and > a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High > Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a > Desktop Microcomputer) > > For more information see: > http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html > ----------------------------------------------------- > Swidbert R. OTT, MSc > Department of Neurobiology > Institute of Zoology > University of Graz, Austria/Europe > voice: +43 316 380 5602, 5702, 5282 > fax: 380 9875 > > > -------------------- > > Dr. Cengizhan Ozturk > ======================= > Johns Hopkins University - Medical Imaging Lab > 407 Traylor Building / 720 Rutland Av. > Baltimore, MD 21205-2196 > Phone: (410) 614 5292 > Fax: (410) 502 6915 > E-mail: cozturk@mri.jhu.edu > http://www.mri.jhu.edu/~cozturk/ > ======================= I can personally vouch for Swidbert R. OTT's Automatch Macro. It run well under both NIH and Object image, is remarkable fast and accurate. I've used it in conjunction with a 7100/80 AV to mosaic images up to 90 frames at a time. You need allow 10-15% overlap on tissue sections, in less detailed images you will need to allow for more overlap. The hardest bit if setting up your stage sensitivity so that it does not drift but allows you fine control at the same time. Even if the stage does drift ,Automatch will still work if there is enough overlap. It is very ram hungry: on my machine, which has 80 MB of physical RAM, 60 -70 MB RAM to NIH and adjusting your undo and clipboard buffer size to the size the image your going to create is ok for 20 MB images, i.e. you will need a lot of RAM. It works well under both Ram Doubler or VM, although you should not give NIH more than your physical ram. The only disadvantage is if you have already captured the images, Automatch does both the capturing and assembly, it will not assemble independently acquired images. The reference for the paper is ........ Ott, SR (1997) Acquisition of High-Resolution Digital Images in Video Microscopy: Automated Image Mosaicking on a Desktop Microcomputer. Microscopy Research and Technique 38: 335-339. *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-d-request@io.ece.drexel.edu Fri Sep 11 05:43 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id FAA15767; Fri, 11 Sep 1998 05:43:10 -0400 (EDT) Date: Fri, 11 Sep 1998 05:43:10 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809110943.FAA15767@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #59 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/59 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 21759 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 59 Today's Topics: Re: spatio-temporal image [ Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: spatio-temporal image Message-Id: Content-Type: text/plain; charset="us-ascii" >Hi all, > >I'm started to use image PC with the Scion CG-7 frame grabber and a Sony >color video camera. >I'd like to write a macro that allows me to make a spatio-temporal image by >recording the same successive selected vertical (or horizontal) line and >choosing time step beetwen the capture of two lines and the number of lines >in order to reconstruct another image. >Has anyone written such a macro for this ? > >Thanks, >_________________________________________________________________________ > >Yves Le Guer >Laboratoire de Transferts Thermiques - UPPA >Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE >Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) >Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 >E-mail : leguer@univ-pau.fr Just capture as usual. (as big fat images!) Put them in a stack. Reslice them along vertical and horizontal lines. Cengizhan Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= ------------------------------ Date: Thu, 10 Sep 1998 19:20:16 +0100 From: mathias@mpi.unibe.ch (mathias rickli) To: nih-image@io.ece.drexel.edu Subject: adjacent image alignment Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit I am rather new to the image analysis world and I have two questions. 1) does anyone work on microstructure analysis of heavy clay ceramics? 2) has anyone written a macro to join adjacent, slightly overlapping images automatically? My idea is to transform 16 (4x4) or more grayscale SEM images from polished sections of ceramics into binary Tiff files and then to merge them together in one file in order to apply object (pore) size measurements. I wonder if this way of image treatment exeeds the capacity of even high performance Mac plattforms. thanks for answering cheers mathias Mathias Rickli [dipl. Min.] Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 home: Freiestrasse 35 CH-3012 Bern Switzerland Tel: +41-31-302-9564 ------------------------------ Date: Thu, 10 Sep 1998 16:03:34 -0400 From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-Id: Content-Type: text/plain; charset="us-ascii" >I am rather new to the image analysis world and I have two questions. >1) does anyone work on microstructure analysis of heavy clay ceramics? >2) has anyone written a macro to join adjacent, slightly overlapping images >automatically? >My idea is to transform 16 (4x4) or more grayscale SEM images from polished >sections of ceramics into binary Tiff files and then to merge them together >in one file in order to apply object (pore) size measurements. I wonder if >this way of image treatment exeeds the capacity of even high performance >Mac plattforms. >thanks for answering > >cheers >mathias ----------------------------------------------------------------- Hi, A little search on mosaic and image puzzle dig up this from my humble "the-best-of-NIH-Image" database. Have fun with it. Cengizhan P.S. My Align will be a bad choice for partial to partial alignment. ____________________ included text below ____________________ On Thu, 25 Jul 1996 magyar@cell.biol.ethz.ch wrote: > Dear Imagers > > In our group, we are working among others with the morphological analysis > of peripheral nerve cross sections. Now, since we want to analyse the > different parameters of single axons (a more or less regular round shape) > and their surrounding myelin sheats (looks like a dark ring around the > axon), I wrote a macro to measure everything as efficient as possible. > The point is, that we collect the pictures with a CCD camera at a certain > magnification. If we take a magnification good enought to have a resolution > of also small axons (63x), then only few (appr. 20) axons are within the > field of view. If we lower the magnification (20x or 40x), then the > resolution of the collected picts is not good enought to make reliable > analysis of all axonal and myelin parameters. > Now I wrote an other macro, which enables one to fit a new overlapping view > into an other allready existing pict. This works astounishingly good, so > that you can nearby not see any transitions. This works by selecting > certain structures while thresholding in one of the pict and then selecting > the same stucture at the same threshold level in the other pict (all picts > are taken in the same angle of view). Using this, you can puzzle together a > pict of originally e.g. 20 or even more CCD camera gained pictures (only > limitation is your RAM). > I am wondering now, whether there are any macros or algorhytms doing the > same job automaticaly e.g. by pattern recognition or so. Could this work > perhaps also by comparison of histogramm values, since the picts are > oriented the same way? > > Thanks for thinking... > > Josef Peter Magyar > > >******************************************************************************* >> * _/_/_/_/_/_/_/_/_/ _/ Eidgenoessische Technische Hochschule >Zuerich * > * _/ _/ _/ _/ Swiss Federal Institute of Technology >Zurich * > * _/_/_/ _/ _/_/_/_/ Ecole polytechnique federale de Zurich >* > * _/ _/ _/ _/ Politecnico federale di Zurigo >* > * _/_/_/_/ _/ _/ _/ >* > * >* > >*-----------------------------------------------------------------------------* >> * Josef Peter Magyar, Ph.D. | Tel: +41/1/633 34 91 >* > * Institute of Cell Biology | +41/1/633 34 92 >* > * Swiss Federal Institute of Technology | Fax: +41/1/633 10 69 >* > * ETH-Hoenggerberg HPM E25 | >* > * CH-8093 Zurich, Switzerland | eMail: >magyar@cell.biol.ethz.ch * > * | >* > >******************************************************************************* >> There are at least two other programs available to accomplish this task -- S. Ott wrote one, which has its own webpage and everything, and I have one at a beta-test stage. Re the first: QUOTE: You might be interested to know that I have released "AutoMatch" a couple of weeks ago which does exactly the same job in NIH Image. Well it doesn't give you a scaled-down map which seems very useful to me. On the other hand, it gives you a full "postview" of the previously captured frame. This 1:1 view is very useful for moving the stage during live acquisition. The algorithm can handle frames of any size, by trading accurracy of alignment versus frame size (of course it does not handle 3000x2000 frames too well...). AutoMatch has a full-featured graphical user interface (not just those basic dialogs the macro language provides) and is written entirely in NIH macro code (yes, you can do that...). Full documentation is included with the package, and a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a Desktop Microcomputer) For more information see: http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html ----------------------------------------------------- Swidbert R. OTT, MSc Department of Neurobiology Institute of Zoology University of Graz, Austria/Europe voice: +43 316 380 5602, 5702, 5282 fax: 380 9875 email: ott@balu.kfunigraz.ac.at WWW: http://wwwzoo.kfunigraz.ac.at/~swidi/home.html ----------------------------------------------------- ENDQUOTE The other approach is mine, which isn't as mature but functions well enough to try out. I call it "Pan-and-Paint", as the goal is to be able to just pan the microscopy stage and paint an image as you go on a video monitor. Pros: 10 seconds per image, builds a real-time montage as you go, works up to a composite of 4x4 times 640x480 greyscale, does the time-consuming work in batch mode after the operator is done collecting the images -- manual override for manual aligning a tricky image is nifty (IMHO) Cons: beta-stage so it changes (improves) more or less weekly. Batch mode is pretty verbose (but ignorable). No web page (yet). The current shareware executable, documentation, and a worked example with stack of actual biomedical images (eg, immunohistochemically stained tissue) can be obtained by anonymous ftp from host "141.214.135.241", in directory "/pub/programs/" which has three equivalent versions -- a macbinary folder, a stuffed version, and a stuffed and binhexed version. Wade Schuette University of Michigan schuette@umich.edu -------------------- Dr. Cengizhan Ozturk ======================= Johns Hopkins University - Medical Imaging Lab 407 Traylor Building / 720 Rutland Av. Baltimore, MD 21205-2196 Phone: (410) 614 5292 Fax: (410) 502 6915 E-mail: cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk/ ======================= ------------------------------ Date: Thu, 10 Sep 1998 14:03:00 -0700 From: Geno Pawlak To: nih-image@io.ece.drexel.edu Subject: Image Capture for PC Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, I'm new to the list so forgive me if this has already been discussed - I'm interested in capturing grayscale images realtime (30fps) to RAM on a PC, most likely from a Hi 8 VCR. I've worked with a Scion LG-3 card on a Mac before and it worked wonderfully, however, I've moved to a new job and have to work with a PC now. Does anyone have any experience with this card on a PC? Capturing from a VCR? On the Mac, the LG-3 would occassionally miss a frame, but this wasn't a problem. In addition I would like to use my NIH Image macros on the PC, with Scion's program - will this work ok? Any other suggestions for framegrabbing hardware are welcome. Thanks, Geno ------------------------------------------- Geno Pawlak University of Washington School of Oceanography Box 357940 Seattle, WA 98195-7940 phone: (206) 543-8543 e-mail: gpawlak@ocean.washington.edu ------------------------------------------- ------------------------------ Date: Fri, 11 Sep 1998 9:34:07 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu Subject: Re: spatio-temporal image Message-ID: <84CB54A52E0@rna.bio.mq.edu.au> >Date: Thu, 10 Sep 1998 12:27:10 -0400 >To: nih-image@io.ece.drexel.edu >From: Cengizhan Ozturk >Subject: Re: spatio-temporal image >> >>I'm started to use image PC with the Scion CG-7 frame grabber and a Sony >>color video camera. >>I'd like to write a macro that allows me to make a spatio-temporal image by >>recording the same successive selected vertical (or horizontal) line and >>choosing time step beetwen the capture of two lines and the number of lines >>in order to reconstruct another image. >>Has anyone written such a macro for this ? >> >>Thanks, >>_________________________________________________________________________ >> >>Yves Le Guer >>Laboratoire de Transferts Thermiques - UPPA >>Helioparc - 2, avenue du President Angot - 64000 PAU - FRANCE >>Tel. : 05 59 84 55 02 (LTT) et 05 59 92 33 76 (IUT GTE) >>Fax : 05 59 84 42 96 Tel. International : 33 5 59 84 55 02 >>E-mail : leguer@univ-pau.fr > >Just capture as usual. (as big fat images!) >Put them in a stack. >Reslice them along vertical and horizontal lines. > >Dr. Cengizhan Ozturk >======================= >Johns Hopkins University - Medical Imaging Lab >407 Traylor Building / 720 Rutland Av. >Baltimore, MD 21205-2196 >Phone: (410) 614 5292 >Fax: (410) 502 6915 >E-mail: cozturk@mri.jhu.edu >http://www.mri.jhu.edu/~cozturk/ >======================= Cengizhan, your reply "Just capture as usual. (as big fat images!)" etc is right on the mark but does also suggest that Yves Le Guer may have missed the obvious ie: "capture" & "make movie" will operate on selections (including long thin rectangular selections either horizontal or vertical) which will allow much faster operation and avoid RAM shortages. Stacks can now be 5000 frames in lastest Image versions. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 11 Sep 1998 10:15:28 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-ID: <84D65615701@rna.bio.mq.edu.au> >Date: Thu, 10 Sep 1998 16:03:34 -0400 > >>I am rather new to the image analysis world and I have two questions. >>1) does anyone work on microstructure analysis of heavy clay ceramics? >>2) has anyone written a macro to join adjacent, slightly overlapping images >>automatically? >>My idea is to transform 16 (4x4) or more grayscale SEM images from polished >>sections of ceramics into binary Tiff files and then to merge them together >>in one file in order to apply object (pore) size measurements. I wonder if >>this way of image treatment exeeds the capacity of even high performance >>Mac plattforms. >>thanks for answering >> >>cheers >>mathias >----------------------------------------------------------------- Cengizhan's very comprehensive reply to this question didn't make direct reference to an extremely useful mechanism in NIH-Image which is applicable in this context, particularly for those new to Image and not everyone would followup the web and macro refererence detail. (I have been unable to raise 141.214.135.241. It may be off "overnight" :-) "Manual" procedures are commonly sufficient particularly for tiled montages where orientation is maintained (eg by microscope stage). The "paste" with "XOR" option is a very powerful tool in this context. Make a new image large enough to accomodate the montage (The old restriction on maximum image width of 4096 has been removed). copy and paste the topleft or some other starting component activate "Show Paste Control(Windows menu" pan (if necessary) so that next paste will be roughly central in the window. copy and paste next component with an overlap. choose "XOR" option in Paste Control Window. pasted ROI can be moved by mouse or, more importantly, by arrow keys till it is accurately placed. "XOR" will make overlapping alignment very apparent as both layers can be readily seen until overlap is accurate. If overlap is identical then the overlap will suddenly go to white (all zeros). The paste option can then be switched to "Replace" or (else the paste "Undo"ne so that the ROI can then be restoreRoi'd, giving accurate position of montage component) This manual procedure can be quite quick and is accurate to the pixel (if the overlaps are properly oriented and undistorted). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 10 Sep 1998 20:52:47 EDT From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-ID: <5bf7dced.35f8745f@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 9/10/98 5:22:01 PM, Mathias Rickli [dipl. Min.] wrote: >2) has anyone written a macro to join adjacent, slightly overlapping images >automatically? > >My idea is to transform 16 (4x4) or more grayscale SEM images from polished >sections of ceramics into binary Tiff files and then to merge them together >in one file in order to apply object (pore) size measurements. I wonder if >this way of image treatment exeeds the capacity of even high performance >Mac plattforms. We have a program (Windows NT, not Mac, although it could be recompiled fairly easily) that will take any array of tiffs - mine are usually 1000x1000 pixels or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on each side and seamlessly stitch them together using cross-correlation in the overlap regions to determine the best alignment (including rotation). It isn't fast - a job like the one above takes several hours - but the results are spectacular. We primarily use it on AFM images, occasionally on SEM, and it has also been used on aerial reconnaissance photos. The program is not presently available to others but if there is enough demand we might consider working out some arrangement for its use. John Russ ------------------------------ Date: Fri, 11 Sep 1998 10:25:34 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-ID: <35F8FA9A.A3B8EC5B@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Cengizhan Ozturk wrote: > >I am rather new to the image analysis world and I have two questions. > >1) does anyone work on microstructure analysis of heavy clay ceramics? > >2) has anyone written a macro to join adjacent, slightly overlapping images > >automatically? > >My idea is to transform 16 (4x4) or more grayscale SEM images from polished > >sections of ceramics into binary Tiff files and then to merge them together > >in one file in order to apply object (pore) size measurements. I wonder if > >this way of image treatment exeeds the capacity of even high performance > >Mac plattforms. > >thanks for answering > > > >cheers > >mathias > ----------------------------------------------------------------- > Hi, > > A little search on mosaic and image puzzle dig up this from my humble > "the-best-of-NIH-Image" database. > Have fun with it. > > Cengizhan > > AutoMatch has a full-featured graphical user interface (not just those basic > dialogs the macro language provides) and is written entirely in NIH macro code > (yes, you can do that...). Full documentation is included with the package, > and > a paper is submitted to Microsc. Res. Tech. (Ott, S R, Acquisition of High > Resolution Digital Images in Video Microscopy: Automated Image Mosaicing on a > Desktop Microcomputer) > > For more information see: > http://wwwzoo.kfunigraz.ac.at/~Swidi/AM/AMhome.html > ----------------------------------------------------- > Swidbert R. OTT, MSc > Department of Neurobiology > Institute of Zoology > University of Graz, Austria/Europe > voice: +43 316 380 5602, 5702, 5282 > fax: 380 9875 > > > -------------------- > > Dr. Cengizhan Ozturk > ======================= > Johns Hopkins University - Medical Imaging Lab > 407 Traylor Building / 720 Rutland Av. > Baltimore, MD 21205-2196 > Phone: (410) 614 5292 > Fax: (410) 502 6915 > E-mail: cozturk@mri.jhu.edu > http://www.mri.jhu.edu/~cozturk/ > ======================= I can personally vouch for Swidbert R. OTT's Automatch Macro. It run well under both NIH and Object image, is remarkable fast and accurate. I've used it in conjunction with a 7100/80 AV to mosaic images up to 90 frames at a time. You need allow 10-15% overlap on tissue sections, in less detailed images you will need to allow for more overlap. The hardest bit if setting up your stage sensitivity so that it does not drift but allows you fine control at the same time. Even if the stage does drift ,Automatch will still work if there is enough overlap. It is very ram hungry: on my machine, which has 80 MB of physical RAM, 60 -70 MB RAM to NIH and adjusting your undo and clipboard buffer size to the size the image your going to create is ok for 20 MB images, i.e. you will need a lot of RAM. It works well under both Ram Doubler or VM, although you should not give NIH more than your physical ram. The only disadvantage is if you have already captured the images, Automatch does both the capturing and assembly, it will not assemble independently acquired images. The reference for the paper is ........ Ott, SR (1997) Acquisition of High-Resolution Digital Images in Video Microscopy: Automated Image Mosaicking on a Desktop Microcomputer. Microscopy Research and Technique 38: 335-339. *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html -------------------------------- End of nih-image-d Digest V98 Issue #59 *************************************** From nih-image-request@io.ece.drexel.edu Fri Sep 11 08:04 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA27542; Fri, 11 Sep 1998 08:04:45 -0400 (EDT) Resent-Date: Fri, 11 Sep 1998 08:04:45 -0400 (EDT) Message-Id: <35F90F1B.5FE6@maroon.tc.umn.edu> Date: Fri, 11 Sep 1998 06:52:59 -0500 From: "Michael J. Herron" Reply-To: Michael J Herron Organization: University of Minnesota X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment References: <5bf7dced.35f8745f@aol.com> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vGZNj3.0.9S6.WyG-r"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/335 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 923 Status: O Dr. Russ, I was under the impression the the edges of SEM images were too distorted for this....wrong impression? Mike DrJohnRuss@aol.com wrote: > > > We have a program (Windows NT, not Mac, although it could be recompiled fairly > easily) that will take any array of tiffs - mine are usually 1000x1000 pixels > or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on > each side and seamlessly stitch them together using cross-correlation in the > overlap regions to determine the best alignment (including rotation). It isn't > fast - a job like the one above takes several hours - but the results are > spectacular. We primarily use it on AFM images, occasionally on SEM, and it > has also been used on aerial reconnaissance photos. The program is not > presently available to others but if there is enough demand we might consider > working out some arrangement for its use. > > John Russ From nih-image-request@io.ece.drexel.edu Fri Sep 11 11:51 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA14667; Fri, 11 Sep 1998 11:50:54 -0400 (EDT) Resent-Date: Fri, 11 Sep 1998 11:50:54 -0400 (EDT) Message-Id: <9809111528.AA16520@acs1.acs.ucalgary.ca> Subject: Re: adjacent image alignment To: nih-image@io.ece.drexel.edu Date: Fri, 11 Sep 98 9:28:24 MDT From: "Doug S. Phillips" Cc: nih-image@io.ece.drexel.edu In-Reply-To: <199809110925.FAA13916@io.ECE.Drexel.EDU>; from "nih-image-d-request@io.ece.drexel.edu" at Sep 11, 1998 5:25 am X-Mailer: ELM [version 2.3 PL11K] Mime-Version: 1.0 Resent-Message-ID: <"YK4vF3.0.4B3.H8K-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/336 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="----------------------------" Content-Length: 1133 Status: O ------------------------------ Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Mathias Rickli asked: > 2) has anyone written a macro to join adjacent, slightly overlapping imag= > es automatically? My idea is to transform 16 (4x4) or more grayscale SEM > images from polished sections of ceramics into binary Tiff files and then to > merge them together in one file in order to apply object (pore) size > measurements. I wonder if this way of image treatment exeeds the capacity of > even high performance Mac plattforms. This is well within reach of any modern Mac. I saw an impressive demo of image stitching at a QuickTime 3 presentation last night. Apple markets a product called QuickTime VR Authoring Studio (http://www.apple.com/quicktime/qtvr/authoringstudio/index.html) that can do automatic alignment of such images. Sincerely, Doug P. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ -------------------------------- From nih-image-request@io.ece.drexel.edu Fri Sep 11 17:37 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA08696; Fri, 11 Sep 1998 17:36:50 -0400 (EDT) Resent-Date: Fri, 11 Sep 1998 17:36:50 -0400 (EDT) X-Sender: smurfette@mst.lanl.gov Message-Id: Mime-Version: 1.0 Date: Fri, 11 Sep 1998 15:24:44 -0600 To: nih-image@io.ece.drexel.edu From: Deanna Busick Subject: Particle Analysis Macros Resent-Message-ID: <"fAZHI.0.At1.gKP-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/337 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 497 Status: O Has anyone had any trouble with Matthew Warfel's particle analysis macros? The macro seems to be running and doing the analysis, but the Size Data (tab) and Fractal Data (tab) files I get out contain no data, just a number of carriage returns equal to the number of particles! Thanks in advance for any help... Deanna ------------------------ DEANNA BUSICK MST-11, MS D429 Los Alamos National Laboratory Los Alamos, NM 87545 e-mail: dnbusick@lanl.gov ph#: (505)667-0561 fax: (505)665-4292 From nih-image-request@io.ece.drexel.edu Fri Sep 11 17:52 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA10040; Fri, 11 Sep 1998 17:52:05 -0400 (EDT) Resent-Date: Fri, 11 Sep 1998 17:52:05 -0400 (EDT) Message-ID: <19980911214538.19621.qmail@pc241.icsl.ucla.edu> To: nih-image@io.ece.drexel.edu cc: jul@seas.ucla.edu Subject: How do I import images in GE SIGNA 5.x format? Date: Fri, 11 Sep 1998 14:45:37 -0700 From: Mark Hasegawa-Johnson Resent-Message-ID: <"LMRx32.0.GG2.FcP-r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/338 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 988 Status: O Pardon the newbie question, but... I'm trying to read in a stack of MR images from a GE SIGNA machine, which I believe to be in 5.x format. Has anybody done this before? Do you know what I'm doing wrong, or can you suggest a different approach which worked for you? Thank you!!! ---------- Things I've tried so far (both from ftp://codon.nih.gov/pub/nih-image/contrib) 1 - mriconverter doesn't recognize the file (the file is grayed out on the "file open" menu). 2 - read.GESIGNA macros seem to read in the correct description data (FOV, slice thickness, image label, etc), but not the correct images. The m option reads a stack of square images of static; the s option reads in two one-pixel-height images of static. ----------- Background: The HFSE stack was created on a 5.x machine, and tarred to a 4mm tape using the following commands, suggested by GE: > cd /usr/g/insite/bin > ximg -l (choose image file from menu) > cd /usr/g/insite/tmp > tar -cvf /dev/nrst8 *E* From nih-image-d-request@io.ece.drexel.edu Sat Sep 12 06:09 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA08540; Sat, 12 Sep 1998 06:09:29 -0400 (EDT) Date: Sat, 12 Sep 1998 06:09:29 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809121009.GAA08540@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #60 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/60 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5287 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 60 Today's Topics: Re: adjacent image alignment [ "Michael J. Herron" ] How do I import images in GE SIGNA 5 [ Mark Hasegawa-Johnson To: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-Id: <35F90F1B.5FE6@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Russ, I was under the impression the the edges of SEM images were too distorted for this....wrong impression? Mike DrJohnRuss@aol.com wrote: > > > We have a program (Windows NT, not Mac, although it could be recompiled fairly > easily) that will take any array of tiffs - mine are usually 1000x1000 pixels > or larger and I often have arrays up to 8x8 - that have overlaps of 10-30% on > each side and seamlessly stitch them together using cross-correlation in the > overlap regions to determine the best alignment (including rotation). It isn't > fast - a job like the one above takes several hours - but the results are > spectacular. We primarily use it on AFM images, occasionally on SEM, and it > has also been used on aerial reconnaissance photos. The program is not > presently available to others but if there is enough demand we might consider > working out some arrangement for its use. > > John Russ ------------------------------ Date: Fri, 11 Sep 98 9:28:24 MDT From: "Doug S. Phillips" To: nih-image@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu Subject: Re: adjacent image alignment Message-Id: <9809111528.AA16520@acs1.acs.ucalgary.ca> Content-Type: multipart/mixed; boundary="----------------------------" Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Mathias Rickli asked: > 2) has anyone written a macro to join adjacent, slightly overlapping imag= > es automatically? My idea is to transform 16 (4x4) or more grayscale SEM > images from polished sections of ceramics into binary Tiff files and then to > merge them together in one file in order to apply object (pore) size > measurements. I wonder if this way of image treatment exeeds the capacity of > even high performance Mac plattforms. This is well within reach of any modern Mac. I saw an impressive demo of image stitching at a QuickTime 3 presentation last night. Apple markets a product called QuickTime VR Authoring Studio (http://www.apple.com/quicktime/qtvr/authoringstudio/index.html) that can do automatic alignment of such images. Sincerely, Doug P. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ - ------------------------------ ------------------------------ Date: Fri, 11 Sep 1998 15:24:44 -0600 From: Deanna Busick To: nih-image@io.ece.drexel.edu Subject: Particle Analysis Macros Message-Id: Content-Type: text/plain; charset="us-ascii" Has anyone had any trouble with Matthew Warfel's particle analysis macros? The macro seems to be running and doing the analysis, but the Size Data (tab) and Fractal Data (tab) files I get out contain no data, just a number of carriage returns equal to the number of particles! Thanks in advance for any help... Deanna ------------------------ DEANNA BUSICK MST-11, MS D429 Los Alamos National Laboratory Los Alamos, NM 87545 e-mail: dnbusick@lanl.gov ph#: (505)667-0561 fax: (505)665-4292 ------------------------------ Date: Fri, 11 Sep 1998 14:45:37 -0700 From: Mark Hasegawa-Johnson To: nih-image@io.ece.drexel.edu cc: jul@seas.ucla.edu Subject: How do I import images in GE SIGNA 5.x format? Message-ID: <19980911214538.19621.qmail@pc241.icsl.ucla.edu> Pardon the newbie question, but... I'm trying to read in a stack of MR images from a GE SIGNA machine, which I believe to be in 5.x format. Has anybody done this before? Do you know what I'm doing wrong, or can you suggest a different approach which worked for you? Thank you!!! ---------- Things I've tried so far (both from ftp://codon.nih.gov/pub/nih-image/contrib) 1 - mriconverter doesn't recognize the file (the file is grayed out on the "file open" menu). 2 - read.GESIGNA macros seem to read in the correct description data (FOV, slice thickness, image label, etc), but not the correct images. The m option reads a stack of square images of static; the s option reads in two one-pixel-height images of static. ----------- Background: The HFSE stack was created on a 5.x machine, and tarred to a 4mm tape using the following commands, suggested by GE: > cd /usr/g/insite/bin > ximg -l (choose image file from menu) > cd /usr/g/insite/tmp > tar -cvf /dev/nrst8 *E* -------------------------------- End of nih-image-d Digest V98 Issue #60 *************************************** From nih-image-request@io.ece.drexel.edu Sun Sep 13 11:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20718; Sun, 13 Sep 1998 11:14:44 -0400 (EDT) Resent-Date: Sun, 13 Sep 1998 11:14:44 -0400 (EDT) Message-ID: <35FBECD9.7EB6190E@netmatters.co.uk> Date: Sun, 13 Sep 1998 16:03:39 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: RGB to HSV References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"5vtpW3.0.kn4.Tvz-r"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/339 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 330 Status: O Is there a macro command for converting a RGB stack into an HSV stack? If not, does anyone know of a plugin of macro that does this? Many thanks Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html From nih-image-d-request@io.ece.drexel.edu Mon Sep 14 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA25216; Mon, 14 Sep 1998 06:13:37 -0400 (EDT) Date: Mon, 14 Sep 1998 06:13:37 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809141013.GAA25216@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #61 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/61 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 983 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 61 Today's Topics: RGB to HSV [ Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: RGB to HSV Message-ID: <35FBECD9.7EB6190E@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Is there a macro command for converting a RGB stack into an HSV stack? If not, does anyone know of a plugin of macro that does this? Many thanks Jeremy *********************************************** Jeremy Brown Moredun Research Institute / The University Of Edinburgh http://users.netmatters.co.uk/brownj/ICHomePage.html -------------------------------- End of nih-image-d Digest V98 Issue #61 *************************************** From nih-image-request@io.ece.drexel.edu Tue Sep 15 06:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA05787; Tue, 15 Sep 1998 06:12:42 -0400 (EDT) Resent-Date: Tue, 15 Sep 1998 06:12:42 -0400 (EDT) Date: Tue, 15 Sep 1998 20:05:38 +1000 From: "Kwang Y. Han" Subject: Mexican Hat, Sombrero & Top-Hat filters To: nih-image@io.ece.drexel.edu Message-id: <000001bde090$63401b20$450ac282@ykhan1> MIME-version: 1.0 X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0 Content-transfer-encoding: 7bit Importance: Normal X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 X-Priority: 3 (Normal) Resent-Message-ID: <"XCEcU2.0.x41.JgZ_r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/341 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 646 Status: O I am student doing some research on electron diffraction (spot) patterns from a TEM. I am confused about the differences (if any) between: - The Mexican Hat filter - Sombrero Filter - the Top-Hat filter. Could someone provide a suggestion for a reference which clarifies these different filters? Also...I am using NIH image and am unsure whether the Top-Hat filter is actually an available plugin/macro under this platform. I have read the paper by Bright and Steel (J. Microscopy, Vol.146, p. 191) and would like to treat my spot diffraction patterns in the same way. The nomenclature is a little confusing. Plenty thanks in advance From nih-image-request@io.ece.drexel.edu Tue Sep 15 07:22 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id HAA12242; Tue, 15 Sep 1998 07:22:00 -0400 (EDT) Resent-Date: Tue, 15 Sep 1998 07:22:00 -0400 (EDT) Message-ID: <35FE4A3A.3EE7@gengenp.rug.ac.be> Date: Tue, 15 Sep 1998 13:06:34 +0200 From: Gerrit Beemster Organization: Lab of Genetics X-Mailer: Mozilla 3.01Gold (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: capturing images with NIH under executor References: <9809111528.AA16520@acs1.acs.ucalgary.ca> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"-JuRi2.0.5c2.fea_r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/342 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 566 Status: O Dear all, Although the subject may be a bit of, I hope someone out there has some experience with this. I'm trying to get NIH-Image running on a PC through Ardi's Executor version 2. It works like a whiz and I'm truly impressed. However, although I have a scion board installed under Executor the NIH program doesn't "see" it. Is there an easy fix for this problem, or is it pretty much a hopeless mission? Thanks for any response. -- Gerrit Beemster Department of Genetics K.L. Ledeganckstraat 35 B-9000 Gent Belgium phone: (32)9/2645010 fax: (32)9/2645349 From nih-image-request@io.ece.drexel.edu Tue Sep 15 08:49 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id IAA20254; Tue, 15 Sep 1998 08:49:10 -0400 (EDT) Resent-Date: Tue, 15 Sep 1998 08:49:10 -0400 (EDT) Message-Id: <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca> X-Sender: mliraj@PO-Box.mcgill.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 15 Sep 1998 08:20:05 -0400 To: nih-image@io.ece.drexel.edu From: "Mario de A. Lira Junior" Subject: Re: capturing images with NIH under executor In-Reply-To: <35FE4A3A.3EE7@gengenp.rug.ac.be> References: <9809111528.AA16520@acs1.acs.ucalgary.ca> Mime-Version: 1.0 Resent-Message-ID: <"a0YqM1.0.4d4.oyb_r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/343 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 307 Status: O >experience with this. I'm trying to get NIH-Image running on a PC >through Ardi's Executor version 2. It works like a whiz and I'm truly Why don't you use the Scion Image por for Windows 9x of NIH-Image ? Generally running a native version makes for better performance and may avoid the problem... Mario From nih-image-request@io.ece.drexel.edu Tue Sep 15 09:18 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA23091; Tue, 15 Sep 1998 09:18:21 -0400 (EDT) Resent-Date: Tue, 15 Sep 1998 09:18:21 -0400 (EDT) Message-ID: <35FE65D9.23E0@gengenp.rug.ac.be> Date: Tue, 15 Sep 1998 15:04:25 +0200 From: Gerrit Beemster Organization: Lab of Genetics X-Mailer: Mozilla 3.01Gold (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: capturing images with NIH under executor References: <9809111528.AA16520@acs1.acs.ucalgary.ca> <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"85k8g.0.AI5.BNc_r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/344 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 704 Status: O Mario de A. Lira Junior wrote: > > >experience with this. I'm trying to get NIH-Image running on a PC > >through Ardi's Executor version 2. It works like a whiz and I'm truly > > Why don't you use the Scion Image por for Windows 9x of NIH-Image ? > Generally running a native version makes for better performance and may > avoid the problem... > Mario Yes, but some of the macro's in the contrib directory (I'm specifically interrested in Automatch) are specific for the mac environment and don't easily port to the ScionImage for as far as I've been able to work out. -- Gerrit Beemster Department of Genetics K.L. Ledeganckstraat 35 B-9000 Gent Belgium phone: (32)9/2645010 fax: (32)9/2645349 From nih-image-d-request@io.ece.drexel.edu Wed Sep 16 06:12 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA27946; Wed, 16 Sep 1998 06:12:28 -0400 (EDT) Date: Wed, 16 Sep 1998 06:12:28 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809161012.GAA27946@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #62 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/62 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4082 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 62 Today's Topics: Mexican Hat, Sombrero & Top-Hat filt [ "Kwang Y. Han" To: nih-image@io.ece.drexel.edu Subject: Mexican Hat, Sombrero & Top-Hat filters Message-id: <000001bde090$63401b20$450ac282@ykhan1> Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit I am student doing some research on electron diffraction (spot) patterns from a TEM. I am confused about the differences (if any) between: - The Mexican Hat filter - Sombrero Filter - the Top-Hat filter. Could someone provide a suggestion for a reference which clarifies these different filters? Also...I am using NIH image and am unsure whether the Top-Hat filter is actually an available plugin/macro under this platform. I have read the paper by Bright and Steel (J. Microscopy, Vol.146, p. 191) and would like to treat my spot diffraction patterns in the same way. The nomenclature is a little confusing. Plenty thanks in advance ------------------------------ Date: Tue, 15 Sep 1998 13:06:34 +0200 From: Gerrit Beemster To: nih-image@io.ece.drexel.edu Subject: capturing images with NIH under executor Message-ID: <35FE4A3A.3EE7@gengenp.rug.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, Although the subject may be a bit of, I hope someone out there has some experience with this. I'm trying to get NIH-Image running on a PC through Ardi's Executor version 2. It works like a whiz and I'm truly impressed. However, although I have a scion board installed under Executor the NIH program doesn't "see" it. Is there an easy fix for this problem, or is it pretty much a hopeless mission? Thanks for any response. -- Gerrit Beemster Department of Genetics K.L. Ledeganckstraat 35 B-9000 Gent Belgium phone: (32)9/2645010 fax: (32)9/2645349 ------------------------------ Date: Tue, 15 Sep 1998 08:20:05 -0400 From: "Mario de A. Lira Junior" To: nih-image@io.ece.drexel.edu Subject: Re: capturing images with NIH under executor Message-Id: <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" >experience with this. I'm trying to get NIH-Image running on a PC >through Ardi's Executor version 2. It works like a whiz and I'm truly Why don't you use the Scion Image por for Windows 9x of NIH-Image ? Generally running a native version makes for better performance and may avoid the problem... Mario ------------------------------ Date: Tue, 15 Sep 1998 15:04:25 +0200 From: Gerrit Beemster To: nih-image@io.ece.drexel.edu Subject: Re: capturing images with NIH under executor Message-ID: <35FE65D9.23E0@gengenp.rug.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mario de A. Lira Junior wrote: > > >experience with this. I'm trying to get NIH-Image running on a PC > >through Ardi's Executor version 2. It works like a whiz and I'm truly > > Why don't you use the Scion Image por for Windows 9x of NIH-Image ? > Generally running a native version makes for better performance and may > avoid the problem... > Mario Yes, but some of the macro's in the contrib directory (I'm specifically interrested in Automatch) are specific for the mac environment and don't easily port to the ScionImage for as far as I've been able to work out. -- Gerrit Beemster Department of Genetics K.L. Ledeganckstraat 35 B-9000 Gent Belgium phone: (32)9/2645010 fax: (32)9/2645349 -------------------------------- End of nih-image-d Digest V98 Issue #62 *************************************** From nih-image-request@io.ece.drexel.edu Wed Sep 16 09:10 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id JAA11784; Wed, 16 Sep 1998 09:09:29 -0400 (EDT) Resent-Date: Wed, 16 Sep 1998 09:09:29 -0400 (EDT) Message-Id: <3.0.6.32.19980916084702.00841280@PO-Box.mcgill.ca> X-Sender: mliraj@PO-Box.mcgill.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 16 Sep 1998 08:47:02 -0400 To: nih-image@io.ece.drexel.edu From: "Mario de A. Lira Junior" Subject: Re: capturing images with NIH under executor In-Reply-To: <35FE65D9.23E0@gengenp.rug.ac.be> References: <9809111528.AA16520@acs1.acs.ucalgary.ca> <3.0.6.32.19980915082005.007f95d0@PO-Box.mcgill.ca> Mime-Version: 1.0 Resent-Message-ID: <"IsV1f2.0.7U2.5Gx_r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/345 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 753 Status: O >> Why don't you use the Scion Image por for Windows 9x of NIH-Image ? >> Generally running a native version makes for better performance and may >> avoid the problem... >> Mario > >Yes, but some of the macro's in the contrib directory (I'm specifically >interrested in Automatch) are specific for the mac environment and don't >easily port to the ScionImage for as far as I've been able to work out. Well, in this case, since both are freeware, you may use both versions, and use the windows version to capture the files you need, save as tifs, go to the mac version and do the analysis there... It is a roundabout, but at least you would be able to start working fast, and could later check out to see if you can do it in a more direct way... Mario From nih-image-request@io.ece.drexel.edu Wed Sep 16 13:00 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA00261; Wed, 16 Sep 1998 13:00:20 -0400 (EDT) Resent-Date: Wed, 16 Sep 1998 13:00:20 -0400 (EDT) Date: Wed, 16 Sep 1998 12:42:29 -0400 (EDT) Sender: Nora Rooney From: Nora Maureen Rooney X-Sender: nora@login4.isis.unc.edu To: nih-image@io.ece.drexel.edu Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Nac4S1.0.027.Hh-_r"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/346 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 599 Status: O I am trying to use the program to decipher cell types on a slide image by their intensity of stain. The cell type that I want to differentiate doesn't become apparent through use of the density slice. Some parts of some of these cells becomes red, but not all of them all of the time. I am trying to use this because it is difficult to decipher between their dark brown color and the dark blue nuclei of cells that are not of interest by simply looking at them. So, I was hoping to have a more quantifiable method of determining which cells are of interest. I would welcome any suggestions. From nih-image-request@io.ece.drexel.edu Wed Sep 16 13:41 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id NAA03516; Wed, 16 Sep 1998 13:41:18 -0400 (EDT) Resent-Date: Wed, 16 Sep 1998 13:41:18 -0400 (EDT) Mime-Version: 1.0 Message-Id: In-Reply-To: Date: Wed, 16 Sep 1998 13:35:26 -0400 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: Re: Unidentified subject! Resent-Message-ID: <"VbnNY2.0.OV.-F__r"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/347 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1418 Status: O Rather than worry about the program not being "smart" enough why not switch to a nuclear stain that can be eliminated by adding a filter to the section. For example if your stain is an immunocytochemical one (ie DAB which is brown) you might want to use Methyl Green as a counterstain. Adding a cyan filter will make the computer "blind" to the nuclei so there won't be any interference. Using a red filter will enhance the nuclear stain . If you can shift your brown stain to black (ie with Nickel DAB) then you might want to use Neutral Red as the nuclear stain. It is eliminated (are at least strongly reduced) by use of a dark red filter. >I am trying to use the program to decipher cell types on a slide image by >their intensity of stain. The cell type that I want to differentiate >doesn't become apparent through use of the density slice. Some parts of >some of these cells becomes red, but not all of them all of the time. I >am trying to use this because it is difficult to decipher between their >dark brown color and the dark blue nuclei of cells that are not of >interest by simply looking at them. So, I was hoping to have a more >quantifiable method of determining which cells are of interest. I would >welcome any suggestions. Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu From nih-image-request@io.ece.drexel.edu Wed Sep 16 20:33 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id UAA15616; Wed, 16 Sep 1998 20:33:21 -0400 (EDT) Resent-Date: Wed, 16 Sep 1998 20:33:21 -0400 (EDT) Date: Wed, 16 Sep 1998 20:24:56 -0500 From: Bill Christens-Barry Subject: Q: explanationof MakeMovie options? To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"mKcwY2.0.pO3.PL50s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/348 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 925 Status: O The NIH Image online manual gives the following for the macro MakeMovie command: MakeMovie('str',frames,interval) Captures a sequence of video frames to a stack. 'str' is some combination of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first', 'trigger each', and 'dialog'. Frames is the number of frames to capture, and interval is the interval between frames in seconds. See the "Movie Making" macro file for examples. Some of the options are not used in the "Movie Making" macro file. For example, the 'str' options 'blind', 'buffer', and 'existing' don't appear. Can anyone explain their usage? Also, the "Movie Making" macro file uses values of -1 for the frames and interval arguments in one of the example macros that uses the 'dialog' argument. What is the meaning of this? Finally, can the MakeMovie command use a sub-second interval, and will this appear in time stamp? Thanks. Bill Christens-Barry From nih-image-request@io.ece.drexel.edu Thu Sep 17 02:35 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA25393; Thu, 17 Sep 1998 02:35:18 -0400 (EDT) Resent-Date: Thu, 17 Sep 1998 02:35:18 -0400 (EDT) Message-Id: <199809170626.OAA15859@nero.rph.health.wa.gov.au> From: "Robert Day" To: nih-image@io.ece.drexel.edu Date: Thu, 17 Sep 1998 14:17:39 +0800 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: Re: How do I import images in GE SIGNA 5.x format? Priority: normal In-reply-to: <19980911214538.19621.qmail@pc241.icsl.ucla.edu> X-mailer: Pegasus Mail for Win32 (v3.01b) Resent-Message-ID: <"d5sMk.0.qk5.JfA0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/349 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2006 Status: O > > Pardon the newbie question, but... > > I'm trying to read in a stack of MR images from a GE SIGNA machine, > which I believe to be in 5.x format. > > Has anybody done this before? Do you know what I'm doing wrong, or > can you suggest a different approach which worked for you? > > Thank you!!! > > ---------- > > Things I've tried so far (both from > ftp://codon.nih.gov/pub/nih-image/contrib) > > 1 - mriconverter doesn't recognize the file (the file is grayed out on the > "file open" menu). Possibly mriconverter is looking for a specific creator/type signature (I don't use this program so I don't know). If you have any examples it will open, use ResEdit (or something a bit safer :-) to look at the signature and change the new files to match. > 2 - read.GESIGNA macros seem to read in the correct description data > (FOV, slice thickness, image label, etc), but not the correct images. The > m option reads a stack of square images of static; the s option reads in > two one-pixel-height images of static. There are several possible reasons for this. 1. The format of GE ximg files has changed in the past. Get ximg to dump the structure of the file and compare that with what the macros are doing (or re-write the macro to suit as needed). The command to do this should be : ximg -g > imageFileOffsets.h which will generate a C include file defining the names and offsets of the fields in the image headers. 2. GE has used machines with different byte orders for its scanners. Try byte swapping just to be sure. 3. The image could have been saved in compressed format. The compression algorithim is given in the Medical Image Format FAQ among other places. In any case, try also the freeware too Dr.RAZZ, as it can read most GE files in my experience. Try : Rob. -- Robert Day rob.day@nero.rph.health.wa.gov.au Project Bioengineer ph +61 8 9224 3227 Royal Perth Hospital fax +61 8 9224 1138 From nih-image-d-request@io.ece.drexel.edu Thu Sep 17 02:35 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA25433; Thu, 17 Sep 1998 02:35:30 -0400 (EDT) Date: Thu, 17 Sep 1998 02:35:30 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809170635.CAA25433@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #63 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/63 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7891 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 63 Today's Topics: Re: capturing images with NIH under [ "Mario de A. Lira Junior" To: nih-image@io.ece.drexel.edu Subject: Re: capturing images with NIH under executor Message-Id: <3.0.6.32.19980916084702.00841280@PO-Box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" >> Why don't you use the Scion Image por for Windows 9x of NIH-Image ? >> Generally running a native version makes for better performance and may >> avoid the problem... >> Mario > >Yes, but some of the macro's in the contrib directory (I'm specifically >interrested in Automatch) are specific for the mac environment and don't >easily port to the ScionImage for as far as I've been able to work out. Well, in this case, since both are freeware, you may use both versions, and use the windows version to capture the files you need, save as tifs, go to the mac version and do the analysis there... It is a roundabout, but at least you would be able to start working fast, and could later check out to see if you can do it in a more direct way... Mario ------------------------------ Date: Wed, 16 Sep 1998 12:42:29 -0400 (EDT) From: Nora Maureen Rooney To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to use the program to decipher cell types on a slide image by their intensity of stain. The cell type that I want to differentiate doesn't become apparent through use of the density slice. Some parts of some of these cells becomes red, but not all of them all of the time. I am trying to use this because it is difficult to decipher between their dark brown color and the dark blue nuclei of cells that are not of interest by simply looking at them. So, I was hoping to have a more quantifiable method of determining which cells are of interest. I would welcome any suggestions. ------------------------------ Date: Wed, 16 Sep 1998 13:35:26 -0400 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: Re: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" Rather than worry about the program not being "smart" enough why not switch to a nuclear stain that can be eliminated by adding a filter to the section. For example if your stain is an immunocytochemical one (ie DAB which is brown) you might want to use Methyl Green as a counterstain. Adding a cyan filter will make the computer "blind" to the nuclei so there won't be any interference. Using a red filter will enhance the nuclear stain . If you can shift your brown stain to black (ie with Nickel DAB) then you might want to use Neutral Red as the nuclear stain. It is eliminated (are at least strongly reduced) by use of a dark red filter. >I am trying to use the program to decipher cell types on a slide image by >their intensity of stain. The cell type that I want to differentiate >doesn't become apparent through use of the density slice. Some parts of >some of these cells becomes red, but not all of them all of the time. I >am trying to use this because it is difficult to decipher between their >dark brown color and the dark blue nuclei of cells that are not of >interest by simply looking at them. So, I was hoping to have a more >quantifiable method of determining which cells are of interest. I would >welcome any suggestions. Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu ------------------------------ Date: Wed, 16 Sep 1998 20:24:56 -0500 From: Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: Q: explanationof MakeMovie options? Message-id: Content-type: text/plain; charset="us-ascii" The NIH Image online manual gives the following for the macro MakeMovie command: MakeMovie('str',frames,interval) Captures a sequence of video frames to a stack. 'str' is some combination of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first', 'trigger each', and 'dialog'. Frames is the number of frames to capture, and interval is the interval between frames in seconds. See the "Movie Making" macro file for examples. Some of the options are not used in the "Movie Making" macro file. For example, the 'str' options 'blind', 'buffer', and 'existing' don't appear. Can anyone explain their usage? Also, the "Movie Making" macro file uses values of -1 for the frames and interval arguments in one of the example macros that uses the 'dialog' argument. What is the meaning of this? Finally, can the MakeMovie command use a sub-second interval, and will this appear in time stamp? Thanks. Bill Christens-Barry ------------------------------ Date: Thu, 17 Sep 1998 14:17:39 +0800 From: "Robert Day" To: nih-image@io.ece.drexel.edu Subject: Re: How do I import images in GE SIGNA 5.x format? Message-Id: <199809170626.OAA15859@nero.rph.health.wa.gov.au> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT > > Pardon the newbie question, but... > > I'm trying to read in a stack of MR images from a GE SIGNA machine, > which I believe to be in 5.x format. > > Has anybody done this before? Do you know what I'm doing wrong, or > can you suggest a different approach which worked for you? > > Thank you!!! > > ---------- > > Things I've tried so far (both from > ftp://codon.nih.gov/pub/nih-image/contrib) > > 1 - mriconverter doesn't recognize the file (the file is grayed out on the > "file open" menu). Possibly mriconverter is looking for a specific creator/type signature (I don't use this program so I don't know). If you have any examples it will open, use ResEdit (or something a bit safer :-) to look at the signature and change the new files to match. > 2 - read.GESIGNA macros seem to read in the correct description data > (FOV, slice thickness, image label, etc), but not the correct images. The > m option reads a stack of square images of static; the s option reads in > two one-pixel-height images of static. There are several possible reasons for this. 1. The format of GE ximg files has changed in the past. Get ximg to dump the structure of the file and compare that with what the macros are doing (or re-write the macro to suit as needed). The command to do this should be : ximg -g > imageFileOffsets.h which will generate a C include file defining the names and offsets of the fields in the image headers. 2. GE has used machines with different byte orders for its scanners. Try byte swapping just to be sure. 3. The image could have been saved in compressed format. The compression algorithim is given in the Medical Image Format FAQ among other places. In any case, try also the freeware too Dr.RAZZ, as it can read most GE files in my experience. Try : Rob. -- Robert Day rob.day@nero.rph.health.wa.gov.au Project Bioengineer ph +61 8 9224 3227 Royal Perth Hospital fax +61 8 9224 1138 -------------------------------- End of nih-image-d Digest V98 Issue #63 *************************************** From nih-image-request@io.ece.drexel.edu Thu Sep 17 04:26 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id EAA08060; Thu, 17 Sep 1998 04:26:50 -0400 (EDT) Resent-Date: Thu, 17 Sep 1998 04:26:50 -0400 (EDT) X-Sender: mathias@ruby.unibe.ch Message-Id: Mime-Version: 1.0 Date: Thu, 17 Sep 1998 10:15:00 +0100 To: nih-image@io.ece.drexel.edu From: mathias@mpi.unibe.ch (mathias rickli) Subject: stereology Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id EAA06198 Resent-Message-ID: <"PLSB13.0.zW1.2HC0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/350 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 504 Status: O Does anybody combine nih image with stereological methods? In more detail I wonder if macros are available to estimate quantities such as: mean particle volume, surface density, mean linear intercept length, star volume,... thanks for answering cheers mathias Mathias Rickli [dipl. Min.] Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 home: Freiestrasse 35 CH-3012 Bern Switzerland Tel: +41-31-302-9564 From nih-image-request@io.ece.drexel.edu Thu Sep 17 15:30 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id PAA08280; Thu, 17 Sep 1998 15:30:01 -0400 (EDT) Resent-Date: Thu, 17 Sep 1998 15:30:01 -0400 (EDT) Message-ID: <36016B73.63C29E5@netmatters.co.uk> Date: Thu, 17 Sep 1998 20:05:14 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Unidentified subject! References: Resent-Message-ID: <"hPZDC2.0.cm1.M-L0s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/351 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="------------C476746C0100839C13B60D38" Content-Length: 5708 Status: O --------------C476746C0100839C13B60D38 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Try 'RGB to HSV' from the Stacks menu. DAB stained cells can be segmented in RGB images, although it is difficult. However, converting the image to the Hue, Saturation, Intensity model should make your DAB stained cells show up really nicely in the HUE channel (1) and the unstained blue nuclei in the Saturation channel (2). DAB is essentially an unsaturated red colour and can be segmented easily from a blue background. Haematoxylin staining, for example, is more saturated in the nuclei but is uniform in Hue. Positive cells should appear bright red on a uniform blue background in the hue channel. Negative cells may then be counted in the Saturation channel, in which DAB due to its low saturation value should not appear. You may want to use a more intense counterstain if you are using DAB to stain cell culture preps. Alternatively you can use the intensity channel (3) to segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to enhance DAB which should be very dark blue/black). Hope this helps, it works well for Neospora in tissue sections and Chlamydia spp in tissue culture. Jeremy Gloria Hoffman wrote: > Rather than worry about the program not being "smart" enough why not switch > to a nuclear stain that can be eliminated by adding a filter to the > section. For example if your stain is an immunocytochemical one (ie DAB > which is brown) you might want to use Methyl Green as a counterstain. > Adding a cyan filter will make the computer "blind" to the nuclei so there > won't be any interference. Using a red filter will enhance the nuclear > stain . If you can shift your brown stain to black (ie with Nickel DAB) > then you might want to use Neutral Red as the nuclear stain. It is > eliminated (are at least strongly reduced) by use of a dark red filter. > > >I am trying to use the program to decipher cell types on a slide image by > >their intensity of stain. The cell type that I want to differentiate > >doesn't become apparent through use of the density slice. Some parts of > >some of these cells becomes red, but not all of them all of the time. I > >am trying to use this because it is difficult to decipher between their > >dark brown color and the dark blue nuclei of cells that are not of > >interest by simply looking at them. So, I was hoping to have a more > >quantifiable method of determining which cells are of interest. I would > >welcome any suggestions. > > Gloria E. Hoffman, Ph.D. > Department of Anatomy and Neurobiology > 685 W Baltimore St > Baltimore MD 21201 > Phone 410 706-2438 > Fax 410 706-2512 > email gehoffma@umaryland.edu --------------C476746C0100839C13B60D38 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Try 'RGB to HSV' from the Stacks menu.

DAB stained cells can be segmented in RGB images, although it is difficult. However, converting the image to the Hue, Saturation, Intensity model should make your DAB stained cells show up really nicely in the HUE channel (1) and the unstained blue nuclei in the Saturation channel (2). DAB is essentially an unsaturated red colour and can be segmented easily from a blue background. Haematoxylin staining, for example, is more saturated in the nuclei but is uniform in Hue. Positive cells should appear bright red on a uniform blue background in the hue channel. Negative cells may then be counted in the Saturation channel, in which DAB due to its low saturation value should not appear.

You may want to use a more intense counterstain if you are using DAB to stain cell culture preps. Alternatively you can use the intensity channel (3) to segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to enhance DAB which should be very dark blue/black).

Hope this helps, it works well for Neospora in tissue sections and Chlamydia spp in tissue culture.

Jeremy

Gloria Hoffman wrote:

Rather than worry about the program not being "smart" enough why not switch
to a nuclear stain that can be eliminated by adding a filter to the
section. For example if your stain is an immunocytochemical one (ie DAB
which is brown) you might want to use Methyl Green as a counterstain.
Adding a cyan filter will make the computer "blind" to the nuclei so there
won't be any interference. Using a red filter will enhance the nuclear
stain . If you can shift your brown stain to black (ie with Nickel DAB)
then you might want to use Neutral Red as the nuclear stain. It is
eliminated (are at least strongly reduced) by use of a dark red filter.

>I am trying to use the program to decipher cell types on a slide image by
>their intensity of stain.  The cell type that I want to differentiate
>doesn't become apparent through use of the density slice.  Some parts of
>some of these cells becomes red, but not all of them all of the time.  I
>am trying to use this because it is difficult to decipher between their
>dark brown color and the dark blue nuclei of cells that are not of
>interest by simply looking at them.  So, I was hoping to have a more
>quantifiable method of determining which cells are of interest.  I would
>welcome any suggestions.

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

  --------------C476746C0100839C13B60D38-- From nih-image-request@io.ece.drexel.edu Thu Sep 17 17:13 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id RAA14995; Thu, 17 Sep 1998 17:12:52 -0400 (EDT) Resent-Date: Thu, 17 Sep 1998 17:12:52 -0400 (EDT) Date: Thu, 17 Sep 1998 13:56:26 -0700 (PDT) From: Maryam Shariati To: nih-image@io.ece.drexel.edu Subject: Questions Regarding NIH Image Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"owhNy3.0.MM3._TN0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/352 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1013 Status: O Hi, I am a Chemical Engineering Ph.D. candidate at USC working on fluid flow through porous media. Recently I downloaded the PC version of the NIH image software from the NIH web site. I am hoping to use this software to analyze images captured when a fluid (1), with a distinct color ( dyed with a dark color), displaces another fluid (2) with a lighter color ( usually not dyed). Hence I am planning to convert the pixel values ( gray scale levels) to concentration using possibly the Beer-Lambert Law. I am hoping to get the concentration gradient across as fluid (1) displaces fluid (2). Given what I have described, I have a couple of questions : o How can one calibrate the system ? o Can one store the pixel values using NIH? You can contact me via email at : shariati@usc.edu. Thanks a lot for your consideration and cooperation in this matter. Your additional suggestions and advice in this matter are greatly appreciated. sincerely, Maryam Shariati shariati@usc.edu From nih-image-request@io.ece.drexel.edu Fri Sep 18 02:15 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA29394; Fri, 18 Sep 1998 02:15:35 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 02:15:35 -0400 (EDT) Date: Thu, 17 Sep 1998 23:06:36 -0700 (PDT) From: Pauline Seta Yaralian To: nih image Subject: gray/white segmentation Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"YhFYw3.0.su6.sXV0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/353 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 359 Status: O Is NIH image capable of automatically segmenting gray and white matter? Also,. is it possible to view 3 planes simultaneously? Pauline S. Yaralian Research Assistant Clinical Neuroscience Laboratory University of Southern California Department of Psychology Los Angeles, Ca. 90089-1061 e mail: yaralian@rcf.usc.edu Office:(213) 740-2220 Fax:(213) 746-9082 From nih-image-d-request@io.ece.drexel.edu Fri Sep 18 02:16 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id CAA29511; Fri, 18 Sep 1998 02:16:25 -0400 (EDT) Date: Fri, 18 Sep 1998 02:16:25 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809180616.CAA29511@io.ECE.Drexel.EDU> Subject: nih-image-d Digest V98 #64 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/64 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9371 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 64 Today's Topics: stereology [ mathias@mpi.unibe.ch (mathias rickl ] Re: Unidentified subject! [ Jeremy Brown Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Does anybody combine nih image with stereological methods? In more detail I wonder if macros are available to estimate quantities such as: mean particle volume, surface density, mean linear intercept length, star volume,... thanks for answering cheers mathias Mathias Rickli [dipl. Min.] Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 home: Freiestrasse 35 CH-3012 Bern Switzerland Tel: +41-31-302-9564 ------------------------------ Date: Thu, 17 Sep 1998 20:05:14 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Unidentified subject! Message-ID: <36016B73.63C29E5@netmatters.co.uk> Content-Type: multipart/alternative; boundary="------------C476746C0100839C13B60D38" --------------C476746C0100839C13B60D38 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Try 'RGB to HSV' from the Stacks menu. DAB stained cells can be segmented in RGB images, although it is difficult. However, converting the image to the Hue, Saturation, Intensity model should make your DAB stained cells show up really nicely in the HUE channel (1) and the unstained blue nuclei in the Saturation channel (2). DAB is essentially an unsaturated red colour and can be segmented easily from a blue background. Haematoxylin staining, for example, is more saturated in the nuclei but is uniform in Hue. Positive cells should appear bright red on a uniform blue background in the hue channel. Negative cells may then be counted in the Saturation channel, in which DAB due to its low saturation value should not appear. You may want to use a more intense counterstain if you are using DAB to stain cell culture preps. Alternatively you can use the intensity channel (3) to segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to enhance DAB which should be very dark blue/black). Hope this helps, it works well for Neospora in tissue sections and Chlamydia spp in tissue culture. Jeremy Gloria Hoffman wrote: > Rather than worry about the program not being "smart" enough why not switch > to a nuclear stain that can be eliminated by adding a filter to the > section. For example if your stain is an immunocytochemical one (ie DAB > which is brown) you might want to use Methyl Green as a counterstain. > Adding a cyan filter will make the computer "blind" to the nuclei so there > won't be any interference. Using a red filter will enhance the nuclear > stain . If you can shift your brown stain to black (ie with Nickel DAB) > then you might want to use Neutral Red as the nuclear stain. It is > eliminated (are at least strongly reduced) by use of a dark red filter. > > >I am trying to use the program to decipher cell types on a slide image by > >their intensity of stain. The cell type that I want to differentiate > >doesn't become apparent through use of the density slice. Some parts of > >some of these cells becomes red, but not all of them all of the time. I > >am trying to use this because it is difficult to decipher between their > >dark brown color and the dark blue nuclei of cells that are not of > >interest by simply looking at them. So, I was hoping to have a more > >quantifiable method of determining which cells are of interest. I would > >welcome any suggestions. > > Gloria E. Hoffman, Ph.D. > Department of Anatomy and Neurobiology > 685 W Baltimore St > Baltimore MD 21201 > Phone 410 706-2438 > Fax 410 706-2512 > email gehoffma@umaryland.edu --------------C476746C0100839C13B60D38 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Try 'RGB to HSV' from the Stacks menu.

DAB stained cells can be segmented in RGB images, although it is difficult. However, converting the image to the Hue, Saturation, Intensity model should make your DAB stained cells show up really nicely in the HUE channel (1) and the unstained blue nuclei in the Saturation channel (2). DAB is essentially an unsaturated red colour and can be segmented easily from a blue background. Haematoxylin staining, for example, is more saturated in the nuclei but is uniform in Hue. Positive cells should appear bright red on a uniform blue background in the hue channel. Negative cells may then be counted in the Saturation channel, in which DAB due to its low saturation value should not appear.

You may want to use a more intense counterstain if you are using DAB to stain cell culture preps. Alternatively you can use the intensity channel (3) to segment DAB stained objects (especially if you are using NiCl2 of CoCl2 to enhance DAB which should be very dark blue/black).

Hope this helps, it works well for Neospora in tissue sections and Chlamydia spp in tissue culture.

Jeremy

Gloria Hoffman wrote:

Rather than worry about the program not being "smart" enough why not switch
to a nuclear stain that can be eliminated by adding a filter to the
section. For example if your stain is an immunocytochemical one (ie DAB
which is brown) you might want to use Methyl Green as a counterstain.
Adding a cyan filter will make the computer "blind" to the nuclei so there
won't be any interference. Using a red filter will enhance the nuclear
stain . If you can shift your brown stain to black (ie with Nickel DAB)
then you might want to use Neutral Red as the nuclear stain. It is
eliminated (are at least strongly reduced) by use of a dark red filter.

>I am trying to use the program to decipher cell types on a slide image by
>their intensity of stain.  The cell type that I want to differentiate
>doesn't become apparent through use of the density slice.  Some parts of
>some of these cells becomes red, but not all of them all of the time.  I
>am trying to use this because it is difficult to decipher between their
>dark brown color and the dark blue nuclei of cells that are not of
>interest by simply looking at them.  So, I was hoping to have a more
>quantifiable method of determining which cells are of interest.  I would
>welcome any suggestions.

Gloria E. Hoffman, Ph.D.
Department of Anatomy and Neurobiology
685 W Baltimore St
Baltimore MD 21201
Phone 410 706-2438
Fax 410 706-2512
email gehoffma@umaryland.edu

  --------------C476746C0100839C13B60D38-- ------------------------------ Date: Thu, 17 Sep 1998 13:56:26 -0700 (PDT) From: Maryam Shariati To: nih-image@io.ece.drexel.edu Subject: Questions Regarding NIH Image Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am a Chemical Engineering Ph.D. candidate at USC working on fluid flow through porous media. Recently I downloaded the PC version of the NIH image software from the NIH web site. I am hoping to use this software to analyze images captured when a fluid (1), with a distinct color ( dyed with a dark color), displaces another fluid (2) with a lighter color ( usually not dyed). Hence I am planning to convert the pixel values ( gray scale levels) to concentration using possibly the Beer-Lambert Law. I am hoping to get the concentration gradient across as fluid (1) displaces fluid (2). Given what I have described, I have a couple of questions : o How can one calibrate the system ? o Can one store the pixel values using NIH? You can contact me via email at : shariati@usc.edu. Thanks a lot for your consideration and cooperation in this matter. Your additional suggestions and advice in this matter are greatly appreciated. sincerely, Maryam Shariati shariati@usc.edu ------------------------------ Date: Thu, 17 Sep 1998 23:06:36 -0700 (PDT) From: Pauline Seta Yaralian To: nih image Subject: gray/white segmentation Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Is NIH image capable of automatically segmenting gray and white matter? Also,. is it possible to view 3 planes simultaneously? Pauline S. Yaralian Research Assistant Clinical Neuroscience Laboratory University of Southern California Department of Psychology Los Angeles, Ca. 90089-1061 e mail: yaralian@rcf.usc.edu Office:(213) 740-2220 Fax:(213) 746-9082 -------------------------------- End of nih-image-d Digest V98 Issue #64 *************************************** From nih-image-request@io.ece.drexel.edu Fri Sep 18 06:33 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id GAA22790; Fri, 18 Sep 1998 06:33:51 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 06:33:51 -0400 (EDT) From: UPongs@tkc.de X-Sender: UPongs@mail.tkc.de Message-Id: Mime-Version: 1.0 Date: Fri, 18 Sep 1998 12:24:06 +0200 To: nih-image@io.ece.drexel.edu Subject: NIH-Image and DT3155 Resent-Message-ID: <"KAmIf.0.9D5.IGZ0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/354 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 255 Status: RO Hi Imagers! Is there anyone of you, who has experiences with a Data Translation Framegrabber DT3155 in a Macintosh (which one - 7300, 7500 or ???) together with NIH-Image? How can I connect both? Any ideas and help is really welcome Uwe Martin Pongs From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:05 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA15513; Fri, 18 Sep 1998 11:04:54 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 11:04:54 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Fri, 18 Sep 1998 10:49:19 -0400 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: gray/white segmentation Resent-Message-ID: <"947VN1.0.HQ3.mBd0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/355 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1077 Status: O >Is NIH image capable of automatically segmenting gray and white matter? >Also,. is it possible to view 3 planes simultaneously? > See object image for 3plane view. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:17 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA16996; Fri, 18 Sep 1998 11:17:36 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 11:17:36 -0400 (EDT) Message-Id: <199809181506.LAA15716@io.ECE.Drexel.EDU> From: Chris Liner Subject: Image/J & linux To: nih-image@io.ece.drexel.edu Date: Fri, 18 Sep 98 10:29:31 CDT Cc: cll@utulsa.edu (Chris Liner) Mailer: Elm [revision: 70.85] Resent-Message-ID: <"k3xnt.0.mr3.ZRd0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/356 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 379 Status: O Has anyone on the list got Image/J running under linux? If so, I would be interested in knowing the procedure. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:26 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA18055; Fri, 18 Sep 1998 11:26:46 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 11:26:46 -0400 (EDT) Message-ID: <3602842F.9363D444@netmatters.co.uk> Date: Fri, 18 Sep 1998 16:02:57 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: gray/white segmentation References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"7b6ao2.0.M24.cZd0s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/357 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1289 Status: O Pauline Seta Yaralian wrote: > Is NIH image capable of automatically segmenting gray and white matter? > Also,. is it possible to view 3 planes simultaneously? > > Pauline S. Yaralian > Research Assistant > Clinical Neuroscience Laboratory > University of Southern California > Department of Psychology > Los Angeles, Ca. 90089-1061 > e mail: yaralian@rcf.usc.edu > Office:(213) 740-2220 > Fax:(213) 746-908 If by three planes simultaneously you mean X,Y,Z axis images, Object Image (a spin-off of NIH Image available from http://simon.bio.uva.nl/object-imageButtons.html or via the NIH site) uses one of the best approaches to this problem I've ever seen. Under the Sacks menu choose slice 2D or slice 3D. These will give you a live 3-planar view of any image stack. This is extremely useful for 3D data sets. Object Image is Mac only, if you are using a PC I am afraid that you will have to make do with drawing a line across you image and then choosing reslice, repeat this lots of times until you find the point in the 3D image you are looking for. Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:27 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA18194; Fri, 18 Sep 1998 11:27:25 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 11:27:25 -0400 (EDT) Message-ID: <3602871F.BE671FB7@netmatters.co.uk> Date: Fri, 18 Sep 1998 16:15:29 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Plug-in wanted for RGB-HSV conversion References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"-3AWI.0.b24.eZd0s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/358 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 673 Status: O Hello all, I still need help with converting RGB images within a macro into HSV images. Is there a plug-in out there that does the job. Alternatively could anyone explain how to convert Red Green and Blue images into Hue Saturation intensity images. I would also appreciate suggestions for a good cytoplasmic counterstain for Macrophages, ones that would work with DAB or FITC staining, preferable one which does not stain acid fast bacteria. Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Fri Sep 18 11:57 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id LAA20925; Fri, 18 Sep 1998 11:57:04 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 11:57:04 -0400 (EDT) Message-ID: Date: 18 Sep 1998 17:44:54 +0200 From: "Mark Wunsch" Subject: labeling area measurements To: "nih questions" X-Mailer: Mail*Link SMTP-QM 4.1.0 Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA19754 Resent-Message-ID: <"K2YrK.0.vq4.__d0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/359 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Length: 669 Status: O Betreff: Uhrzeit:17:35 Uhr MITTEILUNG labeling area measurements Datum:18.09.1998 Hello all, I am studying coral reef communities from underwater video images. I need to measure the size of individuals of different species by surrounding them manually (contrast usually is low), i.e. 10 species in a single image. To transfer the measurements related to the species I would like to find a macro which allows me to label the areas of the individuals with numbers and afterwards to export them to an EXCEL table. Has anybody experience with this kind of application, knows a macro? Cheers Mark From nih-image-request@io.ece.drexel.edu Fri Sep 18 12:14 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA22396; Fri, 18 Sep 1998 12:14:06 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 12:14:06 -0400 (EDT) X-Sender: mathias@ruby.unibe.ch Message-Id: Mime-Version: 1.0 Date: Fri, 18 Sep 1998 18:04:20 +0100 To: nih-image@io.ece.drexel.edu From: mathias@mpi.unibe.ch (mathias rickli) Subject: Analyze Particles... Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id MAA21262 Resent-Message-ID: <"8MXJ91.0.gC5.YFe0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/360 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 491 Status: O Is there a possibility to enlarge the perimeter of the field to analize to over 10000 pixles? This problem arrises when you wish to analize an image which is composed by an aligned set of 4x4 1MB images, for example. Due to resolution requirements I don't want to use lighter (512K) images. Thanks for answering mathias Mathias Rickli, dipl. Min. Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 From nih-image-request@io.ece.drexel.edu Fri Sep 18 12:44 EDT 1998 Received: (from lists@localhost) by io.ECE.Drexel.EDU (8.8.8/8.8.8) id MAA24768; Fri, 18 Sep 1998 12:44:42 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 12:44:42 -0400 (EDT) Message-Id: <36028D3B.B0FBCBCD@purdue.edu> Date: Fri, 18 Sep 1998 11:41:31 -0500 From: Kris Jorgensen Reply-To: kris@purdue.edu Organization: Purdue University X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Peak detection and line scanning References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"r-hRc3.0.2m5.hge0s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/361 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 532 Status: O I need a macro or plugin that will determine the location of a single peak on an image. The peak is actually a ridge since the data is a 2D image and peak extends from top to bottom but is not a simple straight line. If I have to write my own macro any code fragments that would help me would be appriciated. Things like something that would scan each line from top to bottom, etc Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris From nih-image-request@io.ece.drexel.edu Fri Sep 18 14:23 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA01462; Fri, 18 Sep 1998 14:23:05 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 14:23:05 -0400 (EDT) From: SolamereTG@aol.com Message-ID: Date: Fri, 18 Sep 1998 14:09:04 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: labeling area measurements Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"DbYIL.0.U6.O8g0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/362 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 626 Status: O You can use the free hand tool to draw multiple roi's by holding down the shift key between each free hand (surround) operation. You could outline all of the individuals from one species and then use measure to get the area and perimeter for that species. Repeat the operation for each species. Exporting the data to your spread sheet is a straight forward one you have done all of the species outlines. Also if you wish to measure the same set of multiple ROIs thru a stack of images you may use the restoreroi command in a macro to automate the repeating measurement. Good Luck George A. Peeters Solamere Technology Group From nih-image-request@io.ece.drexel.edu Fri Sep 18 18:33 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA18097; Fri, 18 Sep 1998 18:33:40 -0400 (EDT) Resent-Date: Fri, 18 Sep 1998 18:33:40 -0400 (EDT) Message-Id: In-Reply-To: <199809181506.LAA15716@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Fri, 18 Sep 1998 18:27:39 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Image/J & linux Cc: imagej@list.nih.gov Resent-Message-ID: <"Q8Vbt1.0.CB4.Cqj0s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/363 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 626 Status: O >Has anyone on the list got Image/J running under linux? > >If so, I would be interested in knowing the procedure. 1) Download JDK 1.1.6 from http://www.blackdown.org and install it 2) Download the Image/J class files and source code (a single .zip file) from http://rsb.info.nih.gov/ij/ 3) Unzip the .zip file, which creates a directory named ImageJ 4) Change to the ImageJ directory and type "java ij.ImageJ" You will also be able to run Image/J as an applet using the command appletviewer http://rsbweb.nih.gov/~wayne/ij/applet11 There current downloadable version is 0.85, but 0.91 is due in a few days. -wayne From nih-image-d-request@io.ece.drexel.edu Sat Sep 19 06:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA13077; Sat, 19 Sep 1998 06:08:18 -0400 (EDT) Date: Sat, 19 Sep 1998 06:08:18 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809191008.GAA13077@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #65 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/65 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10654 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 65 Today's Topics: NIH-Image and DT3155 [ UPongs@tkc.de ] Re: gray/white segmentation [ Jonathan Nissanov ] Re: labeling area measurements [ SolamereTG@aol.com ] Re: Image/J & linux [ Wayne Rasband ] ------------------------------ Date: Fri, 18 Sep 1998 12:24:06 +0200 From: UPongs@tkc.de To: nih-image@io.ece.drexel.edu Subject: NIH-Image and DT3155 Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Imagers! Is there anyone of you, who has experiences with a Data Translation Framegrabber DT3155 in a Macintosh (which one - 7300, 7500 or ???) together with NIH-Image? How can I connect both? Any ideas and help is really welcome Uwe Martin Pongs ------------------------------ Date: Fri, 18 Sep 1998 10:49:19 -0400 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: gray/white segmentation Message-Id: Content-Type: text/plain; charset="us-ascii" >Is NIH image capable of automatically segmenting gray and white matter? >Also,. is it possible to view 3 planes simultaneously? > See object image for 3plane view. -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Fri, 18 Sep 98 10:29:31 CDT From: Chris Liner To: nih-image@io.ece.drexel.edu Cc: cll@utulsa.edu (Chris Liner) Subject: Image/J & linux Message-Id: <199809181506.LAA15716@io.ECE.Drexel.EDU> Has anyone on the list got Image/J running under linux? If so, I would be interested in knowing the procedure. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] ------------------------------ Date: Fri, 18 Sep 1998 16:02:57 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: gray/white segmentation Message-ID: <3602842F.9363D444@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Pauline Seta Yaralian wrote: > Is NIH image capable of automatically segmenting gray and white matter? > Also,. is it possible to view 3 planes simultaneously? > > Pauline S. Yaralian > Research Assistant > Clinical Neuroscience Laboratory > University of Southern California > Department of Psychology > Los Angeles, Ca. 90089-1061 > e mail: yaralian@rcf.usc.edu > Office:(213) 740-2220 > Fax:(213) 746-908 If by three planes simultaneously you mean X,Y,Z axis images, Object Image (a spin-off of NIH Image available from http://simon.bio.uva.nl/object-imageButtons.html or via the NIH site) uses one of the best approaches to this problem I've ever seen. Under the Sacks menu choose slice 2D or slice 3D. These will give you a live 3-planar view of any image stack. This is extremely useful for 3D data sets. Object Image is Mac only, if you are using a PC I am afraid that you will have to make do with drawing a line across you image and then choosing reslice, repeat this lots of times until you find the point in the 3D image you are looking for. Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Fri, 18 Sep 1998 16:15:29 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Plug-in wanted for RGB-HSV conversion Message-ID: <3602871F.BE671FB7@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hello all, I still need help with converting RGB images within a macro into HSV images. Is there a plug-in out there that does the job. Alternatively could anyone explain how to convert Red Green and Blue images into Hue Saturation intensity images. I would also appreciate suggestions for a good cytoplasmic counterstain for Macrophages, ones that would work with DAB or FITC staining, preferable one which does not stain acid fast bacteria. Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: 18 Sep 1998 17:44:54 +0200 From: "Mark Wunsch" To: "nih questions" Subject: labeling area measurements Message-ID: Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: 8bit Betreff: Uhrzeit:17:35 Uhr MITTEILUNG labeling area measurements Datum:18.09.1998 Hello all, I am studying coral reef communities from underwater video images. I need to measure the size of individuals of different species by surrounding them manually (contrast usually is low), i.e. 10 species in a single image. To transfer the measurements related to the species I would like to find a macro which allows me to label the areas of the individuals with numbers and afterwards to export them to an EXCEL table. Has anybody experience with this kind of application, knows a macro? Cheers Mark ------------------------------ Date: Fri, 18 Sep 1998 18:04:20 +0100 From: mathias@mpi.unibe.ch (mathias rickli) To: nih-image@io.ece.drexel.edu Subject: Analyze Particles... Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Is there a possibility to enlarge the perimeter of the field to analize to over 10000 pixles? This problem arrises when you wish to analize an image which is composed by an aligned set of 4x4 1MB images, for example. Due to resolution requirements I don't want to use lighter (512K) images. Thanks for answering mathias Mathias Rickli, dipl. Min. Mineralogisch-Petrographisches Institut Universitt Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 ------------------------------ Date: Fri, 18 Sep 1998 11:41:31 -0500 From: Kris Jorgensen To: nih-image@io.ece.drexel.edu Subject: Peak detection and line scanning Message-Id: <36028D3B.B0FBCBCD@purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I need a macro or plugin that will determine the location of a single peak on an image. The peak is actually a ridge since the data is a 2D image and peak extends from top to bottom but is not a simple straight line. If I have to write my own macro any code fragments that would help me would be appriciated. Things like something that would scan each line from top to bottom, etc Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris ------------------------------ Date: Fri, 18 Sep 1998 14:09:04 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: labeling area measurements Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit You can use the free hand tool to draw multiple roi's by holding down the shift key between each free hand (surround) operation. You could outline all of the individuals from one species and then use measure to get the area and perimeter for that species. Repeat the operation for each species. Exporting the data to your spread sheet is a straight forward one you have done all of the species outlines. Also if you wish to measure the same set of multiple ROIs thru a stack of images you may use the restoreroi command in a macro to automate the repeating measurement. Good Luck George A. Peeters Solamere Technology Group ------------------------------ Date: Fri, 18 Sep 1998 18:27:39 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Cc: imagej@list.nih.gov Subject: Re: Image/J & linux Message-Id: Content-Type: text/plain; charset="us-ascii" >Has anyone on the list got Image/J running under linux? > >If so, I would be interested in knowing the procedure. 1) Download JDK 1.1.6 from http://www.blackdown.org and install it 2) Download the Image/J class files and source code (a single .zip file) from http://rsb.info.nih.gov/ij/ 3) Unzip the .zip file, which creates a directory named ImageJ 4) Change to the ImageJ directory and type "java ij.ImageJ" You will also be able to run Image/J as an applet using the command appletviewer http://rsbweb.nih.gov/~wayne/ij/applet11 There current downloadable version is 0.85, but 0.91 is due in a few days. -wayne -------------------------------- End of nih-image-d Digest V98 Issue #65 *************************************** From nih-image-request@io.ece.drexel.edu Sat Sep 19 14:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA20665; Sat, 19 Sep 1998 14:16:39 -0400 (EDT) Resent-Date: Sat, 19 Sep 1998 14:16:39 -0400 (EDT) Message-ID: <360400C4.6AACA5C8@netmatters.co.uk> Date: Sat, 19 Sep 1998 19:06:50 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: JCR's Image Processing Handbook Question References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"XmfNO3.0.Nn4.ZA_0s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/364 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 478 Status: O Does anyone know the details of the Range Kernel used in John Russ's Image Processing Handbook on page 363 FIG 21D? Silly question really, I guess John does ;-) Anyway, I would greatly appreciate the details of the kernel. Many thanks as always, Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Sun Sep 20 02:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA14840; Sun, 20 Sep 1998 02:12:13 -0400 (EDT) Resent-Date: Sun, 20 Sep 1998 02:12:13 -0400 (EDT) X-Sender: a_team@pop.dds.nl Message-Id: In-Reply-To: <199809191002.GAA12416@io.ece.drexel.edu> Mime-Version: 1.0 Date: Sat, 19 Sep 1998 20:49:46 +0200 To: nih-image@io.ece.drexel.edu From: "Anneke M.Th. Harbers and Ard Jonker" Subject: Re: nih-image-d Digest V98 #65 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id BAA13543 Resent-Message-ID: <"TtmeB1.0.qJ3.Dc91s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/365 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 741 Status: O >I need a macro or plugin that will determine the location of a single >peak on an image. The peak is actually a ridge since the data is a 2D >image and peak extends from top to bottom but is not a simple straight >line. > >If I have to write my own macro any code fragments that would help me >would be appriciated. Things like something that would scan each line >from top to bottom, etc Hint: add all lines, linewise, top to bottom. That can be done by 'plot profile' by selecting a rectangular area that is wider than it is high (ie. a line that is as wide as your image is high, and is as long as your image is wide). The plot array will contain the summed pixel values. Now only find the maximum plot value. Hope this helps. Ard From nih-image-d-request@io.ece.drexel.edu Sun Sep 20 06:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA03608; Sun, 20 Sep 1998 06:09:01 -0400 (EDT) Date: Sun, 20 Sep 1998 06:09:01 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809201009.GAA03608@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #66 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/66 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2313 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 66 Today's Topics: JCR's Image Processing Handbook Ques [ Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: JCR's Image Processing Handbook Question Message-ID: <360400C4.6AACA5C8@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Does anyone know the details of the Range Kernel used in John Russ's Image Processing Handbook on page 363 FIG 21D? Silly question really, I guess John does ;-) Anyway, I would greatly appreciate the details of the kernel. Many thanks as always, Jeremy ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Sat, 19 Sep 1998 20:49:46 +0200 From: "Anneke M.Th. Harbers and Ard Jonker" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #65 Message-Id: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit >I need a macro or plugin that will determine the location of a single >peak on an image. The peak is actually a ridge since the data is a 2D >image and peak extends from top to bottom but is not a simple straight >line. > >If I have to write my own macro any code fragments that would help me >would be appriciated. Things like something that would scan each line >from top to bottom, etc Hint: add all lines, linewise, top to bottom. That can be done by 'plot profile' by selecting a rectangular area that is wider than it is high (ie. a line that is as wide as your image is high, and is as long as your image is wide). The plot array will contain the summed pixel values. Now only find the maximum plot value. Hope this helps. Ard -------------------------------- End of nih-image-d Digest V98 Issue #66 *************************************** From nih-image-request@io.ece.drexel.edu Sun Sep 20 22:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA07201; Sun, 20 Sep 1998 22:10:12 -0400 (EDT) Resent-Date: Sun, 20 Sep 1998 22:10:12 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Mon, 21 Sep 1998 11:56:43 GMT+1000 Subject: Mail list Archives since changeover 98/7/6? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <93F261A2CB1@rna.bio.mq.edu.au> Resent-Message-ID: <"n4Ha93.0.kT1.C7R1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/366 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 494 Status: O Archives available via http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/ or gopher://gopher.soils.umn.edu dont appear to have been updated since the mail list moved on 98/7/6. Are we in danger of losing this valuable resource ? or is the matter in hand with just some lag at changeover? Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Mon Sep 21 01:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA20031; Mon, 21 Sep 1998 01:16:57 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 01:16:57 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: wacb@aplcomm.jhuapl.edu, nih-image@io.ece.drexel.edu Date: Mon, 21 Sep 1998 15:05:51 GMT+1000 Subject: Re: Q: explanationof MakeMovie options? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <9424D890085@rna.bio.mq.edu.au> Resent-Message-ID: <"mb_p9.0.pd4.RuT1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/367 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2170 Status: O >Date: Wed, 16 Sep 1998 20:24:56 -0500 >From: Bill Christens-Barry >Subject: Q: explanationof MakeMovie options? >To: nih-image@io.ece.drexel.edu > >The NIH Image online manual gives the following for the macro MakeMovie >command: > >MakeMovie('str',frames,interval) >Captures a sequence of video frames to a stack. 'str' is some combination >of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first', >'trigger each', and 'dialog'. Frames is the number of frames to capture, >and interval is the interval between frames in seconds. See the >"Movie Making" macro file for examples. > >Some of the options are not used in the "Movie Making" macro file. For >example, the 'str' options 'blind', 'buffer', and 'existing' don't appear. >Can anyone explain their usage? Also, the "Movie Making" macro file uses >values of -1 for the frames and interval arguments in one of the example >macros that uses the 'dialog' argument. What is the meaning of this? > >Finally, can the MakeMovie command use a sub-second interval, and will this >appear in time stamp? > >Thanks. > >Bill Christens-Barry Bill, 'blind' captures movie without updateing onscreen display so that capture is faster (see your final question). 'existing' refers to 'movie' stack ie write to pre'existing' 'movie' stack or generate new one prior to capture. buffer (I think) refers to use of on-capture-board buffer memory for Scion. -1 values specify use previously assigned values eg by previous makeMovie or dialogue. MakeMovie will use fractional second intervals. Actual capture speed depends on hardware/ capture ROI size (ie smaller frames, faster capture; 'blind' capture is faster than display. With Mac G3/Scion LG3 you should get full 30 (25 CCIR) frames/second but note that interleaved line operation of video will allow split fields of 1/2 vertical resolution at 2 x rate to be obtained (see supplied macros). Timestamps (including sub-second intervals) are recorded. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Mon Sep 21 05:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA06745; Mon, 21 Sep 1998 05:22:33 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 05:22:33 -0400 (EDT) Message-ID: <19980921090358.19439.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Smoothing Histogram Date: Mon, 21 Sep 1998 02:03:58 PDT Resent-Message-ID: <"tqw1V3.0.3J1.WQX1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/368 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 721 Status: O Hello, is there a way to "smoothen" the histogram in the NT-Image with a macro? We want to take the average value between three color values in the histogram. Furthermore, is it possible to get not only the global maximum value from the histogram, but from other maxima, too? Any help would be greatly appreciated. Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Mon Sep 21 08:37 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA19830; Mon, 21 Sep 1998 08:37:26 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 08:37:26 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 21 Sep 1998 08:28:19 -0400 To: "Mark Wunsch" From: Laird Bloom Subject: Re: labeling area measurements Cc: nih-image@io.ece.drexel.edu Resent-Message-ID: <"pRwAj.0.9a4._Ka1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/369 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 10169 Status: O Hi Mark, Here are two sets of macros I've written to do what you described. One is for use with saved images, and the other works well for live images. The "measure areas on scope" set of macros saves data as a single column of numbers which can easily be cut and pasted directly into Excel. You can modify the output to include a sample name; in the Times 'Measure Area [M]' macro, you can define a string variable for the sample name, include a GetString line to allow you to type in the sample name at each step, and add the sample name into the Writeln step. The two-column data table should be pasted into Excel without difficulty. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research Times{The following is a set of instructions for the setup with our microscope; you should copy the two sets of macros below into separate Image files before use. We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Area measurement macros This set of macros will allow you to measure the area of a region you draw, as described above, to get an average of all the areas you measure, and to save the data in a text file and a modified version of your image with the areas drawn in . The output can be imported to Excel for analysis but requires some editing to work efficiently. If you use a lot of saved images, you may want to modify the data output features of the "Area measurement macro" set to be more like that of the "Measure areas on scope" set. >From Scion Image "Special" menu, select "Load Macros" and open the "Area measurement macros" file in the Scion Image folder on the desktop. Then open your first image. Type "S" or select "Set up area measurements" in Special menu. The computer will ask you to name a file for your results. Use one of the outlining tools from the tools palette to outline the region you want to measure. The heart-shaped dotted line allows you to draw freehand regions with the mouse. Then type "M" (or select "Measure area" in the Special menu), and the computer will draw a line around what you just outlined, give the region a number, print the area in pixels in the center of the region, and enter the area in the results file, shown at the bottom of the screen. You can do this repeatedly on the same image. The total area of the image will also be given in the results file. When you have finished with an image, type "F" or select "Finish area measurements" in the Special menu, and the computer will average all of the measurements you made, save the modified image file with a new name ("[your file name] + area measurements"), and ask you which file to open next. (At this point, you need to save the modified images. Just delete them later if you don't want them.) Click on cancel if you don't want to measure other samples. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; {"Area measurement macros": The following set of macros should be in a separate Image file from the preceding set. It was designed for measuring areas on saved files.} { modified area measurement macro; please do not change this file. Each macro uses the global variables listed at the top. } var {Global variable, initially zero} n,d,nLines,j,total,TotalArea:integer; mean:real; nOut,SampleName,ImageName:string; procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; {Fill; Invert; KillRoi;} x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('WithBackground'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; procedure EndProcedure; begin DisposeAll; mean:=total/j; SelectWindow(nOut); Writeln(' Mean area = ',mean:0); Save; {nLines:=nLines+10; Open(nOut); MoveWindow(120,nLines);} Open(' '); total:=0; j:=0; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nOut); Moveto(120,560); If j=1 then write (ImageName,' (image area =',TotalArea,') '); SetFont('Times'); SetFontSize(12); Write(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set Up Area Measurements [S]'; var width,height:integer; begin ImageName:=WindowTitle; nOut:=GetString('name for results file','Results'); NewTextWindow(nOut); MoveWindow(120,550); total:=0; j:=0; SelectWindow(ImageName); SelectAll; Measure; TotalArea:=rArea[rCount]; KillRoi; end; macro 'Finish Area Measurement [F]'; var nSave:string; begin If j=0 then j:=1; SaveAs(ImageName,' + area measurements'); EndProcedure; end; From nih-image-request@io.ece.drexel.edu Mon Sep 21 09:51 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24629; Mon, 21 Sep 1998 09:50:59 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 09:50:59 -0400 (EDT) From: "Grace,John" To: Subject: Re: nih-image-d Digest V98 #66 Message-Id: <0055600003289300000002L002*@MHS> Date: Mon, 21 Sep 1998 08:34:26 -0500 Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA23368 Resent-Message-ID: <"2jk5K2.0.Nj5.TNb1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/370 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 110 Status: O Dear Imagers, Where can I get John Russ's Image Processing Handbook?? Thanks, John Grace Abbott Laboratories From nih-image-request@io.ece.drexel.edu Mon Sep 21 10:51 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28662; Mon, 21 Sep 1998 10:51:20 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 10:51:20 -0400 (EDT) Message-Id: <3.0.32.19980921102930.006a4c50@mailserver3.nist.gov> X-Sender: pbarker@mailserver3.nist.gov X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 21 Sep 1998 10:29:30 -0400 To: nih-image@io.ece.drexel.edu From: "Peter E. Barker, Ph.D." Subject: Re: nih-image-d Digest V98 #66/RUSS BOOK Mime-Version: 1.0 Resent-Message-ID: <"Wqt1V.0.cf6.wCc1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/371 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="=====================_906402570==_" Content-Length: 16436 Status: O --=====================_906402570==_ Content-Type: text/plain; charset="us-ascii" At 08:34 AM 9/21/98 -0500, you wrote: >Dear Imagers, >Where can I get John Russ's Image Processing Handbook?? >Thanks, >John Grace >Abbott Laboratories > > Dear John, See attachment RE: Russ' book. Note there may be a newer edition-check with CRC Press. P. E. Barker, Ph.D. 831.01/NIST U. S. Dept. Commerce Gaithersburg, Maryland 20899-0001 301-975-5402 --=====================_906402570==_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="FYI.htm" =20 Amazon.com: A Glance: The Image Processing Handbook
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Synopsis
= Thoroughly updated to reflect the rapid developments in imaging= technology, this indispensable guide delivers an impressive array of= concepts and techniques to help readers take full advantage of high-end= imaging software. It adds a new dimension to the methods of enhancing= images presented in the bestselling first edition.

Booknews, Inc. , March 1,= 1995
A handbook that presents an extensive collection of= image processing tools so that users of computer-based systems can both= understand those methods provided in packaged software, and program those= additions which may be needed for particular applications. Comparisons are= presented of different algorithms that may be used for similar purposes,= using a selection of representative pictures from light and electron= microscopes, as well as macroscopic, satellite, and astronomical images.= This revised and updated edition adds new chapters on the measurement of= images and the subsequent interpretation of the data, and on printing and= storing images, including the use of image databases. Annotation copyright= Book News, Inc. Portland, Or.

The publisher, CRC Press = http://www.crcpress.com , August 21, 1996
Today's= sophisticated computer professionals need powerful tools to help them= visualize graphic information. Rapid developments in imaging technology= have created a substantial demand for this thoroughly updated Second= Edition of The Image Processing Handbook.

This indispensible guide= delivers an impressive array of concepts and techniques to help you take= full advantage of your high-end imaging software. It adds a new dimension= to the methods of enhancing images presented in the best-selling first= edition:

Acquisition of gray-scale and color images

Methods for= correcting imaging defects, such as geometric distortion and non-uniform= illumination

Selective enhancement of images, such as edge finding,= noise suppression, and texture extraction

Segmentation of images

= Processing of binary images using morphological and Boolean operations

= Three-dimensional imaging using tomographic reconstruction, serial= sections, and volumetric and surface rendering methods

FEATURES:

= Presents a balanced and complete description of frequency space methods= using extensive mathematical presentation and spatial domain= processing

Offers comparisons of different algorithms used for similar= pruposes

Requires only a modest technical background in mathematics or= computers to be able to fully utilize the vcast wealth of material in the= handbook

New data on printing and storing images, including important= coverage of image compression

Advance information on forthcoming= technologies

New chapter on image measurement, including applications of= real-world measurement, topics on densitometry, and color information

= Expanded and updated coverage of image acquisitions, including a discussion= on flatbed scanners

Augmented coverage of 3D image processing

More= than 120 full-color images throughout the book

=20 =20

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=20 --=====================_906402570==_-- From nih-image-request@io.ece.drexel.edu Mon Sep 21 12:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06115; Mon, 21 Sep 1998 12:53:17 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 12:53:17 -0400 (EDT) Content-Return: allowed Date: Mon, 21 Sep 1998 09:07:04 -0400 From: "Dibble, Nicole A" Subject: unsubscribe To: "'nih-image@io.ece.drexel.edu'" Message-Id: <215D10CDFC93D111A11600805FBB7C28211D8F@BILLHALEY> Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Resent-Message-ID: <"aErU91.0.sC1.70e1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/372 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 5 Status: O From nih-image-request@io.ece.drexel.edu Mon Sep 21 20:29 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA10076; Mon, 21 Sep 1998 20:29:06 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 20:29:06 -0400 (EDT) X-Sender: patw@mail.med.usyd.edu.au Message-Id: Mime-Version: 1.0 Date: Tue, 22 Sep 1998 10:22:18 +1000 To: nih-image@io.ece.drexel.edu From: Patricia Waley Subject: PC files Resent-Message-ID: <"mfHTb2.0.L52.ulk1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/373 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 726 Status: O I have recently found problems opening my files in NIH Image with the message "File cannot be opened as the application PC can not be found" appearing. These 8 bit Tiff files have been made on a PC using Optimas and saved on to the floppy disc drive. I have previously only had similar problems opening files if they were saved onto the hard drive and then copied onto a disc. Any suggestions? ________________________________________________________________________________ Patricia Waley Centre for Education and Research on Ageing Concord Hospital Concord NSW 2139 Ph: (02) 9767 6586 Fax: (02) 9767 8315 Email: patw@pathology.usyd.edu.au ________________________________________________________________________________ From nih-image-d-request@io.ece.drexel.edu Mon Sep 21 20:39 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11080; Mon, 21 Sep 1998 20:39:38 -0400 (EDT) Date: Mon, 21 Sep 1998 20:39:38 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809220039.UAA11080@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #67 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/67 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 34980 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 67 Today's Topics: Mail list Archives since changeover [ GJOSS@rna.bio.mq.edu.au ] plugin [ Shawn Makanvand ] Re: nih-image-d Digest V98 #66 [ "Grace,John" Archives available via http://www.soils.agri.umn.edu/infoserv/lists/nih-image/archives/ or gopher://gopher.soils.umn.edu dont appear to have been updated since the mail list moved on 98/7/6. Are we in danger of losing this valuable resource ? or is the matter in hand with just some lag at changeover? Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Sun, 20 Sep 1998 21:23:45 -0700 From: Shawn Makanvand To: nih-image-d@io.ece.drexel.edu Subject: plugin Message-ID: <3605D4D1.64EA@earthlink.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Imagers: I am trying to write a plugin for the NIH Image software on the MAC. I would like to use Metrowerks Code Warrior Pro 2. Any sample projects which I have been able to download so far are all Think C projects. Can anyone help me by either pointing me to a sample plugin which performs image aquisition written in Code Warrior Pro 2, that I could modify to meet my needs, or does anyone have access to a handy converter which will successfully convert these older projects to work with Code Warrior Pro 2. Thank you in advance. Shawn Makanvand shawnmak@earthlink.net ------------------------------ Date: Mon, 21 Sep 1998 15:05:51 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: wacb@aplcomm.jhuapl.edu, nih-image@io.ece.drexel.edu Subject: Re: Q: explanationof MakeMovie options? Message-ID: <9424D890085@rna.bio.mq.edu.au> >Date: Wed, 16 Sep 1998 20:24:56 -0500 >From: Bill Christens-Barry >Subject: Q: explanationof MakeMovie options? >To: nih-image@io.ece.drexel.edu > >The NIH Image online manual gives the following for the macro MakeMovie >command: > >MakeMovie('str',frames,interval) >Captures a sequence of video frames to a stack. 'str' is some combination >of 'blind', 'buffer', 'time stamp', 'existing', 'trigger first', >'trigger each', and 'dialog'. Frames is the number of frames to capture, >and interval is the interval between frames in seconds. See the >"Movie Making" macro file for examples. > >Some of the options are not used in the "Movie Making" macro file. For >example, the 'str' options 'blind', 'buffer', and 'existing' don't appear. >Can anyone explain their usage? Also, the "Movie Making" macro file uses >values of -1 for the frames and interval arguments in one of the example >macros that uses the 'dialog' argument. What is the meaning of this? > >Finally, can the MakeMovie command use a sub-second interval, and will this >appear in time stamp? > >Thanks. > >Bill Christens-Barry Bill, 'blind' captures movie without updateing onscreen display so that capture is faster (see your final question). 'existing' refers to 'movie' stack ie write to pre'existing' 'movie' stack or generate new one prior to capture. buffer (I think) refers to use of on-capture-board buffer memory for Scion. -1 values specify use previously assigned values eg by previous makeMovie or dialogue. MakeMovie will use fractional second intervals. Actual capture speed depends on hardware/ capture ROI size (ie smaller frames, faster capture; 'blind' capture is faster than display. With Mac G3/Scion LG3 you should get full 30 (25 CCIR) frames/second but note that interleaved line operation of video will allow split fields of 1/2 vertical resolution at 2 x rate to be obtained (see supplied macros). Timestamps (including sub-second intervals) are recorded. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Mon, 21 Sep 1998 02:03:58 PDT From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Smoothing Histogram Message-ID: <19980921090358.19439.qmail@hotmail.com> Content-Type: text/plain Hello, is there a way to "smoothen" the histogram in the NT-Image with a macro? We want to take the average value between three color values in the histogram. Furthermore, is it possible to get not only the global maximum value from the histogram, but from other maxima, too? Any help would be greatly appreciated. Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Mon, 21 Sep 1998 08:28:19 -0400 From: Laird Bloom To: "Mark Wunsch" Cc: nih-image@io.ece.drexel.edu Subject: Re: labeling area measurements Message-Id: Content-Type: text/enriched; charset="us-ascii" Hi Mark, Here are two sets of macros I've written to do what you described. One is for use with saved images, and the other works well for live images. The "measure areas on scope" set of macros saves data as a single column of numbers which can easily be cut and pasted directly into Excel. You can modify the output to include a sample name; in the Times 'Measure Area [M]' macro, you can define a string variable for the sample name, include a GetString line to allow you to type in the sample name at each step, and add the sample name into the Writeln step. The two-column data table should be pasted into Excel without difficulty. Please contact me if you have questions. Laird Bloom MIT Center for Cancer Research Times{The following is a set of instructions for the setup with our microscope; you should copy the two sets of macros below into separate Image files before use. We use Scion Image 1.62, essentially the same as NIH Image 1.61. You may need to modify the StartCapturing and StopCapturing commands if the "measure areas on scope" macro, depending on the source of your input. Area measurement macros This set of macros will allow you to measure the area of a region you draw, as described above, to get an average of all the areas you measure, and to save the data in a text file and a modified version of your image with the areas drawn in . The output can be imported to Excel for analysis but requires some editing to work efficiently. If you use a lot of saved images, you may want to modify the data output features of the "Area measurement macro" set to be more like that of the "Measure areas on scope" set. >From Scion Image "Special" menu, select "Load Macros" and open the "Area measurement macros" file in the Scion Image folder on the desktop. Then open your first image. Type "S" or select "Set up area measurements" in Special menu. The computer will ask you to name a file for your results. Use one of the outlining tools from the tools palette to outline the region you want to measure. The heart-shaped dotted line allows you to draw freehand regions with the mouse. Then type "M" (or select "Measure area" in the Special menu), and the computer will draw a line around what you just outlined, give the region a number, print the area in pixels in the center of the region, and enter the area in the results file, shown at the bottom of the screen. You can do this repeatedly on the same image. The total area of the image will also be given in the results file. When you have finished with an image, type "F" or select "Finish area measurements" in the Special menu, and the computer will average all of the measurements you made, save the modified image file with a new name ("[your file name] + area measurements"), and ask you which file to open next. (At this point, you need to save the modified images. Just delete them later if you don't want them.) Click on cancel if you don't want to measure other samples. "Measure areas on scope" macro It is sometimes convenient to measure areas on many parts of a sample without having to save each image and reopen it. To do this and save the areas as a set of numbers suitable for import into Excel, load the "Measure areas on scope" macro file. Data are saved as a single column of numbers for each sample, which can be copied and pasted into a single column in Excel. To start, be sure to close the video camera window. Then type P or pull down the "Set up measurement parameters" macro. It will ask you whether you want to save each image before and after labeling areas, and then it will ask you for the name of your first sample and begin showing live video images. When you have found the image you want, click the mouse button or press the shift, option, or control keys. (You may have to hold the key or mouse button down for a fraction of a second or push it a second time.) Then select a drawing tool, draw around an area you wish to measure, and press the M key when you're ready. The area of each region in pixels (this can be changed to mm, etc from the pulldown menus) will show up in a text file on the right of the screen and is saved after each entry. Be careful if you modify this file while adding data to it (e.g., if the font is too large to let you see all your data); if the text is still highlighted when you measure your next area, all of the highlighted data will be deleted (based on sad but true experience). Keep drawing and pressing M until you're done with that image. Then press V (or pull down "New view of this sample" macro), get your next image, and continue. To score another sample (and save the counts in a new file), press S or pull down "Score next sample" macro. You can open this file in Excel, or copy and paste as a single column into a single Excel file for all of you data (more convenient).} {"Measure areas on scope" macro file follows: modified area measurement macro--use while measuring areas while at microscope. Saves data for each sample in a separate file as a column of numbers; import into Excel for analysis. } var {Global variables} n,d,nLines,j,total,TotalArea:integer; mean:real; SaveMod,nSave,nSample,SampleName,ImageName:string; procedure GetImageToMeasure; begin StartCapturing; Repeat Wait(.1); Until Button or KeyDown('shift') or KeyDown('option') or KeyDown('control'); StopCapturing; SetPicName(nSample,' Image'); SelectWindow(nSample,' Image'); if nSave='Yes' then Save; end procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetBackgroundColor(1); SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('With Background'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nSample); If j=1 then writeln (nSample); SetFont('Times'); SetFontSize(12); Writeln(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set parameters for area measurements [P]'; var width,height:integer; begin nSave:=GetString('Save each image as a 1.2 MB file?','Yes'); SaveMod:=GetString('Save each image with areas marked?','Yes'); nSample:=GetString('name of first sample'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; macro 'New view of current sample [v]'; begin SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); DisposeAll; GetImageToMeasure; end; macro 'New Sample [S]'; begin If j=0 then j:=1; SelectWindow(ImageName); if SaveMod='Yes' then SaveAs(ImageName,' + area measurements'); Dispose; SelectWindow(nSample); mean:=total/j; writeln('Mean ='); write(mean); save; dispose; nSample:=GetString('Name of next sample:'); {Places data window at far right side of screen. You may need to modify this to see it on your screen} NewTextWindow(nSample,80,600); MoveWindow(740,40); total:=0; GetImageToMeasure; j:=0; end; {"Area measurement macros": The following set of macros should be in a separate Image file from the preceding set. It was designed for measuring areas on saved files.} { modified area measurement macro; please do not change this file. Each macro uses the global variables listed at the top. } var {Global variable, initially zero} n,d,nLines,j,total,TotalArea:integer; mean:real; nOut,SampleName,ImageName:string; procedure LabelAreaInCenter; var left, top, width, height, x, y: integer; scale: real; unit: string; begin GetRoi(left,top,width,height); if width=0 then begin PutMessage('This macro requires a selection.'); exit; end; SaveState; InvertY(false); SetForegroundColor(255); {black} SetOptions('Area; Mean; X-Y Center'); GetScale(scale, unit); Measure; DrawBoundary; {Fill; Invert; KillRoi;} x := round(rX[rCount] * scale); y := round(rY[rCount] * scale); MoveTo(x-5, y); SetFont('Times'); SetFontSize(9); SetText('WithBackground'); Writeln('region ',j:0); Write(rArea[rCount]:1:0); RestoreState; end; procedure EndProcedure; begin DisposeAll; mean:=total/j; SelectWindow(nOut); Writeln(' Mean area = ',mean:0); Save; {nLines:=nLines+10; Open(nOut); MoveWindow(120,nLines);} Open(' '); total:=0; j:=0; end; macro 'Measure Area [M]'; begin j:=j+1; LabelAreaInCenter; ImageName:=WindowTitle; SelectWindow(nOut); Moveto(120,560); If j=1 then write (ImageName,' (image area =',TotalArea,') '); SetFont('Times'); SetFontSize(12); Write(' ',rArea[rCount]:1:0); rUser1[j]:=rArea[rCount]; total:=total+rArea[rCount]; Save; SelectWindow(ImageName); end macro 'Set Up Area Measurements [S]'; var width,height:integer; begin ImageName:=WindowTitle; nOut:=GetString('name for results file','Results'); NewTextWindow(nOut); MoveWindow(120,550); total:=0; j:=0; SelectWindow(ImageName); SelectAll; Measure; TotalArea:=rArea[rCount]; KillRoi; end; macro 'Finish Area Measurement [F]'; var nSave:string; begin If j=0 then j:=1; SaveAs(ImageName,' + area measurements'); EndProcedure; end; ------------------------------ Date: Mon, 21 Sep 1998 08:34:26 -0500 From: "Grace,John" To: Subject: Re: nih-image-d Digest V98 #66 Message-Id: <0055600003289300000002L002*@MHS> Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit Dear Imagers, Where can I get John Russ's Image Processing Handbook?? Thanks, John Grace Abbott Laboratories ------------------------------ Date: Mon, 21 Sep 1998 10:29:30 -0400 From: "Peter E. Barker, Ph.D." To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #66/RUSS BOOK Message-Id: <3.0.32.19980921102930.006a4c50@mailserver3.nist.gov> Content-Type: multipart/mixed; boundary="=====================_906402570==_" --=====================_906402570==_ Content-Type: text/plain; charset="us-ascii" At 08:34 AM 9/21/98 -0500, you wrote: >Dear Imagers, >Where can I get John Russ's Image Processing Handbook?? >Thanks, >John Grace >Abbott Laboratories > > Dear John, See attachment RE: Russ' book. Note there may be a newer edition-check with CRC Press. P. E. Barker, Ph.D. 831.01/NIST U. S. Dept. Commerce Gaithersburg, Maryland 20899-0001 301-975-5402 --=====================_906402570==_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="FYI.htm" =20 Amazon.com: A Glance: The Image Processing Handbook
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 The Image Processing Handbook
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Synopsis
= Thoroughly updated to reflect the rapid developments in imaging= technology, this indispensable guide delivers an impressive array of= concepts and techniques to help readers take full advantage of high-end= imaging software. It adds a new dimension to the methods of enhancing= images presented in the bestselling first edition.

Booknews, Inc. , March 1,= 1995
A handbook that presents an extensive collection of= image processing tools so that users of computer-based systems can both= understand those methods provided in packaged software, and program those= additions which may be needed for particular applications. Comparisons are= presented of different algorithms that may be used for similar purposes,= using a selection of representative pictures from light and electron= microscopes, as well as macroscopic, satellite, and astronomical images.= This revised and updated edition adds new chapters on the measurement of= images and the subsequent interpretation of the data, and on printing and= storing images, including the use of image databases. Annotation copyright= Book News, Inc. Portland, Or.

The publisher, CRC Press = http://www.crcpress.com , August 21, 1996
Today's= sophisticated computer professionals need powerful tools to help them= visualize graphic information. Rapid developments in imaging technology= have created a substantial demand for this thoroughly updated Second= Edition of The Image Processing Handbook.

This indispensible guide= delivers an impressive array of concepts and techniques to help you take= full advantage of your high-end imaging software. It adds a new dimension= to the methods of enhancing images presented in the best-selling first= edition:

Acquisition of gray-scale and color images

Methods for= correcting imaging defects, such as geometric distortion and non-uniform= illumination

Selective enhancement of images, such as edge finding,= noise suppression, and texture extraction

Segmentation of images

= Processing of binary images using morphological and Boolean operations

= Three-dimensional imaging using tomographic reconstruction, serial= sections, and volumetric and surface rendering methods

FEATURES:

= Presents a balanced and complete description of frequency space methods= using extensive mathematical presentation and spatial domain= processing

Offers comparisons of different algorithms used for similar= pruposes

Requires only a modest technical background in mathematics or= computers to be able to fully utilize the vcast wealth of material in the= handbook

New data on printing and storing images, including important= coverage of image compression

Advance information on forthcoming= technologies

New chapter on image measurement, including applications of= real-world measurement, topics on densitometry, and color information

= Expanded and updated coverage of image acquisitions, including a discussion= on flatbed scanners

Augmented coverage of 3D image processing

More= than 120 full-color images throughout the book

=20 =20

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=20 --=====================_906402570==_-- ------------------------------ Date: Mon, 21 Sep 1998 09:07:04 -0400 From: "Dibble, Nicole A" To: "'nih-image@io.ece.drexel.edu'" Subject: unsubscribe Message-Id: <215D10CDFC93D111A11600805FBB7C28211D8F@BILLHALEY> Content-Return: allowed Content-Type: text/plain ------------------------------ Date: Tue, 22 Sep 1998 10:22:18 +1000 From: Patricia Waley To: nih-image@io.ece.drexel.edu Subject: PC files Message-Id: Content-Type: text/plain; charset="us-ascii" I have recently found problems opening my files in NIH Image with the message "File cannot be opened as the application PC can not be found" appearing. These 8 bit Tiff files have been made on a PC using Optimas and saved on to the floppy disc drive. I have previously only had similar problems opening files if they were saved onto the hard drive and then copied onto a disc. Any suggestions? ________________________________________________________________________________ Patricia Waley Centre for Education and Research on Ageing Concord Hospital Concord NSW 2139 Ph: (02) 9767 6586 Fax: (02) 9767 8315 Email: patw@pathology.usyd.edu.au ________________________________________________________________________________ -------------------------------- End of nih-image-d Digest V98 Issue #67 *************************************** From nih-image-request@io.ece.drexel.edu Mon Sep 21 20:58 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12773; Mon, 21 Sep 1998 20:57:47 -0400 (EDT) Resent-Date: Mon, 21 Sep 1998 20:57:47 -0400 (EDT) Date: Tue, 22 Sep 1998 10:45:26 +1000 (EST) From: Adrian Whichello Message-Id: <199809220045.KAA18651@cassius.ee.usyd.edu.au> To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #67 Resent-Message-ID: <"OrEMp3.0.Yr2.GDl1s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/374 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1316 Status: O > > I have recently found problems opening my files in NIH Image with the > message "File cannot be opened as the application PC can not be found" > appearing. These 8 bit Tiff files have been made on a PC using Optimas and > saved on to the floppy disc drive. I have previously only had similar > problems opening files if they were saved onto the hard drive and then > copied onto a disc. Any suggestions? Straight off the top of my head, I'd say the filetype has been set to "PC" or somesuch by PC exchange (or whatever you used to read a PC disk on the Mac), hence the whinge. If you get one of the filetype changers from the info-mac archive (sunsite.anu.edu.au/pub/mac/info-mac), such as Snitch, you could change the filetype to one NIH-image expects (I don't know offhand, but check a tiff file that Image can open with no problems). Or open the tiff file with Graphic Converter (also from info-mac) and save it again. -- Dr Adrian Whichello Phone: +61 2 9351 5339 Imaging Science and Engineering Laboratory Fax: +61 2 9351 3847 Sydney University Electrical Engineering Email: adrianw@ee.usyd.edu.au Australia WWW: http://www.ee.usyd.edu.au/~adrianw "I wish to God these calculations had been executed by Steam!" - C. Babbage From nih-image-d-request@io.ece.drexel.edu Tue Sep 22 15:41 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA12088; Tue, 22 Sep 1998 15:41:05 -0400 (EDT) Date: Tue, 22 Sep 1998 15:41:05 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809221941.PAA12088@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #68 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/68 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2602 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 68 Today's Topics: Re: nih-image-d Digest V98 #67 [ Adrian Whichello ] ------------------------------ Date: Tue, 22 Sep 1998 10:45:26 +1000 (EST) From: Adrian Whichello To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #67 Message-Id: <199809220045.KAA18651@cassius.ee.usyd.edu.au> > > I have recently found problems opening my files in NIH Image with the > message "File cannot be opened as the application PC can not be found" > appearing. These 8 bit Tiff files have been made on a PC using Optimas and > saved on to the floppy disc drive. I have previously only had similar > problems opening files if they were saved onto the hard drive and then > copied onto a disc. Any suggestions? Straight off the top of my head, I'd say the filetype has been set to "PC" or somesuch by PC exchange (or whatever you used to read a PC disk on the Mac), hence the whinge. If you get one of the filetype changers from the info-mac archive (sunsite.anu.edu.au/pub/mac/info-mac), such as Snitch, you could change the filetype to one NIH-image expects (I don't know offhand, but check a tiff file that Image can open with no problems). Or open the tiff file with Graphic Converter (also from info-mac) and save it again. -- Dr Adrian Whichello Phone: +61 2 9351 5339 Imaging Science and Engineering Laboratory Fax: +61 2 9351 3847 Sydney University Electrical Engineering Email: adrianw@ee.usyd.edu.au Australia WWW: http://www.ee.usyd.edu.au/~adrianw "I wish to God these calculations had been executed by Steam!" - C. Babbage ------------------------------ Date: Tue, 22 Sep 1998 15:18:04 -0500 From: Laird Bloom To: nih-image-d@io.ece.drexel.edu Subject: vessel area, length, branching measurements Message-Id: Content-Type: text/plain; charset="us-ascii" I'm looking for macros to analyze blood vessel morphology, particularly to measure degrees of branching or branches per unit length. I've heard of the BRANching program; can someone tell me where to find it? Does anyone know of a program that draws a grid and measures how often vessels cross a gridline? Thanks Laird Bloom MIT Center for Cancer Research -------------------------------- End of nih-image-d Digest V98 Issue #68 *************************************** From nih-image-request@io.ece.drexel.edu Wed Sep 23 08:54 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA23269; Wed, 23 Sep 1998 08:52:45 -0400 (EDT) Resent-Date: Wed, 23 Sep 1998 08:52:45 -0400 (EDT) Date: Wed, 23 Sep 1998 14:34:10 +0200 From: Ard Jonker Subject: Autowand/AutoOutline touching edge In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu> X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/375 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 395 Status: O Hello List, I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken. Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate? Regards, Ard From nih-image-request@io.ece.drexel.edu Wed Sep 23 12:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA10866; Wed, 23 Sep 1998 12:08:45 -0400 (EDT) Resent-Date: Wed, 23 Sep 1998 12:08:45 -0400 (EDT) Message-ID: <36092776.B0243E80@netmatters.co.uk> Date: Wed, 23 Sep 1998 16:53:25 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Autowand/AutoOutline touching edge References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"klhTm2.0.NI2.DaH2s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/376 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1951 Status: O Ard Jonker wrote: > Hello List, > > I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken. > > Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate? > > Regards, Ard Ard, the following procedure can be used to delete binary objects touching the edge of a Rectangular ROI. You may be able to make use of it as follow..... Duplicate the image Threshold & make binary Use the procedure below Analyze particle (X,Y) Then use the X,Y coordinates (i=1 to rCount) + the threshold & Autooutline on your original image. In Object image you can then convert each ROI into an object thus saving the roi for further analysis. This is a really nice way of marking up objects non-destructively + you get permanent ROIs and area values stored in the object file. Jeremy Procedure DeleteTouching; begin SetThreshold(1); MakeBinary; WandAutoMeasure(false); GetROI(left,top,width,height); MakeLineROI(left,top,left+width-1,top); Drawboundary; AutoOutline(left,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left,top,left,top+Height-1); Drawboundary; AutoOutline(left,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left+width-1,top,left+width-1,top+Height-1); Drawboundary; AutoOutline(left+width-1,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left,top+Height-1,left+width-1,top+Height-1); Drawboundary; AutoOutline(left,top+Height-1); Clear; SetThreshold(1); MakeBinary; end; ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Wed Sep 23 17:48 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA12385; Wed, 23 Sep 1998 17:48:42 -0400 (EDT) Resent-Date: Wed, 23 Sep 1998 17:48:42 -0400 (EDT) Message-Id: <199809232131.RAA11128@io.ECE.Drexel.EDU> X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Date: Thu, 24 Sep 1998 09:27:03 +1200 To: nih-image@io.ece.drexel.edu From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian) Subject: macro for calibration Resent-Message-ID: <"2N-2m.0.Mk2.AZM2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/377 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 936 Status: O I am an image neophyte and am looking for a macro which will work in Scion-image to achieve the following steps to calibrate a radiographic image: The image has a thin circle of stainless steel for calibration. I need to threshold the image and identify the pixels which are inside the circle on the image. Then use an area based calibration method based on identifying the co-ordinates of all the pixels inside the circle, then calculate the mean and standard deviation of the X co-ordinates and the Y co-ordinates. Then calculate an aspect ratio using the ratio of the standard deviations of the X and Y co-ordinates. I am unfamiliar with writing macros which function inside Scion-image. Can anyone help me with a macro for this series of tasks? Thanks Cristy Trevillian Cristy Trevillian BSc BVMS Assistant Lecturer Equine Studies Massey University Private Bag 11222 Palmerston North, New Zealand 64 6 350 5329 extn 7494 From nih-image-request@io.ece.drexel.edu Wed Sep 23 23:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA13422; Wed, 23 Sep 1998 23:18:06 -0400 (EDT) Resent-Date: Wed, 23 Sep 1998 23:18:06 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu Date: Thu, 24 Sep 1998 13:02:26 GMT+1000 Subject: Re: Autowand/AutoOutline touching edge Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <98843D70C58@rna.bio.mq.edu.au> Resent-Message-ID: <"v5W0b2.0.ao2.1NR2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/378 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2886 Status: O >Received: from SpoolDir by RNA (Mercury 1.43); 23 Sep 98 22:51:39 +1000 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.43) with ESMTP; > 23 Sep 98 22:51:29 +1000 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22869; > Wed, 23 Sep 1998 08:49:24 -0400 (EDT) >Resent-Date: Wed, 23 Sep 1998 08:49:24 -0400 (EDT) >Date: Wed, 23 Sep 1998 14:34:10 +0200 >From: Ard Jonker >Subject: Autowand/AutoOutline touching edge >In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu> >X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl >To: nih-image@io.ece.drexel.edu >Message-id: >MIME-version: 1.0 >Content-type: text/plain; charset="us-ascii" >Content-transfer-encoding: 7BIT >Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/375 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Hello List, > >I want to discard measurements with AutoWand on and AutoOutline, if the >outline touches the edge. The result would be similar to measuring one >particle which touches the edge in AnalyseParticles: no >measurement is taken. > >Is there a clever way, short of checking all outline coordinates for the >condition of x- and y coordinates both being an image edge coordinate? > >Regards, Ard > Ard, Checking x-y coords would in fact be problematic as x-y coordinates as returned by NIH-Image ( and Object-Image etc) do not return coords of outline boundary but the coords for a QuickDraw Region which are a pixel outside Outline along bottom and right ( see archives for many discussions). The function below will simply test if the current ROI touches the edge. (note be wary about changing selectPic to choosePic where restoreRoi is used). var boundaryId:integer; function touchBoundary:boolean; var pid,n,mean,mode,min,max:integer; begin pid:=pidNumber; if not PidExists(boundaryId) then begin selectAll;duplicate('boundary'); boundaryId:=pidNumber;selectPic(pid);restoreRoi; selectPic(boundaryId); setBackGround(0);setForeGround(255);clear;drawBoundary;killroi; selectPic(pid); end; selectPic(boundaryId);restoreRoi; measure;getResults(n,mean,mode,min,max);setCounter(rCount-1); selectPic(pid); if max=0 then touchBoundary:=false else touchBoundary:=true; end macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; Regards, Greg. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Thu Sep 24 06:21 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA26840; Thu, 24 Sep 1998 06:21:21 -0400 (EDT) Date: Thu, 24 Sep 1998 06:21:21 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809241021.GAA26840@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #69 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/69 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7937 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 69 Today's Topics: Autowand/AutoOutline touching edge [ Ard Jonker ] Re: Autowand/AutoOutline touching ed [ Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Autowand/AutoOutline touching edge Message-id: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hello List, I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken. Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate? Regards, Ard ------------------------------ Date: Wed, 23 Sep 1998 16:53:25 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Autowand/AutoOutline touching edge Message-ID: <36092776.B0243E80@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Ard Jonker wrote: > Hello List, > > I want to discard measurements with AutoWand on and AutoOutline, if the outline touches the edge. The result would be similar to measuring one particle which touches the edge in AnalyseParticles: no measurement is taken. > > Is there a clever way, short of checking all outline coordinates for the condition of x- and y coordinates both being an image edge coordinate? > > Regards, Ard Ard, the following procedure can be used to delete binary objects touching the edge of a Rectangular ROI. You may be able to make use of it as follow..... Duplicate the image Threshold & make binary Use the procedure below Analyze particle (X,Y) Then use the X,Y coordinates (i=1 to rCount) + the threshold & Autooutline on your original image. In Object image you can then convert each ROI into an object thus saving the roi for further analysis. This is a really nice way of marking up objects non-destructively + you get permanent ROIs and area values stored in the object file. Jeremy Procedure DeleteTouching; begin SetThreshold(1); MakeBinary; WandAutoMeasure(false); GetROI(left,top,width,height); MakeLineROI(left,top,left+width-1,top); Drawboundary; AutoOutline(left,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left,top,left,top+Height-1); Drawboundary; AutoOutline(left,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left+width-1,top,left+width-1,top+Height-1); Drawboundary; AutoOutline(left+width-1,top); Clear; SetThreshold(1); MakeBinary; MakeLineROI(left,top+Height-1,left+width-1,top+Height-1); Drawboundary; AutoOutline(left,top+Height-1); Clear; SetThreshold(1); MakeBinary; end; ************************************************ Jeremy Brown Moredun Research Institute/Edinburgh University http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Thu, 24 Sep 1998 09:27:03 +1200 From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian) To: nih-image@io.ece.drexel.edu Subject: macro for calibration Message-Id: <199809232131.RAA11128@io.ECE.Drexel.EDU> Content-Type: text/plain; charset="us-ascii" I am an image neophyte and am looking for a macro which will work in Scion-image to achieve the following steps to calibrate a radiographic image: The image has a thin circle of stainless steel for calibration. I need to threshold the image and identify the pixels which are inside the circle on the image. Then use an area based calibration method based on identifying the co-ordinates of all the pixels inside the circle, then calculate the mean and standard deviation of the X co-ordinates and the Y co-ordinates. Then calculate an aspect ratio using the ratio of the standard deviations of the X and Y co-ordinates. I am unfamiliar with writing macros which function inside Scion-image. Can anyone help me with a macro for this series of tasks? Thanks Cristy Trevillian Cristy Trevillian BSc BVMS Assistant Lecturer Equine Studies Massey University Private Bag 11222 Palmerston North, New Zealand 64 6 350 5329 extn 7494 ------------------------------ Date: Thu, 24 Sep 1998 13:02:26 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu Subject: Re: Autowand/AutoOutline touching edge Message-ID: <98843D70C58@rna.bio.mq.edu.au> >Received: from SpoolDir by RNA (Mercury 1.43); 23 Sep 98 22:51:39 +1000 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.43) with ESMTP; > 23 Sep 98 22:51:29 +1000 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22869; > Wed, 23 Sep 1998 08:49:24 -0400 (EDT) >Resent-Date: Wed, 23 Sep 1998 08:49:24 -0400 (EDT) >Date: Wed, 23 Sep 1998 14:34:10 +0200 >From: Ard Jonker >Subject: Autowand/AutoOutline touching edge >In-reply-to: <199809221922.PAA08372@io.ece.drexel.edu> >X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl >To: nih-image@io.ece.drexel.edu >Message-id: >MIME-version: 1.0 >Content-type: text/plain; charset="us-ascii" >Content-transfer-encoding: 7BIT >Resent-Message-ID: <"iEGlV2.0.7H5.8kE2s"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/375 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Hello List, > >I want to discard measurements with AutoWand on and AutoOutline, if the >outline touches the edge. The result would be similar to measuring one >particle which touches the edge in AnalyseParticles: no >measurement is taken. > >Is there a clever way, short of checking all outline coordinates for the >condition of x- and y coordinates both being an image edge coordinate? > >Regards, Ard > Ard, Checking x-y coords would in fact be problematic as x-y coordinates as returned by NIH-Image ( and Object-Image etc) do not return coords of outline boundary but the coords for a QuickDraw Region which are a pixel outside Outline along bottom and right ( see archives for many discussions). The function below will simply test if the current ROI touches the edge. (note be wary about changing selectPic to choosePic where restoreRoi is used). var boundaryId:integer; function touchBoundary:boolean; var pid,n,mean,mode,min,max:integer; begin pid:=pidNumber; if not PidExists(boundaryId) then begin selectAll;duplicate('boundary'); boundaryId:=pidNumber;selectPic(pid);restoreRoi; selectPic(boundaryId); setBackGround(0);setForeGround(255);clear;drawBoundary;killroi; selectPic(pid); end; selectPic(boundaryId);restoreRoi; measure;getResults(n,mean,mode,min,max);setCounter(rCount-1); selectPic(pid); if max=0 then touchBoundary:=false else touchBoundary:=true; end macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; Regards, Greg. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #69 *************************************** From nih-image-request@io.ece.drexel.edu Thu Sep 24 12:45 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05285; Thu, 24 Sep 1998 12:45:36 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 12:45:36 -0400 (EDT) Date: Thu, 24 Sep 1998 12:31:50 -0700 From: Abby Pike Subject: subscribe X-Sender: Pike_c1@email.hnrc.tufts.edu (Unverified) To: nih-image@io.ece.drexel.edu Message-id: <3.0.5.32.19980924123150.00798680@email.hnrc.tufts.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Content-transfer-encoding: 7BIT Resent-Message-ID: <"v_uL7.0.yl.z7d2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/379 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 35 Status: O subscribe nih-image From nih-image-request@io.ece.drexel.edu Thu Sep 24 13:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA07369; Thu, 24 Sep 1998 13:09:33 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 13:09:33 -0400 (EDT) Reply-To: From: "Francis Lamberti" To: Subject: request for a "cell" tracking macro Date: Thu, 24 Sep 1998 09:59:41 -0700 Message-ID: <001b01bde7dc$b8c85500$51b4400c@lamberti> MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2377.0 Importance: Normal In-Reply-To: <199809241015.GAA26131@io.ece.drexel.edu> X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 Resent-Message-ID: <"jgVQf1.0.WQ1.AZd2s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/380 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1407 Status: O Hello Fellow Imagers : I am using NIH image (and Scion's PC Image) to measure the release of dye from a gel particle suspended in wash solutions of varying composition. Currently I have been doing a manual method of creating a stack of time-lapse images, defining a ROI in the center of each bead, measuring the Grey level, and then moving to the next image in the stack while retaining the ROI. A similar series of measurements are performed outside the bead to obtain background grey levels. The ratio of these measurements yields the light transmission through stained bead. By measuring the diameter of the bead, (again in each image of the stack, since the bead swell with time), the concentration of dye can be calculated from the absorbance measurement. Unfortunately, the beads being spherical tend to move around as they swell and release dye. To minimize errors in measurements I am forced to move the ROI of each bead center and each bead background in each image of the stack. Does anyone out there have or know of a macro that allows one to "track" cells (or other objects) through a series of images in a stack; create a mask around cell and measure the grey level at a central ROI in the cell; the grey level at a ROI outside the cell boundary, and the cell size ?? Any help on any part of this would be greatly appreciated. Thanks in advance to all Francis Lamberti Neocrin Company. From nih-image-request@io.ece.drexel.edu Thu Sep 24 15:25 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA21808; Thu, 24 Sep 1998 15:25:15 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 15:25:15 -0400 (EDT) Date: Thu, 24 Sep 1998 12:32:40 -0700 From: Abby Pike Subject: subscribe X-Sender: Pike_c1@email.hnrc.tufts.edu (Unverified) To: nih-image@io.ece.drexel.edu Message-id: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Content-transfer-encoding: 7BIT Resent-Message-ID: <"uw69H1.0.dw4.yXf2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/381 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 35 Status: O subscribe nih-image From nih-image-request@io.ece.drexel.edu Thu Sep 24 15:45 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA23484; Thu, 24 Sep 1998 15:45:18 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 15:45:18 -0400 (EDT) Date: Thu, 24 Sep 1998 15:42:09 -0400 From: lipman_pa@hnrc.tufts.edu (Ruth Lipman) Subject: Re: subscribe X-Sender: lipman_pa@email.hnrc.tufts.edu To: nih-image@io.ece.drexel.edu Message-id: <01J26U9TCGAA9B3SB9@hnrc.tufts.edu> MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"KqGkb3.0.tT5.7wf2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/382 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 67 Status: O >subscribe nih-image Nope, it came through again. From nih-image-request@io.ece.drexel.edu Thu Sep 24 16:55 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA28662; Thu, 24 Sep 1998 16:55:53 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 16:55:53 -0400 (EDT) Message-Id: In-Reply-To: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu> Mime-Version: 1.0 Date: Thu, 24 Sep 1998 16:35:41 -0400 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: subscribe Resent-Message-ID: <"uTAa41.0.rc6.Sqg2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/383 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 3792 Status: O >subscribe nih-image < < TimesThe following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- And remember, the early bird may get the worm, but the second mouse gets the cheese. From nih-image-request@io.ece.drexel.edu Thu Sep 24 20:16 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11576; Thu, 24 Sep 1998 20:16:27 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 20:16:27 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu Date: Fri, 25 Sep 1998 10:07:45 GMT+1000 Subject: Re: Autowand/AutoOutline touching edge Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <99D5B8F5EC5@rna.bio.mq.edu.au> Resent-Message-ID: <"lpCd2.0.CY2.zuj2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/384 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1429 Status: O >Date: Wed, 23 Sep 1998 14:34:10 +0200 >From: Ard Jonker > >I want to discard measurements with AutoWand on and AutoOutline, if the >outline touches the edge. The result would be similar to measuring one >particle which touches the edge in AnalyseParticles: no >measurement is taken. > >Is there a clever way, short of checking all outline coordinates for the >condition of x- and y coordinates both being an image edge coordinate? > >Regards, Ard > I responded to Ard's post yesterday with a macro which tested for the above by measure'ing whether a drawboundary pixel was included in the selection and commented that checking of xycoordinate list would have been problematic. In exchange with Ard, he has since suggested that it would only be necessary to test the coords of the bounding rectangle (available via getRoi()). This is a much simpler and more elegant solution ( avoids problem with x,ycoordinates array values). function touchBoundary:boolean; var x,y,w,h,pw,ph:integer; begin getRoi(x,y,w,h);getPicSize(pw,ph); if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then touchBoundary:=true else touchBoundary:=false; end macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Sep 24 20:54 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA14286; Thu, 24 Sep 1998 20:54:34 -0400 (EDT) Resent-Date: Thu, 24 Sep 1998 20:54:34 -0400 (EDT) Mime-Version: 1.0 X-Sender: scm@128.250.6.196 Message-Id: In-Reply-To: <99D5B8F5EC5@rna.bio.mq.edu.au> Date: Fri, 25 Sep 1998 10:43:58 +1000 To: nih-image@io.ece.drexel.edu From: Steve Martin Subject: Re: Autowand/AutoOutline touching edge Resent-Message-ID: <"FABSY1.0.VH3.VTk2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/385 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1824 Status: O another thought: draw a 1 pixel wide line on all boundaries, and select or fill, starting at 1,1. The fill or selection should include areas touching the boundary which are the same level/binary state. (?) Steve Martin School of Physiotherapy The University of Melbourne At 8:07 PM +1000 on 25/9/98, GJOSS@rna.bio.mq.edu.au wrote: > >Date: Wed, 23 Sep 1998 14:34:10 +0200 > >From: Ard Jonker > > > >I want to discard measurements with AutoWand on and AutoOutline, if the > >outline touches the edge. The result would be similar to measuring one > >particle which touches the edge in AnalyseParticles: no > >measurement is taken. > > > >Is there a clever way, short of checking all outline coordinates for the > >condition of x- and y coordinates both being an image edge coordinate? > > > >Regards, Ard > > > > I responded to Ard's post yesterday with a macro which tested for the >above by > measure'ing whether a drawboundary pixel was included in the selection and > commented that checking of xycoordinate list would have been problematic. > > In exchange with Ard, he has since suggested that it would only be >necessary to > test the coords of the bounding rectangle (available via getRoi()). This >is a > much simpler and more elegant solution ( avoids problem with x,ycoordinates > array values). > > function touchBoundary:boolean; > var x,y,w,h,pw,ph:integer; > begin getRoi(x,y,w,h);getPicSize(pw,ph); > if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then > touchBoundary:=true else touchBoundary:=false; > end > > macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Fri Sep 25 00:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01000; Fri, 25 Sep 1998 00:18:28 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 00:18:28 -0400 (EDT) Message-ID: <360B1A0A.4F14D237@purdue.edu> Date: Thu, 24 Sep 1998 23:20:30 -0500 From: Kris Jorgensen X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image Subject: get current cell Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vXMdx2.0.bE7.CSn2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/386 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 629 Status: O In Object-Image, I need to get the cell number of the open cell. While creating an object in a macro I ask the user for a couple input values that I need to put into static columns so I need to know which row to put those values. If I am always working on the last image listed in the info card then I can use nCount but if I am working on another image I can't get the cell number to store this other information. If anyone has a way to get the current cell please let me know. Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris From nih-image-request@io.ece.drexel.edu Fri Sep 25 01:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA05566; Fri, 25 Sep 1998 01:12:22 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 01:12:22 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: kris@purdue.edu, nih-image@io.ece.drexel.edu Date: Fri, 25 Sep 1998 15:06:42 GMT+1000 Subject: Re: get current cell Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <9A257552679@rna.bio.mq.edu.au> Resent-Message-ID: <"caN5N3.0.o91.CHo2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/387 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1331 Status: O >Date: Thu, 24 Sep 1998 23:20:30 -0500 >From: Kris Jorgensen > >In Object-Image, I need to get the cell number of the open cell. While >creating an object in a macro I ask the user for a couple input values that I >need to put into static columns so I need to know which row to put those >values. If I am always working on the last image listed in the info card then >I can use nCount but if I am working on another image I can't get the cell >number to store this other information. > >If anyone has a way to get the current cell please let me know. > >Kris Function 'selectedCell' does the job as the name implies :-) and the following will demonstrate. Respond '0' or just return to 'cell' query and the 'selectedCell' will be shown. Otherwise enter cell/object and cell/object will be selected and shown. macro'[t]est'; var width, height, slices, pid,cell:integer; name:string; begin cell:=getNumber('cell',0); if cell<>0 then begin selectCell(cell); selectObject(getNumber('Object',1)); GetPicInfo(width, height, slices, pid, name); selectPic(pid); showCell(cell,true); end; showMessage(selectedCell); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Fri Sep 25 05:47 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA27202; Fri, 25 Sep 1998 05:47:34 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 05:47:34 -0400 (EDT) X-Sender: pickerin@utct.ct.utwente.nl Message-Id: Mime-Version: 1.0 Date: Fri, 25 Sep 1998 11:32:50 +0100 To: nih-image@io.ece.drexel.edu From: Jason Pickering Subject: Counting and Sending Pixels Resent-Message-ID: <"ej4_f1.0.uL6.MFs2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/388 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1061 Status: O Hello everyone, I would like to perform a density slice on a live digitized image, and then count the number of pixels that fall within that density slice. Then, I would like to use the Scion LG-3's two analog channels to send a signal proportional to the number of pixels measured. I have written a macro that sucessfully does this, but I would like to modify the source code to increase the performance of this routine. Has anyone had any experience doing something similar? If so, any tips and possible pitfalls would be very much appreciated. Thanks, Jason P. Pickering ___________________________________________________________________________ Jason Pickering |Email: J.P.Pickering@ct.utwente.nl Onderzoeker in opleiding |Tel: xx 31 53 489 3137 Polymeer Materiaalkundevakgroep |Fax: xx 31 53 489 3823 Universiteit Twente |Priv. addr.: Faculteit der Chemische Technologie |van Loenshof 8D Postbus 217 |7511 HG Enschede 7500 AE Enschede | The Netherlands | __________________________________________________________________________ From nih-image-d-request@io.ece.drexel.edu Fri Sep 25 05:56 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA28066; Fri, 25 Sep 1998 05:56:33 -0400 (EDT) Date: Fri, 25 Sep 1998 05:56:33 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809250956.FAA28066@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #70 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/70 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 15872 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 70 Today's Topics: unsubscribe digest [ szczesny@umich.edu ] subscribe [ Abby Pike ] request for a "cell" tracking macro [ "Francis Lamberti" ] Re: subscribe [ lipman_pa@hnrc.tufts.edu (Ruth Lipm ] Re: subscribe [ Jonathan Nissanov ] Re: get current cell [ GJOSS@rna.bio.mq.edu.au ] Counting and Sending Pixels [ Jason Pickering Content-Type: TEXT/PLAIN; CHARSET=US-ASCII ------------------------------ Date: Thu, 24 Sep 1998 12:31:50 -0700 From: Abby Pike To: nih-image@io.ece.drexel.edu Subject: subscribe Message-id: <3.0.5.32.19980924123150.00798680@email.hnrc.tufts.edu> Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT subscribe nih-image ------------------------------ Date: Thu, 24 Sep 1998 09:59:41 -0700 From: "Francis Lamberti" To: Subject: request for a "cell" tracking macro Message-ID: <001b01bde7dc$b8c85500$51b4400c@lamberti> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hello Fellow Imagers : I am using NIH image (and Scion's PC Image) to measure the release of dye from a gel particle suspended in wash solutions of varying composition. Currently I have been doing a manual method of creating a stack of time-lapse images, defining a ROI in the center of each bead, measuring the Grey level, and then moving to the next image in the stack while retaining the ROI. A similar series of measurements are performed outside the bead to obtain background grey levels. The ratio of these measurements yields the light transmission through stained bead. By measuring the diameter of the bead, (again in each image of the stack, since the bead swell with time), the concentration of dye can be calculated from the absorbance measurement. Unfortunately, the beads being spherical tend to move around as they swell and release dye. To minimize errors in measurements I am forced to move the ROI of each bead center and each bead background in each image of the stack. Does anyone out there have or know of a macro that allows one to "track" cells (or other objects) through a series of images in a stack; create a mask around cell and measure the grey level at a central ROI in the cell; the grey level at a ROI outside the cell boundary, and the cell size ?? Any help on any part of this would be greatly appreciated. Thanks in advance to all Francis Lamberti Neocrin Company. ------------------------------ Date: Thu, 24 Sep 1998 12:32:40 -0700 From: Abby Pike To: nih-image@io.ece.drexel.edu Subject: subscribe Message-id: <3.0.5.32.19980924123240.0079c160@email.hnrc.tufts.edu> Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT subscribe nih-image ------------------------------ Date: Thu, 24 Sep 1998 15:42:09 -0400 From: lipman_pa@hnrc.tufts.edu (Ruth Lipman) To: nih-image@io.ece.drexel.edu Subject: Re: subscribe Message-id: <01J26U9TCGAA9B3SB9@hnrc.tufts.edu> Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT >subscribe nih-image Nope, it came through again. ------------------------------ Date: Thu, 24 Sep 1998 16:35:41 -0400 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: subscribe Message-Id: Content-Type: text/enriched; charset="us-ascii" >subscribe nih-image < < TimesThe following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- And remember, the early bird may get the worm, but the second mouse gets the cheese. ------------------------------ Date: Fri, 25 Sep 1998 10:07:45 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: a.jonker@AMC.UVA.NL, nih-image@io.ece.drexel.edu Subject: Re: Autowand/AutoOutline touching edge Message-ID: <99D5B8F5EC5@rna.bio.mq.edu.au> >Date: Wed, 23 Sep 1998 14:34:10 +0200 >From: Ard Jonker > >I want to discard measurements with AutoWand on and AutoOutline, if the >outline touches the edge. The result would be similar to measuring one >particle which touches the edge in AnalyseParticles: no >measurement is taken. > >Is there a clever way, short of checking all outline coordinates for the >condition of x- and y coordinates both being an image edge coordinate? > >Regards, Ard > I responded to Ard's post yesterday with a macro which tested for the above by measure'ing whether a drawboundary pixel was included in the selection and commented that checking of xycoordinate list would have been problematic. In exchange with Ard, he has since suggested that it would only be necessary to test the coords of the bounding rectangle (available via getRoi()). This is a much simpler and more elegant solution ( avoids problem with x,ycoordinates array values). function touchBoundary:boolean; var x,y,w,h,pw,ph:integer; begin getRoi(x,y,w,h);getPicSize(pw,ph); if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then touchBoundary:=true else touchBoundary:=false; end macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 25 Sep 1998 10:43:58 +1000 From: Steve Martin To: nih-image@io.ece.drexel.edu Subject: Re: Autowand/AutoOutline touching edge Message-Id: Content-Type: text/plain; charset="us-ascii" another thought: draw a 1 pixel wide line on all boundaries, and select or fill, starting at 1,1. The fill or selection should include areas touching the boundary which are the same level/binary state. (?) Steve Martin School of Physiotherapy The University of Melbourne At 8:07 PM +1000 on 25/9/98, GJOSS@rna.bio.mq.edu.au wrote: > >Date: Wed, 23 Sep 1998 14:34:10 +0200 > >From: Ard Jonker > > > >I want to discard measurements with AutoWand on and AutoOutline, if the > >outline touches the edge. The result would be similar to measuring one > >particle which touches the edge in AnalyseParticles: no > >measurement is taken. > > > >Is there a clever way, short of checking all outline coordinates for the > >condition of x- and y coordinates both being an image edge coordinate? > > > >Regards, Ard > > > > I responded to Ard's post yesterday with a macro which tested for the >above by > measure'ing whether a drawboundary pixel was included in the selection and > commented that checking of xycoordinate list would have been problematic. > > In exchange with Ard, he has since suggested that it would only be >necessary to > test the coords of the bounding rectangle (available via getRoi()). This >is a > much simpler and more elegant solution ( avoids problem with x,ycoordinates > array values). > > function touchBoundary:boolean; > var x,y,w,h,pw,ph:integer; > begin getRoi(x,y,w,h);getPicSize(pw,ph); > if (x<=0) or (y<=0) or (x+w>=pw) or (y+h>=ph) then > touchBoundary:=true else touchBoundary:=false; > end > > macro'/0 does ROI touch [B]oundary'; begin showMessage(touchBoundary);end; > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 24 Sep 1998 23:20:30 -0500 From: Kris Jorgensen To: nih-image Subject: get current cell Message-ID: <360B1A0A.4F14D237@purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In Object-Image, I need to get the cell number of the open cell. While creating an object in a macro I ask the user for a couple input values that I need to put into static columns so I need to know which row to put those values. If I am always working on the last image listed in the info card then I can use nCount but if I am working on another image I can't get the cell number to store this other information. If anyone has a way to get the current cell please let me know. Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris ------------------------------ Date: Fri, 25 Sep 1998 15:06:42 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: kris@purdue.edu, nih-image@io.ece.drexel.edu Subject: Re: get current cell Message-ID: <9A257552679@rna.bio.mq.edu.au> >Date: Thu, 24 Sep 1998 23:20:30 -0500 >From: Kris Jorgensen > >In Object-Image, I need to get the cell number of the open cell. While >creating an object in a macro I ask the user for a couple input values that I >need to put into static columns so I need to know which row to put those >values. If I am always working on the last image listed in the info card then >I can use nCount but if I am working on another image I can't get the cell >number to store this other information. > >If anyone has a way to get the current cell please let me know. > >Kris Function 'selectedCell' does the job as the name implies :-) and the following will demonstrate. Respond '0' or just return to 'cell' query and the 'selectedCell' will be shown. Otherwise enter cell/object and cell/object will be selected and shown. macro'[t]est'; var width, height, slices, pid,cell:integer; name:string; begin cell:=getNumber('cell',0); if cell<>0 then begin selectCell(cell); selectObject(getNumber('Object',1)); GetPicInfo(width, height, slices, pid, name); selectPic(pid); showCell(cell,true); end; showMessage(selectedCell); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 25 Sep 1998 11:32:50 +0100 From: Jason Pickering To: nih-image@io.ece.drexel.edu Subject: Counting and Sending Pixels Message-Id: Content-Type: text/plain; charset="us-ascii" Hello everyone, I would like to perform a density slice on a live digitized image, and then count the number of pixels that fall within that density slice. Then, I would like to use the Scion LG-3's two analog channels to send a signal proportional to the number of pixels measured. I have written a macro that sucessfully does this, but I would like to modify the source code to increase the performance of this routine. Has anyone had any experience doing something similar? If so, any tips and possible pitfalls would be very much appreciated. Thanks, Jason P. Pickering ___________________________________________________________________________ Jason Pickering |Email: J.P.Pickering@ct.utwente.nl Onderzoeker in opleiding |Tel: xx 31 53 489 3137 Polymeer Materiaalkundevakgroep |Fax: xx 31 53 489 3823 Universiteit Twente |Priv. addr.: Faculteit der Chemische Technologie |van Loenshof 8D Postbus 217 |7511 HG Enschede 7500 AE Enschede | The Netherlands | __________________________________________________________________________ -------------------------------- End of nih-image-d Digest V98 Issue #70 *************************************** From nih-image-request@io.ece.drexel.edu Fri Sep 25 09:27 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA14910; Fri, 25 Sep 1998 09:27:32 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 09:27:32 -0400 (EDT) Message-Id: <360B9980.4E74F69A@purdue.edu> Date: Fri, 25 Sep 1998 08:24:16 -0500 From: Kris Jorgensen Reply-To: kris@purdue.edu Organization: Purdue University X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: get current cell References: <9A257552679@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"jn8r13.0.iK3.dRv2s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/389 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1752 Status: O GJOSS@rna.bio.mq.edu.au wrote: > > >Date: Thu, 24 Sep 1998 23:20:30 -0500 > >From: Kris Jorgensen > > > >In Object-Image, I need to get the cell number of the open cell. While > >creating an object in a macro I ask the user for a couple input values that I > >need to put into static columns so I need to know which row to put those > >values. If I am always working on the last image listed in the info card then > >I can use nCount but if I am working on another image I can't get the cell > >number to store this other information. > > > >If anyone has a way to get the current cell please let me know. > > > >Kris > > Function 'selectedCell' does the job as the name implies :-) > and the following will demonstrate. > Respond '0' or just return to 'cell' query and the 'selectedCell' will be > shown. Otherwise enter cell/object and cell/object will be selected and shown. > > macro'[t]est'; > var width, height, slices, pid,cell:integer; > name:string; > begin > cell:=getNumber('cell',0); > if cell<>0 then begin > selectCell(cell); > selectObject(getNumber('Object',1)); > GetPicInfo(width, height, slices, pid, name); > selectPic(pid); > showCell(cell,true); > end; > showMessage(selectedCell); > end I want to make the process automatic without user intervention. selectedCell doesn't return the cell that is currently open since it is not selected. All I get is 0. It is only after the cell is closed and one of its objects is manually selected will selectedCell work. I don't want to rely on the user selecting the cell. Maybe we need an openCell function. -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris From nih-image-request@io.ece.drexel.edu Fri Sep 25 10:52 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA21360; Fri, 25 Sep 1998 10:52:44 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 10:52:44 -0400 (EDT) X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48] Message-Id: In-Reply-To: <360B9980.4E74F69A@purdue.edu> References: <9A257552679@rna.bio.mq.edu.au> Mime-Version: 1.0 Date: Fri, 25 Sep 1998 16:43:53 +0200 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: get current cell Resent-Message-ID: <"SiOyj.0.zw4.Ziw2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/390 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2350 Status: O Kris I can offer you a work-around which may help you (see below). The problem is that an open cell has no number until it is closed. When it is closed and you work in insert mode (i.e. not on the last image of the image list), the cell will obtain the highest number in that image, while the remaining cells are renumbered (shuffled up). Cells within an image or stack always have contiguous numbers, but can be random across stack slices. Below is a macro function which returns the highest cell number of the front image, so you hopefully can continue until the problem is solved more elegantly. Note that a cell index can easily change when cells are deleted or inserted. Instead of using index-value- pairs, you should consider to put your additional user information into a dynamic column which maintains always correctly linked. By macro, you can create a dynamic column with Makeresultcolumn('name'), *not* followed by 'PutOperand' or 'PutAlgrorithm'. You also can use InitColumn('name'), which has a similar effect, but if a column with this name already exists, it will be cleared without warning. You also can create dynamic column manually, by choosing Define objects, clicking on 'NewResult' and supplying the operation 'None'. OpenCell is indeed a macro which is already implemented in the newest version (due mid-october; I am currently looking for beta-testers), but it has the meaning that you can re-open a previously closed cell and add/delete objects, thus it doesn't address your problem. function HighestCell: integer; {in Object-Image, the highest cell number in the current image is returned} var width, height, slices, pid, im, foundcell, thecell: real; name: string; begin foundcell:= 0; for im:= 1 to nImages do begin thecell := LastCell(im); SelectCell(thecell); GetPicInfo(width, height, slices, pid, name); if PidNumber = Pid then foundcell := thecell; end; HighestCell:= foundcell; end; macro 'Show Highest Cell'; begin ShowMessage('HighestCell= ', HighestCell); end; Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html From nih-image-request@io.ece.drexel.edu Fri Sep 25 11:49 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26316; Fri, 25 Sep 1998 11:49:05 -0400 (EDT) Resent-Date: Fri, 25 Sep 1998 11:49:05 -0400 (EDT) Message-Id: <3.0.6.32.19980925113232.007f7870@PO-Box.mcgill.ca> X-Sender: mliraj@PO-Box.mcgill.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Fri, 25 Sep 1998 11:32:32 -0400 To: nih-image@io.ece.drexel.edu From: "Mario de A. Lira Junior" Subject: Particle analysis Mime-Version: 1.0 Resent-Message-ID: <"6wQxo.0.E56.dVx2s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/391 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 532 Status: O Hello List, I am a beginner on Scion Image (PC side) and one of the measurements I'm doing is a particle analysis, for which I'll be obtaining both Major and Minor axis. I know those measures are for the hypothetical best approach of an ellipse to the real data. Would I be reasonably correct and using a Major/Minor value as an indication of the "sphericity" of the particles ? If so, is it possible to add a self-created parameter to Particle Analysis like the User1 and such for full image analysis ? Thanks for the help, Mario From nih-image-d-request@io.ece.drexel.edu Sat Sep 26 06:13 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14120; Sat, 26 Sep 1998 06:13:07 -0400 (EDT) Date: Sat, 26 Sep 1998 06:13:07 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809261013.GAA14120@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #71 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/71 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6506 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 71 Today's Topics: Re: get current cell [ Kris Jorgensen ] Re: get current cell [ Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: get current cell Message-Id: <360B9980.4E74F69A@purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit GJOSS@rna.bio.mq.edu.au wrote: > > >Date: Thu, 24 Sep 1998 23:20:30 -0500 > >From: Kris Jorgensen > > > >In Object-Image, I need to get the cell number of the open cell. While > >creating an object in a macro I ask the user for a couple input values that I > >need to put into static columns so I need to know which row to put those > >values. If I am always working on the last image listed in the info card then > >I can use nCount but if I am working on another image I can't get the cell > >number to store this other information. > > > >If anyone has a way to get the current cell please let me know. > > > >Kris > > Function 'selectedCell' does the job as the name implies :-) > and the following will demonstrate. > Respond '0' or just return to 'cell' query and the 'selectedCell' will be > shown. Otherwise enter cell/object and cell/object will be selected and shown. > > macro'[t]est'; > var width, height, slices, pid,cell:integer; > name:string; > begin > cell:=getNumber('cell',0); > if cell<>0 then begin > selectCell(cell); > selectObject(getNumber('Object',1)); > GetPicInfo(width, height, slices, pid, name); > selectPic(pid); > showCell(cell,true); > end; > showMessage(selectedCell); > end I want to make the process automatic without user intervention. selectedCell doesn't return the cell that is currently open since it is not selected. All I get is 0. It is only after the cell is closed and one of its objects is manually selected will selectedCell work. I don't want to rely on the user selecting the cell. Maybe we need an openCell function. -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris ------------------------------ Date: Fri, 25 Sep 1998 16:43:53 +0200 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: get current cell Message-Id: Content-Type: text/plain; charset="us-ascii" Kris I can offer you a work-around which may help you (see below). The problem is that an open cell has no number until it is closed. When it is closed and you work in insert mode (i.e. not on the last image of the image list), the cell will obtain the highest number in that image, while the remaining cells are renumbered (shuffled up). Cells within an image or stack always have contiguous numbers, but can be random across stack slices. Below is a macro function which returns the highest cell number of the front image, so you hopefully can continue until the problem is solved more elegantly. Note that a cell index can easily change when cells are deleted or inserted. Instead of using index-value- pairs, you should consider to put your additional user information into a dynamic column which maintains always correctly linked. By macro, you can create a dynamic column with Makeresultcolumn('name'), *not* followed by 'PutOperand' or 'PutAlgrorithm'. You also can use InitColumn('name'), which has a similar effect, but if a column with this name already exists, it will be cleared without warning. You also can create dynamic column manually, by choosing Define objects, clicking on 'NewResult' and supplying the operation 'None'. OpenCell is indeed a macro which is already implemented in the newest version (due mid-october; I am currently looking for beta-testers), but it has the meaning that you can re-open a previously closed cell and add/delete objects, thus it doesn't address your problem. function HighestCell: integer; {in Object-Image, the highest cell number in the current image is returned} var width, height, slices, pid, im, foundcell, thecell: real; name: string; begin foundcell:= 0; for im:= 1 to nImages do begin thecell := LastCell(im); SelectCell(thecell); GetPicInfo(width, height, slices, pid, name); if PidNumber = Pid then foundcell := thecell; end; HighestCell:= foundcell; end; macro 'Show Highest Cell'; begin ShowMessage('HighestCell= ', HighestCell); end; Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html ------------------------------ Date: Fri, 25 Sep 1998 11:32:32 -0400 From: "Mario de A. Lira Junior" To: nih-image@io.ece.drexel.edu Subject: Particle analysis Message-Id: <3.0.6.32.19980925113232.007f7870@PO-Box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" Hello List, I am a beginner on Scion Image (PC side) and one of the measurements I'm doing is a particle analysis, for which I'll be obtaining both Major and Minor axis. I know those measures are for the hypothetical best approach of an ellipse to the real data. Would I be reasonably correct and using a Major/Minor value as an indication of the "sphericity" of the particles ? If so, is it possible to add a self-created parameter to Particle Analysis like the User1 and such for full image analysis ? Thanks for the help, Mario ------------------------------ Date: Fri, 25 Sep 1998 17:09:02 -0400 From: Neal Sullivan To: nih-image-d@io.ece.drexel.edu Subject: Image cross-correlation macro Message-ID: Content-Type: text/plain Greetings, I am looking for a SCION IMAGE compatible image cross-correlation macro... Thanks in advance Neal Sullivan Schlumberger ATE / Verification Systems -------------------------------- End of nih-image-d Digest V98 Issue #71 *************************************** From nih-image-request@io.ece.drexel.edu Mon Sep 28 08:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22782; Mon, 28 Sep 1998 08:10:19 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 08:10:19 -0400 (EDT) X-Sender: pickerin@utct.ct.utwente.nl Message-Id: In-Reply-To: <199809261003.GAA13222@io.ece.drexel.edu> Mime-Version: 1.0 Date: Mon, 28 Sep 1998 13:43:02 +0100 To: nih-image@io.ece.drexel.edu From: Jason Pickering Subject: Scion LG-3 Questions Resent-Message-ID: <"9NiiN2.0.T25.JRt3s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/392 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1006 Status: O Dear NIH Imagers, Can anyone tell me how to set the scion[4] channel from the source code? I need to trigger an outside event using the data out channel of the ScionLG-3 board. I have done this though a macro command such as: scion[4]:=BitOr(scion[4],8); scion[4]:=BitOr(scion[4],7); Any suggestions? Also, any hints as to how to read the scion[3] channel from the source code? I used similar commands with the macro language, but I would like to accomplish the same thing with compiled code. Cheers, Jason Pickering ___________________________________________________________________________ Jason Pickering |Email: J.P.Pickering@ct.utwente.nl Onderzoeker in opleiding |Tel: xx 31 53 489 3137 Polymeer Materiaalkundevakgroep |Fax: xx 31 53 489 3823 Universiteit Twente |Priv. addr.: Faculteit der Chemische Technologie |van Loenshof 8D Postbus 217 |7511 HG Enschede 7500 AE Enschede | The Netherlands | __________________________________________________________________________ From nih-image-request@io.ece.drexel.edu Mon Sep 28 13:48 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA18317; Mon, 28 Sep 1998 13:48:56 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 13:48:56 -0400 (EDT) Date: Mon, 28 Sep 1998 13:32:59 -0700 From: Abby Pike Subject: measuring X-Sender: Pike_c1@email.hnrc.tufts.edu To: nih-image@io.ece.drexel.edu Message-id: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Content-transfer-encoding: 7BIT Resent-Message-ID: <"veqBC2.0.I24.4Py3s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/393 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 340 Status: O Does anybody know if it is possible to set a distance for how far from the starting point the free hand drawing tool goes in? For example: to start from the end of a curved line and following to line untill the drawing tool has reached .3 of the length of the curve. Any help would be appreciated, thanks Abby Pike Pike_c1@hnrc.tufts.edu From nih-image-request@io.ece.drexel.edu Mon Sep 28 15:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA23550; Mon, 28 Sep 1998 14:59:59 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 14:59:59 -0400 (EDT) Date: Mon, 28 Sep 1998 14:37:20 -0400 From: "Richard A. Fluck" Subject: combining images X-Sender: R_Fluck@acad.fandm.edu To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"pkQef.0.vK5.qTz3s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/394 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 681 Status: O I have double-stained cells with two fluorescent dyes that I image with separate filter sets. Is there a way, within NIH Image, to capture images via each filter set and then combine the images in some way so that the fluorescence within each image shows up as separate colors, for example, rhodamine as red and Hoechst 33258 as blue? I see this done often in the literature but have never done it myself. Images in the literature also show yet a third color where the two original images overlap in their fluorescence. Richard A. Fluck, Dept. of Biology, Franklin and Marshall College, P.O. Box 3003, Lancaster, PA 17604-3003 USA; voice, (717)291-4152; fax, (717) 399-4548 From nih-image-request@io.ece.drexel.edu Mon Sep 28 17:26 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03527; Mon, 28 Sep 1998 17:26:40 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 17:26:40 -0400 (EDT) Message-Id: <199809282103.RAA16729@codon.nih.gov> X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Date: Mon, 28 Sep 1998 17:05:02 -0400 To: nih-image@io.ece.drexel.edu From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) Subject: QuickCam & ADB port Resent-Message-ID: <"tSKCV1.0.UQ.ie_3s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/395 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="ISO-2022-JP" Content-Length: 883 Status: O Hello Imagers, I am using Logitech (previously connectix) Color QuickCam to capture images with NIH Image. QuickCam works using the power from ADB port and my Powerbook G3 does not seem to give enough power to it from its ADB port. That is, my powerbook can capture images from it with NIH Image when ADB plug of the QuickCam is connected with the ADB port of another mac. Does anyone know if there is any way to increase the power to the ADB port on Powerbooks? Any suggestions will be greatly appreciated. Tsuyoshi ________________________________________ Tsuyoshi Miyakawa, Ph. D. Section on Behavioral Neuropharmacology Experimental Therapeutics Branch National Institute of Mental Health Building 10 Room 4D11 Bethesda, MD 20892-1375 Lab phone#: 301-496-4838 or 301-496-4839 Lab fax#: 301-480-1164 E-mail tsuyoshi@codon.nih.gov ________________________________________ From nih-image-request@io.ece.drexel.edu Mon Sep 28 19:05 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA11513; Mon, 28 Sep 1998 19:05:48 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 19:05:48 -0400 (EDT) From: jludtke@facstaff.wisc.edu Date: Mon, 28 Sep 1998 17:50:09 -0500 Message-Id: <199809282250.RAA94496@mail1.doit.wisc.edu> Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: combining images Resent-Message-ID: <"BXGPw2.0.sQ2.nA14s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/396 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 249 Status: O There is a set of macros in the NIH image folder called "color". You just "load macro" under the special menu and choose "color". Then, under special, you should find "color merge two images". Give it a try. Jim Ludtke jludtke@facstaff.wisc.edu From nih-image-request@io.ece.drexel.edu Mon Sep 28 20:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA17576; Mon, 28 Sep 1998 20:22:40 -0400 (EDT) Resent-Date: Mon, 28 Sep 1998 20:22:40 -0400 (EDT) Message-Id: Date: Tue, 29 Sep 1998 01:59:38 +0200 To: nih-image@io.ece.drexel.edu Subject: kein Betreff X-Mailer: T-Online eMail 2.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8BIT X-Sender: 0421374363-0001@t-online.de From: 0421374363-0001@t-online.de (Hermann Kleemeyer) Resent-Message-ID: <"gZyw_1.0.5t3.TE24s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/397 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 70 Status: O search NIH-image|listproc/nih-image all TLC&thinlayer chromatography From nih-image-request@io.ece.drexel.edu Tue Sep 29 04:13 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA26657; Tue, 29 Sep 1998 04:13:19 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 04:13:19 -0400 (EDT) Date: Tue, 29 Sep 1998 09:57:05 +0200 (CEST) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Quicktime to NIH.Animation... In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"uGWQx1.0.286.uC94s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/398 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 132 Status: O HI! Is it possible to convert a quicktime animation to a TIFF format, such that I would be able to open it in NIH Image? Gary. From nih-image-d-request@io.ece.drexel.edu Tue Sep 29 04:16 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA27175; Tue, 29 Sep 1998 04:16:53 -0400 (EDT) Date: Tue, 29 Sep 1998 04:16:53 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809290816.EAA27175@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #72 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/72 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6149 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 72 Today's Topics: Scion LG-3 Questions [ Jason Pickering ] combining images [ "Richard A. Fluck" ] ------------------------------ Date: Mon, 28 Sep 1998 13:43:02 +0100 From: Jason Pickering To: nih-image@io.ece.drexel.edu Subject: Scion LG-3 Questions Message-Id: Content-Type: text/plain; charset="us-ascii" Dear NIH Imagers, Can anyone tell me how to set the scion[4] channel from the source code? I need to trigger an outside event using the data out channel of the ScionLG-3 board. I have done this though a macro command such as: scion[4]:=BitOr(scion[4],8); scion[4]:=BitOr(scion[4],7); Any suggestions? Also, any hints as to how to read the scion[3] channel from the source code? I used similar commands with the macro language, but I would like to accomplish the same thing with compiled code. Cheers, Jason Pickering ___________________________________________________________________________ Jason Pickering |Email: J.P.Pickering@ct.utwente.nl Onderzoeker in opleiding |Tel: xx 31 53 489 3137 Polymeer Materiaalkundevakgroep |Fax: xx 31 53 489 3823 Universiteit Twente |Priv. addr.: Faculteit der Chemische Technologie |van Loenshof 8D Postbus 217 |7511 HG Enschede 7500 AE Enschede | The Netherlands | __________________________________________________________________________ ------------------------------ Date: Mon, 28 Sep 1998 13:32:59 -0700 From: Abby Pike To: nih-image@io.ece.drexel.edu Subject: measuring Message-id: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu> Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Does anybody know if it is possible to set a distance for how far from the starting point the free hand drawing tool goes in? For example: to start from the end of a curved line and following to line untill the drawing tool has reached .3 of the length of the curve. Any help would be appreciated, thanks Abby Pike Pike_c1@hnrc.tufts.edu ------------------------------ Date: Mon, 28 Sep 1998 14:37:20 -0400 From: "Richard A. Fluck" To: nih-image@io.ece.drexel.edu Subject: combining images Message-id: Content-type: text/plain; charset="us-ascii" I have double-stained cells with two fluorescent dyes that I image with separate filter sets. Is there a way, within NIH Image, to capture images via each filter set and then combine the images in some way so that the fluorescence within each image shows up as separate colors, for example, rhodamine as red and Hoechst 33258 as blue? I see this done often in the literature but have never done it myself. Images in the literature also show yet a third color where the two original images overlap in their fluorescence. Richard A. Fluck, Dept. of Biology, Franklin and Marshall College, P.O. Box 3003, Lancaster, PA 17604-3003 USA; voice, (717)291-4152; fax, (717) 399-4548 ------------------------------ Date: Mon, 28 Sep 1998 17:05:02 -0400 From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) To: nih-image@io.ece.drexel.edu Subject: QuickCam & ADB port Message-Id: <199809282103.RAA16729@codon.nih.gov> Content-Type: text/plain; charset="ISO-2022-JP" Hello Imagers, I am using Logitech (previously connectix) Color QuickCam to capture images with NIH Image. QuickCam works using the power from ADB port and my Powerbook G3 does not seem to give enough power to it from its ADB port. That is, my powerbook can capture images from it with NIH Image when ADB plug of the QuickCam is connected with the ADB port of another mac. Does anyone know if there is any way to increase the power to the ADB port on Powerbooks? Any suggestions will be greatly appreciated. Tsuyoshi ________________________________________ Tsuyoshi Miyakawa, Ph. D. Section on Behavioral Neuropharmacology Experimental Therapeutics Branch National Institute of Mental Health Building 10 Room 4D11 Bethesda, MD 20892-1375 Lab phone#: 301-496-4838 or 301-496-4839 Lab fax#: 301-480-1164 E-mail tsuyoshi@codon.nih.gov ________________________________________ ------------------------------ Date: Mon, 28 Sep 1998 17:50:09 -0500 From: jludtke@facstaff.wisc.edu To: nih-image@io.ece.drexel.edu Subject: Re: combining images Message-Id: <199809282250.RAA94496@mail1.doit.wisc.edu> Content-Type: text/plain; charset="us-ascii" There is a set of macros in the NIH image folder called "color". You just "load macro" under the special menu and choose "color". Then, under special, you should find "color merge two images". Give it a try. Jim Ludtke jludtke@facstaff.wisc.edu ------------------------------ Date: Tue, 29 Sep 1998 01:59:38 +0200 From: 0421374363-0001@t-online.de (Hermann Kleemeyer) To: nih-image@io.ece.drexel.edu Subject: kein Betreff Message-Id: Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT search NIH-image|listproc/nih-image all TLC&thinlayer chromatography ------------------------------ Date: Tue, 29 Sep 1998 09:57:05 +0200 (CEST) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Quicktime to NIH.Animation... Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII HI! Is it possible to convert a quicktime animation to a TIFF format, such that I would be able to open it in NIH Image? Gary. -------------------------------- End of nih-image-d Digest V98 Issue #72 *************************************** From nih-image-request@io.ece.drexel.edu Tue Sep 29 07:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA12404; Tue, 29 Sep 1998 07:18:14 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 07:18:14 -0400 (EDT) X-Sender: zuppinge@baba.ethz.ch Message-Id: In-Reply-To: References: Mime-Version: 1.0 Date: Tue, 29 Sep 1998 13:00:40 +0200 To: nih-image@io.ece.drexel.edu From: Christian Zuppinger Subject: Re: Quicktime to NIH.Animation... Resent-Message-ID: <"Djebo1.0.8g2.5uB4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/399 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 801 Status: O >HI! > >Is it possible to convert a quicktime animation to a TIFF format, such >that I would be able to open it in NIH Image? > >Gary. It is actually possible to open QuickTime movies directly in the latest NIH Image version (1.62). However if you have access to a movie processing software such as Adobe premiere, you can export a variety of movie formats as a picture series, that can be opened in NIH Image. Christian Dipl Biol Christian Zuppinger ETH Hoenggerberg Institut fuer Zellbiologie, HPM F27 CH-8093 Zurich Switzerland Tel: + 441 1 633 33 54 Fax: + 441 1 633 10 69 Email: zuppinge@cell.biol.ethz.ch or czuppinger@access.ch WWW: Institute http://www.rereth.ethz.ch/biol/zellbiologie/zellbiologie.prof_overview.html private http://www.access.ch/whoswho/showwho?czuppinger From nih-image-request@io.ece.drexel.edu Tue Sep 29 07:37 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA14139; Tue, 29 Sep 1998 07:37:32 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 07:37:32 -0400 (EDT) Message-ID: <3610D1EA.8F3AE44D@netmatters.co.uk> Date: Tue, 29 Sep 1998 12:26:21 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: measuring References: <3.0.5.32.19980928133259.0079b6b0@email.hnrc.tufts.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"y0q2w1.0.w93.eDC4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/400 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 679 Status: O Abby Pike wrote: > Does anybody know if it is possible to set a distance for how far from the > starting point the free hand drawing tool goes in? For example: to start > from the end of a curved line and following to line untill the drawing tool > has reached .3 of the length of the curve. Any help would be appreciated, > thanks > > Abby Pike > Pike_c1@hnrc.tufts.edu Try Object Image, if I understand you correctly it has the facility you need. Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Tue Sep 29 08:02 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA16662; Tue, 29 Sep 1998 08:02:19 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 08:02:19 -0400 (EDT) Message-ID: <19980929114614.20773.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Counting fibres Date: Tue, 29 Sep 1998 04:46:14 PDT Resent-Message-ID: <"ZHiAA1.0.Ne3.dYC4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/401 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 665 Status: O Hello, we are trying to count fibres dispersed on a glass plate. We get the 3d image Stack from a confocal microscope. However, between the fibres are some smaller "dirt"-specks, which we don't want to count. We already told Image not to count objects smaller than 30 Pixels, however larger "crumbs" are still counted. How can we get Image to recognize only large objects, that are "fibre-like" (i.e. long and thin and not compact like a crumb)? We already found a cell counting macro, that recognizes circle like cells, and leaves out the rest... ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Tue Sep 29 10:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28135; Tue, 29 Sep 1998 10:09:29 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 10:09:29 -0400 (EDT) Message-ID: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: Reliable Storage and Formats to save Date: Tue, 29 Sep 1998 09:42:52 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"0DuwR2.0.FM6.kME4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/402 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1320 Status: O Hi everyone, Basically, a lot of CT and X-ray images will be scanned for 100's of patient (file size will be min.7 meg to max. 20 meg.). I would like to save, compress (Stuffit/Winzip), label and store them in reliable storage like optical or ZIP or any other media which I do not know which one is better. Later, I would like to search images by name, date and display as thumbnails and then retrieve for research. We have G3's and NT boxes as mixed plotforms. Any suggestion for followings will be appreciated and I will post the results here: * Q1. What will be the best losseless format to save files without loosing anything? TIFF or JPEG or other * Q2. After saving files with selected formats such as TIFF, What will be the best application to compress and save space? such as Disk Doubler, Stuffit or Winzip or other * Q3. The best reliable media, such as recordable CD, DVD, ZIP or other? * Q4. After storing images, What will be the best application to retrieve and display images EASILY? or do you suggest any software to search patient names, retrieve and display stored images EASILY?. I have paintshop pro and PhotoDeluxe and we are planning to buy IMAGEPRO later. Appreciated Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-Univ. of Mich. Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-request@io.ece.drexel.edu Tue Sep 29 10:33 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00583; Tue, 29 Sep 1998 10:33:21 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 10:33:21 -0400 (EDT) From: johannes.barsig@pharma.Novartis.com X-Lotus-FromDomain: PH@N1 To: nih-image@io.ece.drexel.edu Message-ID: <4125668E.005269AC.00@nts1.novartis.com> Date: Tue, 29 Sep 1998 16:08:05 +0100 Subject: wound area measurements Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"zvJCR.0.Ov6.rfE4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/403 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 609 Status: O We are tracing wound areas of mice on glass slides. The circles we get should be digitalized using a graphics tablet. Image should detect, when the circle is closed an measure the area of the circle. Then, the next circle could be drawn. In results, the measurements should be listed. The areas are about two square cm. First question, which graphics tablet would be best for this task together with NIH Image. Second question, is there a macro around that could control the sequential measuring process described. I appreciate every hint. Johannes Barsig, Ph.D. Novartis Research Institute Vienna, Austria From nih-image-request@io.ece.drexel.edu Tue Sep 29 11:03 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02984; Tue, 29 Sep 1998 11:03:27 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 11:03:27 -0400 (EDT) Message-Id: <3610F469.E9745F44@purdue.edu> Date: Tue, 29 Sep 1998 09:53:29 -0500 From: Kris Jorgensen Reply-To: kris@purdue.edu Organization: Purdue University X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu, Mehmet.Dondurur.ph.d@jvc.org Subject: Re: Reliable Storage and Formats to save References: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"pBzOc2.0.qJ.87F4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/404 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1399 Status: O Mehmet Dondurur, Ph. D. wrote: > > Any suggestion for followings will be appreciated and I will post the > results here: > > * Q2. After saving files with selected formats such as TIFF, What > will be the best application to compress and save space? such as Disk > Doubler, Stuffit or Winzip or other I have found that compressing images that are already in a compressed form (jpeg) generally has only limited usefulness. Some will actually get bigger, so the answer to Q1 may be more important. > * Q3. The best reliable media, such as recordable CD, DVD, ZIP or > other? I would not use a ZIP. The mean time to failure is far to short for them or any random access magnetic media. I would us an optical format like CD or DVD. Since you have both Macs and NT machines you can write them in dual format and still have access to them from both machines. > * Q4. After storing images, What will be the best application to > retrieve and display images EASILY? or > do you suggest any software to search patient names, retrieve and > display stored images EASILY?. You should be able to us something like FileMaker to write your own database interface to your files. Again, look at a cross platfrom solution. Hope this helps Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris From nih-image-request@io.ece.drexel.edu Tue Sep 29 12:07 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09047; Tue, 29 Sep 1998 12:07:36 -0400 (EDT) <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org> Resent-Date: Tue, 29 Sep 1998 12:07:36 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org> Mime-Version: 1.0 Date: Tue, 29 Sep 1998 11:54:19 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: Reliable Storage and Formats to save Resent-Message-ID: <"Abxm-1.0.Dk1.X6G4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/405 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1958 Status: O >* Q1. What will be the best losseless format to save files without >loosing anything? TIFF or JPEG or other JPEG is not lossless. TIFF is when the LZW compressed TIFF format is used, otherwise TIFF isn't compressed. >* Q2. After saving files with selected formats such as TIFF, What >will be the best application to compress and save space? such as Disk >Doubler, Stuffit or Winzip or other Choose a compression application that runs on as many platforms as possible. Stuffit may have a windoze version, there are Mac-based Zippers, and there are other compressors that originated in the UNIX world that have MacOS versions. >* Q3. The best reliable media, such as recordable CD, DVD, ZIP or >other? I wouldn't choose magnetic media for archival storage. This rules out Zip storage. In addition, I've heard rumors of hardware problems with Zip mechanisms that damage the media. DVD is too new for my tastes, but CD seems a reasonable choice. >* Q4. After storing images, What will be the best application to >retrieve and display images EASILY? or >do you suggest any software to search patient names, retrieve and >display stored images EASILY?. Keep a simple FileMaker database with references to storage volume ID, file path, etc., as well as any other needed data. With FileMaker, you can also store thumbnails of the images if you wish. Back it up to CD often - you don't want to have to reconstruct it. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Tue Sep 29 13:51 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA16740; Tue, 29 Sep 1998 13:51:17 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 13:51:17 -0400 (EDT) Message-Id: In-Reply-To: <4125668E.005269AC.00@nts1.novartis.com> Mime-Version: 1.0 Date: Tue, 29 Sep 1998 12:25:34 -0600 To: nih-image@io.ece.drexel.edu From: Arnout Ruifrok Subject: Re: wound area measurements Resent-Message-ID: <"PAgK63.0.cc3.lWH4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/406 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1168 Status: O >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria I can reccomend the Wacom digitizing tablet. I have a 15.5*21cm tablet which works for me, but other sizes are also available. It has a cordless pen, and relative and absolute positioning, scaling and pressure sensitivity all can be set to your own liking. Since I have the tablet, I don't use the mouse anymore. For the measuring process you decribe you don't necessarily need a macro, depending on how you want you output. Outlining each areas and doing 'measure' (apple-1) will generate a list of measurements in the 'results' window. Arnout From nih-image-request@io.ece.drexel.edu Tue Sep 29 14:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA18982; Tue, 29 Sep 1998 14:17:18 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 14:17:18 -0400 (EDT) Message-Id: <199809291749.NAA14662@kanga.INS.CWRU.Edu> Date: Tue, 29 Sep 1998 13:49:13 -0400 (EDT) From: nbd@po.cwru.edu (Nagendu B. Dev) To: nih-image@io.ece.drexel.edu Subject: Re: wound area measurements Reply-To: nbd@po.cwru.edu (Nagendu B. Dev) Resent-Message-ID: <"ciSQY.0.824.isH4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/407 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 964 Status: O Dr.Barsig: If you are interested only in the area measurement for a circle, you could use sigmascan digitizing tablet with the sigmascan program, areas are automatically logged into the sigmascan table. Hope, this solves your problem. from: nbd@po.cwru.edu ### Reply to message from johannes.barsig@pharma.Novartis.com of Tue, 29 Sep > >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria > > > > From nih-image-request@io.ece.drexel.edu Tue Sep 29 15:20 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA24197; Tue, 29 Sep 1998 15:20:40 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 15:20:40 -0400 (EDT) Message-Id: <3610F6A7.55B@cirl.meei.harvard.edu> Date: Tue, 29 Sep 1998 15:03:03 +0000 From: src Reply-To: srcramer@cirl.meei.harvard.edu Organization: HMS/MEEI X-Mailer: Mozilla 3.0 (Macintosh; I; 68K) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: S-Video and nih-image Content-Transfer-Encoding: 7bit Resent-Message-ID: <"LRf2n1.0.od5.h_I4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/408 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 452 Status: O To All; I wondered if anyone had information on how to use the S-Video option with RGB colors when trying to capture images from within nih-image? We are using a microscope/camera setup which is connected to an S-Video port on a PowerMac 8600. Is there a seperate video card we need to get from nih? Thanks in advance for any information. Scott Cramer Woods Hole Oceanographic Institution/Mass. Eye & Ear Infirmary srcramer@cirl.meei.harvard.edu From nih-image-request@io.ece.drexel.edu Tue Sep 29 16:58 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA01201; Tue, 29 Sep 1998 16:58:55 -0400 (EDT) Resent-Date: Tue, 29 Sep 1998 16:58:55 -0400 (EDT) Message-ID: <19980929204608.5529.qmail@pc241.icsl.ucla.edu> To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save In-Reply-To: Your message of "Tue, 29 Sep 1998 11:54:19 EDT." Date: Tue, 29 Sep 1998 13:46:08 -0700 From: Mark Hasegawa-Johnson Resent-Message-ID: <"gUkXE3.0.rG7.rPK4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/409 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 456 Status: O >>* Q1. What will be the best losseless format to save files without >>loosing anything? TIFF or JPEG or other You should also consider that many medical images store 16 bits of grayscale data per pixel, while most non-medical formats store up to 8 bits grayscale, or up to 24 bits color. I usually choose a range of interest for each set of images, quantize that range of interest to 8-bit precision, and then save as 8-bit grayscale TIFF. - Mark From nih-image-request@io.ece.drexel.edu Wed Sep 30 04:59 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02488; Wed, 30 Sep 1998 04:58:58 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 04:58:58 -0400 (EDT) Message-ID: <19980930084539.2826.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save Date: Wed, 30 Sep 1998 01:45:39 PDT Resent-Message-ID: <"fD6tt.0.LE.M_U4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/410 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1613 Status: O >* Q1. What will be the best losseless format to save files without >loosing anything? TIFF or JPEG or other A1: If you don't want to loose anything, then JPEG is the one NOT to choose (since it's compression ALWAYS causes loss in quality.) Save it uncompressed, and try a pack-utility like WinZip (see A2) >* Q2. After saving files with selected formats such as TIFF, What >will be the best application to compress and save space? such as Disk >Doubler, Stuffit or Winzip or other A2 Use WinZip (or any other ZIP-Archiver) for compression of your uncompressed images (compressing already compressed images is not that easily possible). Use ZIP since it is understood by most systems and since Thumbs can read it (see A4) >* Q3. The best reliable media, such as recordable CD, DVD, ZIP or >other? For long term archivation I suggest a DAT tape (only for storage, since seek times are pretty long for tapes). For working with these images I suggest putting some on Rewritable MO's or CD-RW's >* Q4. After storing images, What will be the best application to >retrieve and display images EASILY? or >do you suggest any software to search patient names, retrieve and >display stored images EASILY?. A4 As others suggested, use a FileManager to catalogize your files. However, if you found the tape/disk with your ZIPped images, use Thumbs Plus (for Windows) at http://www.cerious.com to view the Images directly in a ZIP-packed archieve. I hope this helps. Sincerely Michael Arm ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-d-request@io.ece.drexel.edu Wed Sep 30 04:59 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02569; Wed, 30 Sep 1998 04:59:17 -0400 (EDT) Date: Wed, 30 Sep 1998 04:59:17 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199809300859.EAA02569@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #73 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/73 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 16815 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 73 Today's Topics: Re: Quicktime to NIH.Animation... [ Christian Zuppinger ] Re: Reliable Storage and Formats to [ Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: Quicktime to NIH.Animation... Message-Id: Content-Type: text/plain; charset="us-ascii" >HI! > >Is it possible to convert a quicktime animation to a TIFF format, such >that I would be able to open it in NIH Image? > >Gary. It is actually possible to open QuickTime movies directly in the latest NIH Image version (1.62). However if you have access to a movie processing software such as Adobe premiere, you can export a variety of movie formats as a picture series, that can be opened in NIH Image. Christian Dipl Biol Christian Zuppinger ETH Hoenggerberg Institut fuer Zellbiologie, HPM F27 CH-8093 Zurich Switzerland Tel: + 441 1 633 33 54 Fax: + 441 1 633 10 69 Email: zuppinge@cell.biol.ethz.ch or czuppinger@access.ch WWW: Institute http://www.rereth.ethz.ch/biol/zellbiologie/zellbiologie.prof_overview.html private http://www.access.ch/whoswho/showwho?czuppinger ------------------------------ Date: Tue, 29 Sep 1998 12:26:21 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: measuring Message-ID: <3610D1EA.8F3AE44D@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Abby Pike wrote: > Does anybody know if it is possible to set a distance for how far from the > starting point the free hand drawing tool goes in? For example: to start > from the end of a curved line and following to line untill the drawing tool > has reached .3 of the length of the curve. Any help would be appreciated, > thanks > > Abby Pike > Pike_c1@hnrc.tufts.edu Try Object Image, if I understand you correctly it has the facility you need. Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Tue, 29 Sep 1998 04:46:14 PDT From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Counting fibres Message-ID: <19980929114614.20773.qmail@hotmail.com> Content-Type: text/plain Hello, we are trying to count fibres dispersed on a glass plate. We get the 3d image Stack from a confocal microscope. However, between the fibres are some smaller "dirt"-specks, which we don't want to count. We already told Image not to count objects smaller than 30 Pixels, however larger "crumbs" are still counted. How can we get Image to recognize only large objects, that are "fibre-like" (i.e. long and thin and not compact like a crumb)? We already found a cell counting macro, that recognizes circle like cells, and leaves out the rest... ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Tue, 29 Sep 1998 09:42:52 -0400 From: "Mehmet Dondurur, Ph. D." To: "'nih-image@io.ece.drexel.edu'" Subject: Reliable Storage and Formats to save Message-ID: <69B43248FE73D11197BB00A0C99AB0678953@jvcserver.vanguardweb.org> Content-Type: text/plain Hi everyone, Basically, a lot of CT and X-ray images will be scanned for 100's of patient (file size will be min.7 meg to max. 20 meg.). I would like to save, compress (Stuffit/Winzip), label and store them in reliable storage like optical or ZIP or any other media which I do not know which one is better. Later, I would like to search images by name, date and display as thumbnails and then retrieve for research. We have G3's and NT boxes as mixed plotforms. Any suggestion for followings will be appreciated and I will post the results here: * Q1. What will be the best losseless format to save files without loosing anything? TIFF or JPEG or other * Q2. After saving files with selected formats such as TIFF, What will be the best application to compress and save space? such as Disk Doubler, Stuffit or Winzip or other * Q3. The best reliable media, such as recordable CD, DVD, ZIP or other? * Q4. After storing images, What will be the best application to retrieve and display images EASILY? or do you suggest any software to search patient names, retrieve and display stored images EASILY?. I have paintshop pro and PhotoDeluxe and we are planning to buy IMAGEPRO later. Appreciated Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-Univ. of Mich. Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Tue, 29 Sep 1998 16:08:05 +0100 From: johannes.barsig@pharma.Novartis.com To: nih-image@io.ece.drexel.edu Subject: wound area measurements Message-ID: <4125668E.005269AC.00@nts1.novartis.com> Content-type: text/plain; charset=us-ascii Content-Disposition: inline We are tracing wound areas of mice on glass slides. The circles we get should be digitalized using a graphics tablet. Image should detect, when the circle is closed an measure the area of the circle. Then, the next circle could be drawn. In results, the measurements should be listed. The areas are about two square cm. First question, which graphics tablet would be best for this task together with NIH Image. Second question, is there a macro around that could control the sequential measuring process described. I appreciate every hint. Johannes Barsig, Ph.D. Novartis Research Institute Vienna, Austria ------------------------------ Date: Tue, 29 Sep 1998 09:53:29 -0500 From: Kris Jorgensen To: nih-image@io.ece.drexel.edu, Mehmet.Dondurur.ph.d@jvc.org Subject: Re: Reliable Storage and Formats to save Message-Id: <3610F469.E9745F44@purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mehmet Dondurur, Ph. D. wrote: > > Any suggestion for followings will be appreciated and I will post the > results here: > > * Q2. After saving files with selected formats such as TIFF, What > will be the best application to compress and save space? such as Disk > Doubler, Stuffit or Winzip or other I have found that compressing images that are already in a compressed form (jpeg) generally has only limited usefulness. Some will actually get bigger, so the answer to Q1 may be more important. > * Q3. The best reliable media, such as recordable CD, DVD, ZIP or > other? I would not use a ZIP. The mean time to failure is far to short for them or any random access magnetic media. I would us an optical format like CD or DVD. Since you have both Macs and NT machines you can write them in dual format and still have access to them from both machines. > * Q4. After storing images, What will be the best application to > retrieve and display images EASILY? or > do you suggest any software to search patient names, retrieve and > display stored images EASILY?. You should be able to us something like FileMaker to write your own database interface to your files. Again, look at a cross platfrom solution. Hope this helps Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris ------------------------------ Date: Tue, 29 Sep 1998 11:54:19 -0400 From: Carl Gustafson To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save Message-Id: Content-Type: text/plain; charset="us-ascii" >* Q1. What will be the best losseless format to save files without >loosing anything? TIFF or JPEG or other JPEG is not lossless. TIFF is when the LZW compressed TIFF format is used, otherwise TIFF isn't compressed. >* Q2. After saving files with selected formats such as TIFF, What >will be the best application to compress and save space? such as Disk >Doubler, Stuffit or Winzip or other Choose a compression application that runs on as many platforms as possible. Stuffit may have a windoze version, there are Mac-based Zippers, and there are other compressors that originated in the UNIX world that have MacOS versions. >* Q3. The best reliable media, such as recordable CD, DVD, ZIP or >other? I wouldn't choose magnetic media for archival storage. This rules out Zip storage. In addition, I've heard rumors of hardware problems with Zip mechanisms that damage the media. DVD is too new for my tastes, but CD seems a reasonable choice. >* Q4. After storing images, What will be the best application to >retrieve and display images EASILY? or >do you suggest any software to search patient names, retrieve and >display stored images EASILY?. Keep a simple FileMaker database with references to storage volume ID, file path, etc., as well as any other needed data. With FileMaker, you can also store thumbnails of the images if you wish. Back it up to CD often - you don't want to have to reconstruct it. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Tue, 29 Sep 1998 12:25:34 -0600 From: Arnout Ruifrok To: nih-image@io.ece.drexel.edu Subject: Re: wound area measurements Message-Id: Content-Type: text/plain; charset="us-ascii" >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria I can reccomend the Wacom digitizing tablet. I have a 15.5*21cm tablet which works for me, but other sizes are also available. It has a cordless pen, and relative and absolute positioning, scaling and pressure sensitivity all can be set to your own liking. Since I have the tablet, I don't use the mouse anymore. For the measuring process you decribe you don't necessarily need a macro, depending on how you want you output. Outlining each areas and doing 'measure' (apple-1) will generate a list of measurements in the 'results' window. Arnout ------------------------------ Date: Tue, 29 Sep 1998 13:49:13 -0400 (EDT) From: nbd@po.CWRU.Edu (Nagendu B. Dev) To: nih-image@io.ece.drexel.edu Subject: Re: wound area measurements Message-Id: <199809291749.NAA14662@kanga.INS.CWRU.Edu> Dr.Barsig: If you are interested only in the area measurement for a circle, you could use sigmascan digitizing tablet with the sigmascan program, areas are automatically logged into the sigmascan table. Hope, this solves your problem. from: nbd@po.cwru.edu ### Reply to message from johannes.barsig@pharma.Novartis.com of Tue, 29 Sep > >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria > > > > ------------------------------ Date: Tue, 29 Sep 1998 15:03:03 +0000 From: src To: nih-image@io.ece.drexel.edu Subject: S-Video and nih-image Message-Id: <3610F6A7.55B@cirl.meei.harvard.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To All; I wondered if anyone had information on how to use the S-Video option with RGB colors when trying to capture images from within nih-image? We are using a microscope/camera setup which is connected to an S-Video port on a PowerMac 8600. Is there a seperate video card we need to get from nih? Thanks in advance for any information. Scott Cramer Woods Hole Oceanographic Institution/Mass. Eye & Ear Infirmary srcramer@cirl.meei.harvard.edu ------------------------------ Date: Tue, 29 Sep 1998 13:46:08 -0700 From: Mark Hasegawa-Johnson To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save Message-ID: <19980929204608.5529.qmail@pc241.icsl.ucla.edu> >>* Q1. What will be the best losseless format to save files without >>loosing anything? TIFF or JPEG or other You should also consider that many medical images store 16 bits of grayscale data per pixel, while most non-medical formats store up to 8 bits grayscale, or up to 24 bits color. I usually choose a range of interest for each set of images, quantize that range of interest to 8-bit precision, and then save as 8-bit grayscale TIFF. - Mark ------------------------------ Date: Wed, 30 Sep 1998 01:45:39 PDT From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save Message-ID: <19980930084539.2826.qmail@hotmail.com> Content-Type: text/plain >* Q1. What will be the best losseless format to save files without >loosing anything? TIFF or JPEG or other A1: If you don't want to loose anything, then JPEG is the one NOT to choose (since it's compression ALWAYS causes loss in quality.) Save it uncompressed, and try a pack-utility like WinZip (see A2) >* Q2. After saving files with selected formats such as TIFF, What >will be the best application to compress and save space? such as Disk >Doubler, Stuffit or Winzip or other A2 Use WinZip (or any other ZIP-Archiver) for compression of your uncompressed images (compressing already compressed images is not that easily possible). Use ZIP since it is understood by most systems and since Thumbs can read it (see A4) >* Q3. The best reliable media, such as recordable CD, DVD, ZIP or >other? For long term archivation I suggest a DAT tape (only for storage, since seek times are pretty long for tapes). For working with these images I suggest putting some on Rewritable MO's or CD-RW's >* Q4. After storing images, What will be the best application to >retrieve and display images EASILY? or >do you suggest any software to search patient names, retrieve and >display stored images EASILY?. A4 As others suggested, use a FileManager to catalogize your files. However, if you found the tape/disk with your ZIPped images, use Thumbs Plus (for Windows) at http://www.cerious.com to view the Images directly in a ZIP-packed archieve. I hope this helps. Sincerely Michael Arm ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com -------------------------------- End of nih-image-d Digest V98 Issue #73 *************************************** From nih-image-request@io.ece.drexel.edu Wed Sep 30 05:06 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA03412; Wed, 30 Sep 1998 05:06:35 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 05:06:35 -0400 (EDT) Message-ID: <19980930085710.13766.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Counting Fibres (the complete message) Date: Wed, 30 Sep 1998 01:57:10 PDT Resent-Message-ID: <"bGOrd3.0.XZ.8AV4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/411 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1270 Status: O Sorry, it seemed, as if the last part of my previous mail was cut off. Hello, we are trying to count fibres dispersed on a glass plate. We get the 3d image Stack from a confocal microscope. However, between the fibres are some smaller "dirt"-specks, which we don't want to count. We already told Image not to count objects smaller than 30 Pixels, however larger "crumbs" are still counted. How can we get Image to recognize only large objects, that are "fibre-like" (i.e. long and thin and not compact like a crumb)? We already found a cell counting macro, that recognizes circle like cells, and leaves out the rest... Is there a way to tell a macro only to count long, thin objects? Putting an ellipse into a ROI-selected fibre often doesn't work, since some are slightly bent like a parenthesis "("... Any suggestions would be greatly appreciated. Sincerely Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA23713; Wed, 30 Sep 1998 09:09:55 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 09:09:55 -0400 (EDT) Message-ID: <3612A7AE.C952D464@de.ms.philips.com> Date: Wed, 30 Sep 1998 14:50:38 -0700 From: Johann Borchers Organization: Philips Medizin Systeme X-Mailer: Mozilla 4.06 [en] (Win16; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save References: <199809300850.EAA01432@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"zVaNX.0.jL5.laY4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/412 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-2 Content-Length: 986 Status: O > > >* Q1. What will be the best losseless format to save files without > >loosing anything? TIFF or JPEG or other > > A1: If you don't want to loose anything, then JPEG is the one NOT to > choose (since it's compression ALWAYS causes loss in quality.) Save it > uncompressed, and try a pack-utility like WinZip (see A2) > -- Dear Imagers, the ACR-NEMA group proposed a "JPEG Lossles" compression for DICOM 3.0 compliant devices. Without loss of any pixel-information, you can achieve compression rates of 2-3 with typical grayscale images. ---------------------------------------------------------------------- Johann Borchers Voice : 49 40 5078-2071 Philips Medical Systems Hamburg FAX : 49 40 5078-2301 Medical-Information-Techn. Mobile : 49 171 5544566 e-mail : johann.borchers@de.ms.philips.com ---------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:20 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24710; Wed, 30 Sep 1998 09:20:55 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 09:20:55 -0400 (EDT) From: Stephen Keenan Sender: k9425608@qub.ac.uk To: nih-image@io.ece.drexel.edu Subject: Watersheds for Scion PC Image? Message-ID: Date: Wed, 30 Sep 1998 14:05:44 -0400 (EDT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"CYmD42.0.Fg5.SoY4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/413 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 357 Status: O Does anyone know if a watersheds pluggin exists for Scion PC Image. I know that this pluggin exists for NIH image for the Mac but so far I haven'tbeen able to find a pluggin for the PC version. If anyone could point me in the right direction I would be extremely grateful. Thanks in advance, Stephen Keenan, Ph.D Student, Queen's University Belfast From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:40 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA26491; Wed, 30 Sep 1998 09:40:11 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 09:40:11 -0400 (EDT) Message-ID: <36123F46.7110EF3@netmatters.co.uk> Date: Wed, 30 Sep 1998 14:25:12 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"XqTmT2.0.I56.33Z4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/414 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 775 Status: O Stephen Keenan wrote: > Does anyone know if a watersheds pluggin exists for Scion > PC Image. I know that this pluggin exists for NIH image for the > Mac but so far I haven'tbeen able to find a pluggin for the PC > version. > If anyone could point me in the right direction I would be extremely > grateful. > > Thanks in advance, > > Stephen Keenan, > Ph.D Student, > Queen's University Belfast There should be a watershed command in the binary processes associated with the Process menu. It is should also be executable via the macro language. Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Wed Sep 30 09:52 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27650; Wed, 30 Sep 1998 09:52:19 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 09:52:19 -0400 (EDT) Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> From: "Kirk, Todd Jason" To: nih-image@io.ece.drexel.edu Subject: Meridian InSIGHT and MAC Date: Wed, 30 Sep 1998 08:30:55 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"i-SXE3.0.5G6.EAZ4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/415 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 622 Status: O Has anyone connected a Mac to a Merdian Insight plus? We had a PC connected to it, now we have a Mac. We used the serial port on the PC to change filters, open the shutter etc. Now that the Mac is going to be used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin out seems to be different and it is not sending the data (using the openserial( ) command), to change the filters etc. Apple said that I have to become a developer to get this info., and cannot help. It seems simple, has anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. Todd Kirk Indiana University Medical Center From nih-image-request@io.ece.drexel.edu Wed Sep 30 10:20 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00138; Wed, 30 Sep 1998 10:20:17 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 10:20:17 -0400 (EDT) Date: Wed, 30 Sep 1998 23:59:40 +1000 (EST) Message-Id: <199809301359.XAA01783@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: Summing Macro Resent-Message-ID: <"PgX2p.0.mw6.tbZ4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/417 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 447 Status: O Greetings imagers, Does anyone out there know of a macro which can; - sum up a list of already calculated (area) values (usually less than 50) from the results window. - take this sum and divide it by the total area of the image and display the result. Any help would be much appreciated as I desperately need some code to include in my final year project. Thanx in advance, Cormac McCann Final year Mechanical Engineering student, CQU. From nih-image-request@io.ece.drexel.edu Wed Sep 30 10:20 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA00170; Wed, 30 Sep 1998 10:20:33 -0400 (EDT) <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> Resent-Date: Wed, 30 Sep 1998 10:20:33 -0400 (EDT) X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48] Message-Id: In-Reply-To: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> Mime-Version: 1.0 Date: Wed, 30 Sep 1998 16:02:21 +0200 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Meridian InSIGHT and MAC Resent-Message-ID: <"XgCq3.0.5t6.kZZ4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/416 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1384 Status: O > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be used, >I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin >out seems to be different and it is not sending the data (using the >openserial( ) command), to change the filters etc. Apple said that I have to >become a developer to get this info., and cannot help. It seems simple, has >anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. > >Todd Kirk >Indiana University Medical Center One complication of the NIH Image serial access is that it alway expects handshake to be active. In my version of object-Image (see web site), you can switch handshake off. This often helped without resoldering the cable. OpenSerial('Options') Besides parity, speed and stop bits, two more parameters are recognized in Object-Image: 'no DTR' disables the input hardware handshake 'no XonXoff' disables the input software handshake. Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html From nih-image-request@io.ece.drexel.edu Wed Sep 30 11:39 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA06365; Wed, 30 Sep 1998 11:39:08 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 11:39:08 -0400 (EDT) Message-ID: <36124888.45D4A4EE@sdsc.edu> Date: Wed, 30 Sep 1998 08:04:40 -0700 From: Harvey Karten Reply-To: hjkarten@UCSD.EDU Organization: UCSD X-Mailer: Mozilla 4.04 [en] (Win95; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re:Reliable format and saving files References: <199809300855.EAA01981@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ipC5m3.0.1-._da4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/418 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2433 Status: O The issue that has not been addressed in the other replies is the matter of databasing. While FileMaker Pro is a useful tool for storing and saving text based information, it has only limited ability for dealing with images. You can create a portal/container for displaying an image, but FileMaker has no facility for generating the needed thumbnails. It is best to use FileMaker in conjunction with an image gallery database product, such as Thumbsplus, Canto Cumulus or a few other lesser products. I have found Thumbsplus to be the most flexible in being able to read the widest variety of file formats, including 8, 12 and 16 bits files. It can read complex Multi-TIFF files (e.g. stacks of double or triple labeled images in an extended Z-series, etc.). IImage Gallery Database programs generate thumbnail images of all files on a disk or series of disks, display them on the screen, and you can then click on the image of interest. It will bring up the oriignla image, you can then edit it and re-save it. As in the case of most Image Gallery Databasing Programs (Thumbsplus, Canto Cumulus, Extensis Portfolio, Search 3.1, and possibly others) Thumbsplus will autmoatically scan a disk looking for previously uncatalogued image files. It will generate a thumbnail image of a size you choose, read the original collection parameters (possibly including patient's names, experimental protocol, etc.), and make these available across a network. It will do all this and more for less than $100. The next version promises to have direct input to ODBC compliant database programs. FileMaker Pro will soon be ODBC compliant, so that will make it easier to work with. Both FileMaker Pro and Thumbsplus are available for Mac, Windows 95 and NT platforms. You can buy Thumbsplus from http://www.cerious.com No, I don't work Thumbsplus, but I have worked with them and found them to be the most responsive of companies. They are a small operation, and are willing to adapt their software to the needs of the scientific community. And you can't beat the price! regards, Harvey -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09332; Wed, 30 Sep 1998 12:12:05 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 12:12:05 -0400 (EDT) Message-Id: <9809301547.AA131782@acs1.acs.ucalgary.ca> Subject: Re: detecting fibres To: nih-image@io.ece.drexel.edu Date: Wed, 30 Sep 98 9:47:42 MDT From: "Doug S. Phillips" Cc: arminator@hotmail.com In-Reply-To: <199809300846.EAA00974@io.ece.drexel.edu>; from "nih-image-d-request@io.ece.drexel.edu" at Sep 30, 1998 4:46 am X-Mailer: ELM [version 2.3 PL11K] Mime-Version: 1.0 Resent-Message-ID: <"hioo6.0.Pn1.sBb4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/419 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="----------------------------" Content-Length: 2104 Status: O ------------------------------ Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Michael Arm wrote: > How can we get Image to recognize only large objects, that are > "fibre-like" (i.e. long and thin and not compact like a crumb)? Here is a macro I use for the opposite purpose - detecting whether an object is sufficiently round (aspect ratio less than 4 in the following example). By changing the "aspect" value in the following, and changing the if rUser1[j] < aspect then begin to if rUser1[j] > aspect then begin it should do what you want. {=================================================================} macro 'Find focus'; {Try to measure the position of the white square in each picture of a stack} var i,j,jfocus,numslices: integer; aspect: real; begin { Open a window for the data. } NewTextWindow('Focus position',250,250); MoveWindow(250,320); Writeln('Frame, X, Y, Area, Major, Minor'); SaveState; numslices:=nSlices; SetParticleSize(5,500); LabelParticles(true); OutlineParticles(true); SetOptions('X-Y Center, Area, Major, Minor'); for i:=1 to numslices do begin ChooseSlice(i); ChangeValues(255,255,254); SetDensitySlice(215,254); MakeBinary; Dilate; AnalyzeParticles; SelectWindow('Focus position'); aspect:=4.0; if rCount > 0 then begin for j:=1 to rCount do begin rUser1[j]:=rMajor[j]/rMinor[j]; end; for j:=1 to rCount do begin if rUser1[j] < aspect then begin aspect:=rUser1[j]; jfocus:=j; end; end; Writeln(i:5:0,',',rX[jfocus]:5:0,',',rY[jfocus]:5:0,',',rArea[jfocus]:5:0,',',rMajor[jfocus]:5:0,',',rMinor[jfocus]:5:0); end; end; RestoreState; end; Sincerely, Doug P. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ -------------------------------- From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:19 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09909; Wed, 30 Sep 1998 12:19:09 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 12:19:09 -0400 (EDT) From: Stephen Keenan Sender: k9425608@qub.ac.uk To: brownj@netmatters.co.uk cc: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? In-Reply-To: <36123F46.7110EF3@netmatters.co.uk> Message-ID: Date: Wed, 30 Sep 1998 16:54:12 -0400 (EDT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"zReQR1.0.2u1.WGb4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/420 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 294 Status: O Jeremy, Thank you for taking the time to answer my request. I do not seem to have a watersheds command in the binary processes associated with my Process menu. Do I need to obtain any additional modules/macros to enable this function? Thanks again ---------------------- Stephen Keenan From nih-image-request@io.ece.drexel.edu Wed Sep 30 12:50 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12347; Wed, 30 Sep 1998 12:50:08 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 12:50:08 -0400 (EDT) Message-Id: In-Reply-To: References: <36123F46.7110EF3@netmatters.co.uk> Mime-Version: 1.0 Date: Wed, 30 Sep 1998 12:39:27 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Watersheds for Scion PC Image? Resent-Message-ID: <"CXZsK2.0.Uj2.crb4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/421 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 270 Status: O >Jeremy, > >Thank you for taking the time to answer my request. > >I do not seem to have a watersheds command in the binary >processes associated with my Process menu. The Watershed command is in Scion Image for Windows beta 3, but it doesn't appear to work. -wayne From nih-image-request@io.ece.drexel.edu Wed Sep 30 16:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA00522; Wed, 30 Sep 1998 16:12:03 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 16:12:03 -0400 (EDT) X-Authentication-Warning: morpheus.cis.yale.edu: feke owned process doing -bs Date: Wed, 30 Sep 1998 15:52:48 -0400 (EDT) From: Gilbert D Feke X-Sender: feke@morpheus.cis.yale.edu To: nih-image@io.ece.drexel.edu Subject: real-time row&column averaging Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"qYFdL1.0.237.Rme4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/422 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 655 Status: O I am trying to find some combination of CCD camera, frame grabber (either digital or analog), DSP, and/or software which allows me to perform real-time averaging of rows and columns. For example, if I have a 512x512 image input, then I would like the real-time processing to output both a 1x512 image and a 512x1 image which I can save to memory or disk. Line scan cameras are not an option since I need both the row and column averaging from the same camera. If anyone has any suggestions of how I could do this or some company I should contact, please reply. Thank you. Gilbert Feke Yale University Dept. of Applied Physics gilbert.feke@yale.edu From nih-image-request@io.ece.drexel.edu Wed Sep 30 20:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18849; Wed, 30 Sep 1998 20:08:04 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 20:08:04 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: arminator@hotmail.com, nih-image@io.ece.drexel.edu Date: Thu, 1 Oct 1998 9:50:01 GMT+1000 Subject: Re: Counting Fibres (the complete message) Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"y-zwK3.0.5F4.2Di4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/423 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2673 Status: O >From: "Michael Arm" >To: nih-image@io.ece.drexel.edu >Subject: Counting Fibres (the complete message) >Date: Wed, 30 Sep 1998 01:57:10 PDT >.... >we are trying to count fibres dispersed on a glass plate. We get the 3d >image Stack from a confocal microscope. >However, between the fibres are some smaller "dirt"-specks, which we >don't want to count. We already told Image not to count objects smaller >than 30 Pixels, however larger "crumbs" are still counted. >How can we get Image to recognize only large objects, that are >"fibre-like" (i.e. long and thin and not compact like a crumb)? >We already found a cell counting macro, that recognizes circle like >cells, and leaves out the rest... > >Is there a way to tell a macro only to count long, thin objects? Putting >an ellipse into a ROI-selected fibre often doesn't work, since some are >slightly bent like a parenthesis "("... > >Any suggestions would be greatly appreciated. > >Sincerely >Michael Arm > Michael, you cant "tell a macro only to count long, thin objects" but having counted objects which satisfy size criteria, you can scan the results tables by macro to attempt further qualification of counted particles. You can then count those in the results table that meet the further imposed criteria or effectively delete them from the table (by shuffling others over them). It is not clear to me what the significance of the 3D is but I would expect to be able to effectively exclude the larger "crumbs" by using the ratio rArea[i]/rLength[i]: for i:= rCount do begin rUser1[i]:=rArea[i]/rLength[i]; { rLength is particle perimeter for analyzeParticles for long thin fibre particles, rUser1[i] should be average halfwidth << rLength[i]/2 ~= length } You might also consider making a binary image, and then a Euclidean distance map (binary(Process menu before analyzeParticles. Particles with larger cross-sections can be excluded by densitySlice'ing the distance map; MakeBinary; binary('map');enhanceContrast; setDensitySlice(1,maxHalfwidth); analyzeParticles; then rMax[i] will be a measure of particle's maximum halfwidth which in turn should be close to average halfwidth in rUser1. If you really want to nitpick the particles by macro, then use analyzeParticles results table locations to autoOutline each particle in turn but you would be much better off to use Object-Image in that case as it records rTop,rLeft for that autoOutline(rTop[i],rLeft[i]); purpose. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Wed Sep 30 20:29 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA20814; Wed, 30 Sep 1998 20:29:45 -0400 (EDT) Resent-Date: Wed, 30 Sep 1998 20:29:45 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: johannes.barsig@pharma.Novartis.com, nih-image@io.ece.drexel.edu Date: Thu, 1 Oct 1998 10:16:09 GMT+1000 Subject: Re: wound area measurements Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"NVewJ.0.oj4.lai4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/424 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1430 Status: O >From: johannes.barsig@pharma.Novartis.com >To: nih-image@io.ece.drexel.edu >Date: Tue, 29 Sep 1998 16:08:05 +0100 >Subject: wound area measurements > >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria > I would have thought that you would find that an inexpensive video or digital camera attached to a dissecting microscope would be a much more flexible and efficient approach with potential for (semi)automated analysis by NIH-Image and offering much better documentation of results. Object-Image has a very nice extension to NIH-Image for computer-assisted outlining of density-sliced images: points are collected by (option) "sparking" to nearest density-sliced edge. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Wed Sep 30 20:36 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA21986; Wed, 30 Sep 1998 20:36:33 -0400 (EDT) Date: Wed, 30 Sep 1998 20:36:33 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810010036.UAA21986@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #74 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/74 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 21160 Status: O ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 74 Today's Topics: Counting Fibres (the complete messag [ "Michael Arm" ] Re: Watersheds for Scion PC Image? [ Jeremy Brown ] Re:Reliable format and saving files [ Harvey Karten ] Re: detecting fibres [ "Doug S. Phillips" ] Re: Watersheds for Scion PC Image? [ Wayne Rasband ] real-time row&column averaging [ Gilbert D Feke To: nih-image@io.ece.drexel.edu Subject: Counting Fibres (the complete message) Message-ID: <19980930085710.13766.qmail@hotmail.com> Content-Type: text/plain Sorry, it seemed, as if the last part of my previous mail was cut off. Hello, we are trying to count fibres dispersed on a glass plate. We get the 3d image Stack from a confocal microscope. However, between the fibres are some smaller "dirt"-specks, which we don't want to count. We already told Image not to count objects smaller than 30 Pixels, however larger "crumbs" are still counted. How can we get Image to recognize only large objects, that are "fibre-like" (i.e. long and thin and not compact like a crumb)? We already found a cell counting macro, that recognizes circle like cells, and leaves out the rest... Is there a way to tell a macro only to count long, thin objects? Putting an ellipse into a ROI-selected fibre often doesn't work, since some are slightly bent like a parenthesis "("... Any suggestions would be greatly appreciated. Sincerely Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Wed, 30 Sep 1998 14:50:38 -0700 From: Johann Borchers To: nih-image@io.ece.drexel.edu Subject: Re: Reliable Storage and Formats to save Message-ID: <3612A7AE.C952D464@de.ms.philips.com> Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit > > >* Q1. What will be the best losseless format to save files without > >loosing anything? TIFF or JPEG or other > > A1: If you don't want to loose anything, then JPEG is the one NOT to > choose (since it's compression ALWAYS causes loss in quality.) Save it > uncompressed, and try a pack-utility like WinZip (see A2) > -- Dear Imagers, the ACR-NEMA group proposed a "JPEG Lossles" compression for DICOM 3.0 compliant devices. Without loss of any pixel-information, you can achieve compression rates of 2-3 with typical grayscale images. ---------------------------------------------------------------------- Johann Borchers Voice : 49 40 5078-2071 Philips Medical Systems Hamburg FAX : 49 40 5078-2301 Medical-Information-Techn. Mobile : 49 171 5544566 e-mail : johann.borchers@de.ms.philips.com ---------------------------------------------------------------------- ------------------------------ Date: Wed, 30 Sep 1998 14:05:44 -0400 (EDT) From: Stephen Keenan To: nih-image@io.ece.drexel.edu Subject: Watersheds for Scion PC Image? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Does anyone know if a watersheds pluggin exists for Scion PC Image. I know that this pluggin exists for NIH image for the Mac but so far I haven'tbeen able to find a pluggin for the PC version. If anyone could point me in the right direction I would be extremely grateful. Thanks in advance, Stephen Keenan, Ph.D Student, Queen's University Belfast ------------------------------ Date: Wed, 30 Sep 1998 14:25:12 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? Message-ID: <36123F46.7110EF3@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Stephen Keenan wrote: > Does anyone know if a watersheds pluggin exists for Scion > PC Image. I know that this pluggin exists for NIH image for the > Mac but so far I haven'tbeen able to find a pluggin for the PC > version. > If anyone could point me in the right direction I would be extremely > grateful. > > Thanks in advance, > > Stephen Keenan, > Ph.D Student, > Queen's University Belfast There should be a watershed command in the binary processes associated with the Process menu. It is should also be executable via the macro language. Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Wed, 30 Sep 1998 08:30:55 -0500 From: "Kirk, Todd Jason" To: nih-image@io.ece.drexel.edu Subject: Meridian InSIGHT and MAC Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> Content-Type: text/plain Has anyone connected a Mac to a Merdian Insight plus? We had a PC connected to it, now we have a Mac. We used the serial port on the PC to change filters, open the shutter etc. Now that the Mac is going to be used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin out seems to be different and it is not sending the data (using the openserial( ) command), to change the filters etc. Apple said that I have to become a developer to get this info., and cannot help. It seems simple, has anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. Todd Kirk Indiana University Medical Center ------------------------------ Date: Wed, 30 Sep 1998 16:02:21 +0200 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Meridian InSIGHT and MAC Message-Id: Content-Type: text/plain; charset="us-ascii" > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be used, >I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin >out seems to be different and it is not sending the data (using the >openserial( ) command), to change the filters etc. Apple said that I have to >become a developer to get this info., and cannot help. It seems simple, has >anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. > >Todd Kirk >Indiana University Medical Center One complication of the NIH Image serial access is that it alway expects handshake to be active. In my version of object-Image (see web site), you can switch handshake off. This often helped without resoldering the cable. OpenSerial('Options') Besides parity, speed and stop bits, two more parameters are recognized in Object-Image: 'no DTR' disables the input hardware handshake 'no XonXoff' disables the input software handshake. Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html ------------------------------ Date: Wed, 30 Sep 1998 23:59:40 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: Summing Macro Message-Id: <199809301359.XAA01783@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" Greetings imagers, Does anyone out there know of a macro which can; - sum up a list of already calculated (area) values (usually less than 50) from the results window. - take this sum and divide it by the total area of the image and display the result. Any help would be much appreciated as I desperately need some code to include in my final year project. Thanx in advance, Cormac McCann Final year Mechanical Engineering student, CQU. ------------------------------ Date: Wed, 30 Sep 1998 08:04:40 -0700 From: Harvey Karten To: nih-image@io.ece.drexel.edu Subject: Re:Reliable format and saving files Message-ID: <36124888.45D4A4EE@sdsc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The issue that has not been addressed in the other replies is the matter of databasing. While FileMaker Pro is a useful tool for storing and saving text based information, it has only limited ability for dealing with images. You can create a portal/container for displaying an image, but FileMaker has no facility for generating the needed thumbnails. It is best to use FileMaker in conjunction with an image gallery database product, such as Thumbsplus, Canto Cumulus or a few other lesser products. I have found Thumbsplus to be the most flexible in being able to read the widest variety of file formats, including 8, 12 and 16 bits files. It can read complex Multi-TIFF files (e.g. stacks of double or triple labeled images in an extended Z-series, etc.). IImage Gallery Database programs generate thumbnail images of all files on a disk or series of disks, display them on the screen, and you can then click on the image of interest. It will bring up the oriignla image, you can then edit it and re-save it. As in the case of most Image Gallery Databasing Programs (Thumbsplus, Canto Cumulus, Extensis Portfolio, Search 3.1, and possibly others) Thumbsplus will autmoatically scan a disk looking for previously uncatalogued image files. It will generate a thumbnail image of a size you choose, read the original collection parameters (possibly including patient's names, experimental protocol, etc.), and make these available across a network. It will do all this and more for less than $100. The next version promises to have direct input to ODBC compliant database programs. FileMaker Pro will soon be ODBC compliant, so that will make it easier to work with. Both FileMaker Pro and Thumbsplus are available for Mac, Windows 95 and NT platforms. You can buy Thumbsplus from http://www.cerious.com No, I don't work Thumbsplus, but I have worked with them and found them to be the most responsive of companies. They are a small operation, and are willing to adapt their software to the needs of the scientific community. And you can't beat the price! regards, Harvey -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org ------------------------------ Date: Wed, 30 Sep 98 9:47:42 MDT From: "Doug S. Phillips" To: nih-image@io.ece.drexel.edu Cc: arminator@hotmail.com Subject: Re: detecting fibres Message-Id: <9809301547.AA131782@acs1.acs.ucalgary.ca> Content-Type: multipart/mixed; boundary="----------------------------" Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Michael Arm wrote: > How can we get Image to recognize only large objects, that are > "fibre-like" (i.e. long and thin and not compact like a crumb)? Here is a macro I use for the opposite purpose - detecting whether an object is sufficiently round (aspect ratio less than 4 in the following example). By changing the "aspect" value in the following, and changing the if rUser1[j] < aspect then begin to if rUser1[j] > aspect then begin it should do what you want. {=================================================================} macro 'Find focus'; {Try to measure the position of the white square in each picture of a stack} var i,j,jfocus,numslices: integer; aspect: real; begin { Open a window for the data. } NewTextWindow('Focus position',250,250); MoveWindow(250,320); Writeln('Frame, X, Y, Area, Major, Minor'); SaveState; numslices:=nSlices; SetParticleSize(5,500); LabelParticles(true); OutlineParticles(true); SetOptions('X-Y Center, Area, Major, Minor'); for i:=1 to numslices do begin ChooseSlice(i); ChangeValues(255,255,254); SetDensitySlice(215,254); MakeBinary; Dilate; AnalyzeParticles; SelectWindow('Focus position'); aspect:=4.0; if rCount > 0 then begin for j:=1 to rCount do begin rUser1[j]:=rMajor[j]/rMinor[j]; end; for j:=1 to rCount do begin if rUser1[j] < aspect then begin aspect:=rUser1[j]; jfocus:=j; end; end; Writeln(i:5:0,',',rX[jfocus]:5:0,',',rY[jfocus]:5:0,',',rArea[jfocus]:5:0,',',rMajor[jfocus]:5:0,',',rMinor[jfocus]:5:0); end; end; RestoreState; end; Sincerely, Doug P. Doug S. Phillips Internet: phillips@ucalgary.ca University Computing Services Phone:(403)220-8445 FAX:(403)282-9199 The University of Calgary WWW: http://www.acs.ucalgary.ca/~phillips/ - ------------------------------ ------------------------------ Date: Wed, 30 Sep 1998 16:54:12 -0400 (EDT) From: Stephen Keenan To: brownj@netmatters.co.uk cc: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Jeremy, Thank you for taking the time to answer my request. I do not seem to have a watersheds command in the binary processes associated with my Process menu. Do I need to obtain any additional modules/macros to enable this function? Thanks again ---------------------- Stephen Keenan ------------------------------ Date: Wed, 30 Sep 1998 12:39:27 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? Message-Id: Content-Type: text/plain; charset="us-ascii" >Jeremy, > >Thank you for taking the time to answer my request. > >I do not seem to have a watersheds command in the binary >processes associated with my Process menu. The Watershed command is in Scion Image for Windows beta 3, but it doesn't appear to work. -wayne ------------------------------ Date: Wed, 30 Sep 1998 15:52:48 -0400 (EDT) From: Gilbert D Feke To: nih-image@io.ece.drexel.edu Subject: real-time row&column averaging Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to find some combination of CCD camera, frame grabber (either digital or analog), DSP, and/or software which allows me to perform real-time averaging of rows and columns. For example, if I have a 512x512 image input, then I would like the real-time processing to output both a 1x512 image and a 512x1 image which I can save to memory or disk. Line scan cameras are not an option since I need both the row and column averaging from the same camera. If anyone has any suggestions of how I could do this or some company I should contact, please reply. Thank you. Gilbert Feke Yale University Dept. of Applied Physics gilbert.feke@yale.edu ------------------------------ Date: Thu, 1 Oct 1998 9:50:01 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: arminator@hotmail.com, nih-image@io.ece.drexel.edu Subject: Re: Counting Fibres (the complete message) Message-ID: >From: "Michael Arm" >To: nih-image@io.ece.drexel.edu >Subject: Counting Fibres (the complete message) >Date: Wed, 30 Sep 1998 01:57:10 PDT >.... >we are trying to count fibres dispersed on a glass plate. We get the 3d >image Stack from a confocal microscope. >However, between the fibres are some smaller "dirt"-specks, which we >don't want to count. We already told Image not to count objects smaller >than 30 Pixels, however larger "crumbs" are still counted. >How can we get Image to recognize only large objects, that are >"fibre-like" (i.e. long and thin and not compact like a crumb)? >We already found a cell counting macro, that recognizes circle like >cells, and leaves out the rest... > >Is there a way to tell a macro only to count long, thin objects? Putting >an ellipse into a ROI-selected fibre often doesn't work, since some are >slightly bent like a parenthesis "("... > >Any suggestions would be greatly appreciated. > >Sincerely >Michael Arm > Michael, you cant "tell a macro only to count long, thin objects" but having counted objects which satisfy size criteria, you can scan the results tables by macro to attempt further qualification of counted particles. You can then count those in the results table that meet the further imposed criteria or effectively delete them from the table (by shuffling others over them). It is not clear to me what the significance of the 3D is but I would expect to be able to effectively exclude the larger "crumbs" by using the ratio rArea[i]/rLength[i]: for i:= rCount do begin rUser1[i]:=rArea[i]/rLength[i]; { rLength is particle perimeter for analyzeParticles for long thin fibre particles, rUser1[i] should be average halfwidth << rLength[i]/2 ~= length } You might also consider making a binary image, and then a Euclidean distance map (binary(Process menu before analyzeParticles. Particles with larger cross-sections can be excluded by densitySlice'ing the distance map; MakeBinary; binary('map');enhanceContrast; setDensitySlice(1,maxHalfwidth); analyzeParticles; then rMax[i] will be a measure of particle's maximum halfwidth which in turn should be close to average halfwidth in rUser1. If you really want to nitpick the particles by macro, then use analyzeParticles results table locations to autoOutline each particle in turn but you would be much better off to use Object-Image in that case as it records rTop,rLeft for that autoOutline(rTop[i],rLeft[i]); purpose. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 1 Oct 1998 10:16:09 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: johannes.barsig@pharma.Novartis.com, nih-image@io.ece.drexel.edu Subject: Re: wound area measurements Message-ID: >From: johannes.barsig@pharma.Novartis.com >To: nih-image@io.ece.drexel.edu >Date: Tue, 29 Sep 1998 16:08:05 +0100 >Subject: wound area measurements > >We are tracing wound areas of mice on glass slides. The circles we get >should be digitalized using a graphics tablet. Image should detect, when >the circle is closed an measure the area of the circle. Then, the next >circle could be drawn. In results, the measurements should be listed. The >areas are about two square cm. First question, which graphics tablet would >be best for this task together with NIH Image. Second question, is there a >macro around that could control the sequential measuring process described. >I appreciate every hint. >Johannes Barsig, Ph.D. >Novartis Research Institute >Vienna, Austria > I would have thought that you would find that an inexpensive video or digital camera attached to a dissecting microscope would be a much more flexible and efficient approach with potential for (semi)automated analysis by NIH-Image and offering much better documentation of results. Object-Image has a very nice extension to NIH-Image for computer-assisted outlining of density-sliced images: points are collected by (option) "sparking" to nearest density-sliced edge. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #74 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 1 00:56 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA13264; Thu, 1 Oct 1998 00:56:29 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 00:56:29 -0400 (EDT) Date: 30 Sep 98 21:35:15 -0600 From: Steven Moore Subject: [1]RE>Re: wound area measurements To: "nih-image" X-Mailer: QuickMail Pro 1.5.2 (Windows32) X-Priority: 3 Reply-To: Steven Moore MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Message-ID: <1304931229-2795399@mailhost.cipe.com> Resent-Message-ID: <"weLoP.0.Lm2.SPm4s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/425 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-Ascii" Content-Length: 1876 Status: O Thanks for the message! Please note that I'm out of the office for two weeks. I will return on October 15. If you need immediate attention, call (800) 322-9884. Press 0 (zero). Thanks. Steven Moore, CIPE On 10/1/98, nih-image wrote: >>From: johannes.barsig@pharma.Novartis.com >>To: nih-image@io.ece.drexel.edu >>Date: Tue, 29 Sep 1998 16:08:05 +0100 >>Subject: wound area measurements >> >>We are tracing wound areas of mice on glass slides. The circles we get >>should be digitalized using a graphics tablet. Image should detect, when >>the circle is closed an measure the area of the circle. Then, the next >>circle could be drawn. In results, the measurements should be listed. The >>areas are about two square cm. First question, which graphics tablet would >>be best for this task together with NIH Image. Second question, is there a >>macro around that could control the sequential measuring process described. >>I appreciate every hint. >>Johannes Barsig, Ph.D. >>Novartis Research Institute >>Vienna, Austria >> >I would have thought that you would find that an inexpensive video or digital >camera attached to a dissecting microscope would be a much more flexible and >efficient approach with potential for (semi)automated analysis by NIH-Image and >offering much better documentation of results. > >Object-Image has a very nice extension to NIH-Image for computer-assisted >outlining of density-sliced images: points are collected by (option) "sparking" >to nearest density-sliced edge. >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia > >. > Steven D. Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ stevem@cipe.com http://www.cipe.com (800) 322-9884 ext. 125 From nih-image-request@io.ece.drexel.edu Thu Oct 1 09:44 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA28877; Thu, 1 Oct 1998 09:44:42 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 09:44:42 -0400 (EDT) From: Stephen Keenan Sender: k9425608@qub.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? In-Reply-To: Message-ID: Date: Thu, 1 Oct 1998 14:26:19 -0400 (EDT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"JtBTH1.0.RS6.XCu4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/426 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 459 Status: RO Wayne, I obtained Scion Image Beta 3b. The Watershed command does seem to work for me. The results I obtained aren't very good but I suspect this may be something to do with the images I am using. Thanks for your help. On Wed, 30 Sep 1998 12:39:27 -0400 Wayne Rasband wrote: > The Watershed command is in Scion Image for Windows beta 3, but it doesn't > appear to work. > > -wayne > > ---------------------- Stephen Keenan From nih-image-request@io.ece.drexel.edu Thu Oct 1 09:45 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA28927; Thu, 1 Oct 1998 09:44:54 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 09:44:54 -0400 (EDT) Posted-Date: Thu, 01 Oct 1998 15:30:09 +0000 Sender: marmotta@hmg.inpg.fr Message-Id: <3613A001.3C21@hmg.inpg.fr> Date: Thu, 01 Oct 1998 15:30:09 +0000 From: MARMOTTANT Philippe Organization: LEGI X-Mailer: Mozilla 3.01 (X11; I; HP-UX A.09.05 9000/715) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Seed Fill plug-in ? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"UWiTH.0.JX6.MEu4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/427 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 617 Status: O Hello subcribers, To eliminate discontinous edges, resulting from image anaysis of water drops, I'd like to have a macro that seed fills images, as the paint bucket does. A Pascal procedure was proposed in the archives , but I only have a Think C 5.0 language, so I thought about a including a Photoshop compatible Plug-in. Does anyone know about a C code that performs this operation as a Photoshop plug-in ? ******************* Philippe Marmottant Laboratoire des Ecoulements Geophysiques et Industriels BP 53 X, 38041 Grenoble Cedex FRANCE Home : 15 bd Marechal Leclerc, 38000 Grenoble tel : 04 76 00 01 66 From nih-image-request@io.ece.drexel.edu Thu Oct 1 09:46 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA29173; Thu, 1 Oct 1998 09:46:38 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 09:46:38 -0400 (EDT) From: David M Roof Message-Id: <199810011333.JAA14879@mail.med.upenn.edu> Subject: serial connections:Meridian InSIGHT and MAC To: nih-image@io.ece.drexel.edu Date: Thu, 1 Oct 1998 09:33:13 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"75zj11.0.we6.XIu4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/428 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 850 Status: O Re: serial connections In addition to checking out the features of Object Image, you can learn all about interfacing Mac serial ports to lab equipment at: http://www.mindspring.com/~jc1/serial/main.html -David > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be >used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but >the pin out seems to be different and it is not sending the data (using >the openserial( ) command), to change the filters etc. Apple said that I >have to become a developer to get this info., and cannot help. It seems >simple, has anyone used a "regular" (DB25 pinout) modem on an apple? >Thanks. > >Todd Kirk >Indiana University Medical Center From nih-image-request@io.ece.drexel.edu Thu Oct 1 10:13 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02444; Thu, 1 Oct 1998 10:13:11 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 10:13:11 -0400 (EDT) Message-Id: <199810011359.AA10691@na3.dow.com> From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Watersheds for Scion PC Image? Date: Thu, 1 Oct 1998 09:53:08 -0400 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"vH6Yu1.0.sA.Phu4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/429 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 383 Status: O Folks: I brought this up with Scion a little while ago and their response was that this feature is there, but has not been fully debugged, so you should double-check your results against your original. I found that it sometimes appeared to work, other times it crashed the program. I have not yet verified the Euclidean Distance Map result. Bill Heeschen Dow Chemical Midland, MI From nih-image-request@io.ece.drexel.edu Thu Oct 1 10:14 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02622; Thu, 1 Oct 1998 10:14:22 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 10:14:22 -0400 (EDT) Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FD5@cheetah.uits.iupui.edu> From: "Kirk, Todd Jason" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: serial connections:Meridian InSIGHT and MAC Date: Thu, 1 Oct 1998 09:00:39 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"mDC0H1.0.1D.Diu4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/430 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 683 Status: O Hey, Thanks to everyone that replied, listserves are the BEST! What Apple could not provide me with USRobotics could. I found a pin out on their site and it works perfectly with the Scion version of NIH Image. Thanks again! Todd > -----Original Message----- > From: David M Roof [SMTP:roof@mail.med.upenn.edu] > Sent: Thursday, October 01, 1998 8:33 AM > To: nih-image@io.ece.drexel.edu > Subject: serial connections:Meridian InSIGHT and MAC > > Re: serial connections > > In addition to checking out the features of Object Image, you can learn > all about interfacing Mac serial ports to lab equipment at: > http://www.mindspring.com/~jc1/serial/main.html > > -David > From nih-image-request@io.ece.drexel.edu Thu Oct 1 13:52 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA23692; Thu, 1 Oct 1998 13:52:06 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 13:52:06 -0400 (EDT) Date: Thu, 01 Oct 1998 13:30:40 -0400 From: Bill Christens-Barry Subject: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices? To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"tx42z1.0.KD5.smx4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/431 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 809 I'm looking for a method of calculating (preferably within the macro language) a best-fitting 3D ellipsoid from contours of an object spanning a series of slices. I have saved the contour coordinates as a series of XYcoordinate text files with known slice spacing and scale etc. By 'best-fitting', I mean the ellipsoid that minimizes the sum of square deviations of points on the contours from the ellipsoid surface. Thus, the contour coordinates constitute a subset of a complete object surface description. Can anyone suggest a method that can be implemented in the macro language? Standard unix library or source code? Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- From nih-image-d-request@io.ece.drexel.edu Thu Oct 1 16:21 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA06720; Thu, 1 Oct 1998 16:21:18 -0400 (EDT) Date: Thu, 1 Oct 1998 16:21:18 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810012021.QAA06720@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #75 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/75 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10324 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 75 Today's Topics: [1]RE>Re: wound area measurements [ Steven Moore ] Re: Watersheds for Scion PC Image? [ Stephen Keenan ] Seed Fill plug-in ? [ MARMOTTANT Philippe To: "nih-image" Subject: [1]RE>Re: wound area measurements Message-ID: <1304931229-2795399@mailhost.cipe.com> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-Ascii" Thanks for the message! Please note that I'm out of the office for two weeks. I will return on October 15. If you need immediate attention, call (800) 322-9884. Press 0 (zero). Thanks. Steven Moore, CIPE On 10/1/98, nih-image wrote: >>From: johannes.barsig@pharma.Novartis.com >>To: nih-image@io.ece.drexel.edu >>Date: Tue, 29 Sep 1998 16:08:05 +0100 >>Subject: wound area measurements >> >>We are tracing wound areas of mice on glass slides. The circles we get >>should be digitalized using a graphics tablet. Image should detect, when >>the circle is closed an measure the area of the circle. Then, the next >>circle could be drawn. In results, the measurements should be listed. The >>areas are about two square cm. First question, which graphics tablet would >>be best for this task together with NIH Image. Second question, is there a >>macro around that could control the sequential measuring process described. >>I appreciate every hint. >>Johannes Barsig, Ph.D. >>Novartis Research Institute >>Vienna, Austria >> >I would have thought that you would find that an inexpensive video or digital >camera attached to a dissecting microscope would be a much more flexible and >efficient approach with potential for (semi)automated analysis by NIH-Image and >offering much better documentation of results. > >Object-Image has a very nice extension to NIH-Image for computer-assisted >outlining of density-sliced images: points are collected by (option) "sparking" >to nearest density-sliced edge. >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia > >. > Steven D. Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ stevem@cipe.com http://www.cipe.com (800) 322-9884 ext. 125 ------------------------------ Date: Thu, 1 Oct 1998 14:26:19 -0400 (EDT) From: Stephen Keenan To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Watersheds for Scion PC Image? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Wayne, I obtained Scion Image Beta 3b. The Watershed command does seem to work for me. The results I obtained aren't very good but I suspect this may be something to do with the images I am using. Thanks for your help. On Wed, 30 Sep 1998 12:39:27 -0400 Wayne Rasband wrote: > The Watershed command is in Scion Image for Windows beta 3, but it doesn't > appear to work. > > -wayne > > ---------------------- Stephen Keenan ------------------------------ Date: Thu, 01 Oct 1998 15:30:09 +0000 From: MARMOTTANT Philippe To: nih-image@io.ece.drexel.edu Subject: Seed Fill plug-in ? Message-Id: <3613A001.3C21@hmg.inpg.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello subcribers, To eliminate discontinous edges, resulting from image anaysis of water drops, I'd like to have a macro that seed fills images, as the paint bucket does. A Pascal procedure was proposed in the archives , but I only have a Think C 5.0 language, so I thought about a including a Photoshop compatible Plug-in. Does anyone know about a C code that performs this operation as a Photoshop plug-in ? ******************* Philippe Marmottant Laboratoire des Ecoulements Geophysiques et Industriels BP 53 X, 38041 Grenoble Cedex FRANCE Home : 15 bd Marechal Leclerc, 38000 Grenoble tel : 04 76 00 01 66 ------------------------------ Date: Thu, 1 Oct 1998 09:33:13 -0400 (EDT) From: David M Roof To: nih-image@io.ece.drexel.edu Subject: serial connections:Meridian InSIGHT and MAC Message-Id: <199810011333.JAA14879@mail.med.upenn.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Re: serial connections In addition to checking out the features of Object Image, you can learn all about interfacing Mac serial ports to lab equipment at: http://www.mindspring.com/~jc1/serial/main.html -David > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be >used, I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but >the pin out seems to be different and it is not sending the data (using >the openserial( ) command), to change the filters etc. Apple said that I >have to become a developer to get this info., and cannot help. It seems >simple, has anyone used a "regular" (DB25 pinout) modem on an apple? >Thanks. > >Todd Kirk >Indiana University Medical Center ------------------------------ Date: Thu, 1 Oct 1998 09:53:08 -0400 From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Watersheds for Scion PC Image? Message-Id: <199810011359.AA10691@na3.dow.com> Content-Type: text/plain Folks: I brought this up with Scion a little while ago and their response was that this feature is there, but has not been fully debugged, so you should double-check your results against your original. I found that it sometimes appeared to work, other times it crashed the program. I have not yet verified the Euclidean Distance Map result. Bill Heeschen Dow Chemical Midland, MI ------------------------------ Date: Thu, 1 Oct 1998 09:00:39 -0500 From: "Kirk, Todd Jason" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: serial connections:Meridian InSIGHT and MAC Message-ID: <9D916278299FD111A7E100805FA7C2BA4B9FD5@cheetah.uits.iupui.edu> Content-Type: text/plain Hey, Thanks to everyone that replied, listserves are the BEST! What Apple could not provide me with USRobotics could. I found a pin out on their site and it works perfectly with the Scion version of NIH Image. Thanks again! Todd > -----Original Message----- > From: David M Roof [SMTP:roof@mail.med.upenn.edu] > Sent: Thursday, October 01, 1998 8:33 AM > To: nih-image@io.ece.drexel.edu > Subject: serial connections:Meridian InSIGHT and MAC > > Re: serial connections > > In addition to checking out the features of Object Image, you can learn > all about interfacing Mac serial ports to lab equipment at: > http://www.mindspring.com/~jc1/serial/main.html > > -David > ------------------------------ Date: Thu, 01 Oct 1998 13:30:40 -0400 From: Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices? Message-id: Content-type: text/plain; charset="us-ascii" I'm looking for a method of calculating (preferably within the macro language) a best-fitting 3D ellipsoid from contours of an object spanning a series of slices. I have saved the contour coordinates as a series of XYcoordinate text files with known slice spacing and scale etc. By 'best-fitting', I mean the ellipsoid that minimizes the sum of square deviations of points on the contours from the ellipsoid surface. Thus, the contour coordinates constitute a subset of a complete object surface description. Can anyone suggest a method that can be implemented in the macro language? Standard unix library or source code? Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- ------------------------------ Date: Thu, 1 Oct 1998 15:48:57 -0400 (EDT) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Thu, 1 Oct 1998, Bill Christens-Barry wrote: > I'm looking for a method of calculating (preferably within the macro > language) a best-fitting 3D ellipsoid from contours of an object spanning a > series of slices. I have saved the contour coordinates as a series of > XYcoordinate text files with known slice spacing and scale etc. By > 'best-fitting', I mean the ellipsoid that minimizes the sum of square > deviations of points on the contours from the ellipsoid surface. Thus, the > contour coordinates constitute a subset of a complete object surface > description. > > Can anyone suggest a method that can be implemented in the macro language? > Standard unix library or source code? > > Thanks. > > Bill Christens-Barry > ------------------------- > Bill Christens-Barry, PhD > Johns Hopkins University Applied Physics Laboratory > wacb@aplcomm.jhuapl.edu > ------------------------- > > -------------------------------- End of nih-image-d Digest V98 Issue #75 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 1 16:24 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA06976; Thu, 1 Oct 1998 16:24:01 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 16:24:01 -0400 (EDT) Date: Thu, 1 Oct 1998 15:48:57 -0400 (EDT) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: Q: calculating best-fitting ellipsoid of a 3D object spanning multiple slices? In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"XbkS32.0.sv.noz4s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/432 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1179 -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Thu, 1 Oct 1998, Bill Christens-Barry wrote: > I'm looking for a method of calculating (preferably within the macro > language) a best-fitting 3D ellipsoid from contours of an object spanning a > series of slices. I have saved the contour coordinates as a series of > XYcoordinate text files with known slice spacing and scale etc. By > 'best-fitting', I mean the ellipsoid that minimizes the sum of square > deviations of points on the contours from the ellipsoid surface. Thus, the > contour coordinates constitute a subset of a complete object surface > description. > > Can anyone suggest a method that can be implemented in the macro language? > Standard unix library or source code? > > Thanks. > > Bill Christens-Barry > ------------------------- > Bill Christens-Barry, PhD > Johns Hopkins University Applied Physics Laboratory > wacb@aplcomm.jhuapl.edu > ------------------------- > > From nih-image-request@io.ece.drexel.edu Thu Oct 1 20:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA26474; Thu, 1 Oct 1998 20:16:43 -0400 (EDT) Resent-Date: Thu, 1 Oct 1998 20:16:43 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu Date: Fri, 2 Oct 1998 9:50:37 GMT+1000 Subject: Re: Seed Fill plug-in ? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"WLyrm1.0.km5.FJ15s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/433 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1518 >Date: Thu, 01 Oct 1998 15:30:09 +0000 >From: MARMOTTANT Philippe >... > To eliminate discontinous edges, resulting from image anaysis of water >drops, I'd like to have a macro that seed fills images, as the paint >bucket does. A Pascal procedure was proposed in the archives , but I >only have a Think C 5.0 language, so I thought about a including a >Photoshop compatible Plug-in. > >Does anyone know about a C code that performs this operation as a >Photoshop plug-in ? > >******************* >Philippe Marmottant >Laboratoire des Ecoulements Geophysiques et Industriels >BP 53 X, 38041 Grenoble Cedex FRANCE >Home : >15 bd Marechal Leclerc, 38000 Grenoble >tel : 04 76 00 01 66 Object-Image is an extended version of W. Rasband's image processing program 'NIH-Image'. by Norbert Vischer (vischer@bio.uva.nl) it is available at: http://simon.bio.uva.nl/Object-Image.html it has SeedFill(x, y) Same as clicking with the paint bucket on (x, y) along with many other extremely useful extentions. I am curious as to how you would use a seedFill "To eliminate discontinous edges, resulting from image anaysis of water drops, as the paint bucket does". It seems to me that you would need to segment the drop as a Roi/selection before you use seedFill. How does it help with segmentation? Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Fri Oct 2 08:20 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA11850; Fri, 2 Oct 1998 08:20:38 -0400 (EDT) Resent-Date: Fri, 2 Oct 1998 08:20:38 -0400 (EDT) Posted-Date: Fri, 02 Oct 1998 14:09:15 +0000 Sender: marmotta@hmg.inpg.fr Message-Id: <3614DE8B.1C2F@hmg.inpg.fr> Date: Fri, 02 Oct 1998 14:09:15 +0000 From: MARMOTTANT Philippe Organization: LEGI X-Mailer: Mozilla 3.01 (X11; I; HP-UX A.09.05 9000/715) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Seed Fill plug-in ? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"Iek0w2.0.eW2.P8C5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/434 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2068 GJOSS@rna.bio.mq.edu.au wrote: > Object-Image is an extended version of W. Rasband's > image processing program 'NIH-Image'. > by Norbert Vischer (vischer@bio.uva.nl) > it is available at: > http://simon.bio.uva.nl/Object-Image.html > > it has SeedFill(x, y) > Same as clicking with the paint bucket on (x, y) > along with many other extremely useful extentions. > > I am curious as to how you would use a seedFill "To eliminate discontinous > edges, resulting from image anaysis of water drops, as the paint bucket does". > It seems to me that you would need to segment the drop as a Roi/selection > before you use seedFill. > > How does it help with segmentation? > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia Here are some explanations on my image analysis of non spherical water drops produced by atomisation experiments: I first perform a FindEdges-like operation, that I programmed as a C Photoshop compatible plug-in, by plotting the normalized rms of the 8 neighbouring pixels of each pixel (a filter called Sigma). A threshold on this result allows to eliminate out-focus drop edges, because the rms on these edges is lower than with sharp edges. Out-focus are eliminated because of being outside calibration. After a squelettonize I then obtain closed and unclosed loops. Unclosed loops are due to the superposition of an out focus drop with an in-focus drop. I don't want this edge with an unknown part. Here is where I perform the SeedFill in black, same color as the edges, that fills the unclosed loops, and make them disappear. I can thus have size measurements on single in-focus drops, represented by closed loops, with the Analyze particle NIH function. Hoping I help you see clearer on my segmentation process, -- ******************* Philippe Marmottant Laboratoire des Ecoulements Geophysiques et Industriels Universite Joseph Fourier, BP 53 X, 38041 Grenoble Cedex France From nih-image-request@io.ece.drexel.edu Fri Oct 2 11:50 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02458; Fri, 2 Oct 1998 11:50:16 -0400 (EDT) Resent-Date: Fri, 2 Oct 1998 11:50:16 -0400 (EDT) From: beverly@umich.edu Date: Fri, 2 Oct 1998 11:33:34 -0400 (EDT) X-Sender: beverly@qbert.rs.itd.umich.edu To: nih-image@io.ece.drexel.edu Subject: Help with Frame Grabber Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Yjo0l2.0.j9.J9F5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/435 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1115 To whom it may concern: We are interested in using the NIH Image program to help us count crystals through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light microscope. We have an old Mac IIcx that we would like to use as computer to control the program. However, I can't seem to find a Frame Grabber Card that I can use on an older mac. If memory serves correctly, it is only equipped with NuBus slots. According to the NIH Image manual, the VG-5 is a NuBus Card (Appendix B of the manual) however according to the tech support specs at the SCION website, this card is PCI only. Where can I find a NuBus card that we can use in this Mac? Would this mac have sufficient computing power to run the program affectively. We don't need to capture live video just still images. Thanks for any support you can provide. I have copied this message to both Sales and Tech Support because I'm not sure who would be the best group to talk to about this. Thanks again Beverly C. Langevin R.Ph., M.S. University of Michigan College of Pharmacy, Room 3018 beverly@umich.edu Office: (734) 647-2219 From nih-image-d-request@io.ece.drexel.edu Fri Oct 2 11:50 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA02529; Fri, 2 Oct 1998 11:50:37 -0400 (EDT) Date: Fri, 2 Oct 1998 11:50:37 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810021550.LAA02529@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #76 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/76 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5976 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 76 Today's Topics: Re: Seed Fill plug-in ? [ GJOSS@rna.bio.mq.edu.au ] Re: Seed Fill plug-in ? [ MARMOTTANT Philippe >Date: Thu, 01 Oct 1998 15:30:09 +0000 >From: MARMOTTANT Philippe >... > To eliminate discontinous edges, resulting from image anaysis of water >drops, I'd like to have a macro that seed fills images, as the paint >bucket does. A Pascal procedure was proposed in the archives , but I >only have a Think C 5.0 language, so I thought about a including a >Photoshop compatible Plug-in. > >Does anyone know about a C code that performs this operation as a >Photoshop plug-in ? > >******************* >Philippe Marmottant >Laboratoire des Ecoulements Geophysiques et Industriels >BP 53 X, 38041 Grenoble Cedex FRANCE >Home : >15 bd Marechal Leclerc, 38000 Grenoble >tel : 04 76 00 01 66 Object-Image is an extended version of W. Rasband's image processing program 'NIH-Image'. by Norbert Vischer (vischer@bio.uva.nl) it is available at: http://simon.bio.uva.nl/Object-Image.html it has SeedFill(x, y) Same as clicking with the paint bucket on (x, y) along with many other extremely useful extentions. I am curious as to how you would use a seedFill "To eliminate discontinous edges, resulting from image anaysis of water drops, as the paint bucket does". It seems to me that you would need to segment the drop as a Roi/selection before you use seedFill. How does it help with segmentation? Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 02 Oct 1998 14:09:15 +0000 From: MARMOTTANT Philippe To: nih-image@io.ece.drexel.edu Subject: Re: Seed Fill plug-in ? Message-Id: <3614DE8B.1C2F@hmg.inpg.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit GJOSS@rna.bio.mq.edu.au wrote: > Object-Image is an extended version of W. Rasband's > image processing program 'NIH-Image'. > by Norbert Vischer (vischer@bio.uva.nl) > it is available at: > http://simon.bio.uva.nl/Object-Image.html > > it has SeedFill(x, y) > Same as clicking with the paint bucket on (x, y) > along with many other extremely useful extentions. > > I am curious as to how you would use a seedFill "To eliminate discontinous > edges, resulting from image anaysis of water drops, as the paint bucket does". > It seems to me that you would need to segment the drop as a Roi/selection > before you use seedFill. > > How does it help with segmentation? > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia Here are some explanations on my image analysis of non spherical water drops produced by atomisation experiments: I first perform a FindEdges-like operation, that I programmed as a C Photoshop compatible plug-in, by plotting the normalized rms of the 8 neighbouring pixels of each pixel (a filter called Sigma). A threshold on this result allows to eliminate out-focus drop edges, because the rms on these edges is lower than with sharp edges. Out-focus are eliminated because of being outside calibration. After a squelettonize I then obtain closed and unclosed loops. Unclosed loops are due to the superposition of an out focus drop with an in-focus drop. I don't want this edge with an unknown part. Here is where I perform the SeedFill in black, same color as the edges, that fills the unclosed loops, and make them disappear. I can thus have size measurements on single in-focus drops, represented by closed loops, with the Analyze particle NIH function. Hoping I help you see clearer on my segmentation process, -- ******************* Philippe Marmottant Laboratoire des Ecoulements Geophysiques et Industriels Universite Joseph Fourier, BP 53 X, 38041 Grenoble Cedex France ------------------------------ Date: Fri, 2 Oct 1998 11:33:34 -0400 (EDT) From: beverly@umich.edu To: nih-image@io.ece.drexel.edu Subject: Help with Frame Grabber Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII To whom it may concern: We are interested in using the NIH Image program to help us count crystals through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light microscope. We have an old Mac IIcx that we would like to use as computer to control the program. However, I can't seem to find a Frame Grabber Card that I can use on an older mac. If memory serves correctly, it is only equipped with NuBus slots. According to the NIH Image manual, the VG-5 is a NuBus Card (Appendix B of the manual) however according to the tech support specs at the SCION website, this card is PCI only. Where can I find a NuBus card that we can use in this Mac? Would this mac have sufficient computing power to run the program affectively. We don't need to capture live video just still images. Thanks for any support you can provide. I have copied this message to both Sales and Tech Support because I'm not sure who would be the best group to talk to about this. Thanks again Beverly C. Langevin R.Ph., M.S. University of Michigan College of Pharmacy, Room 3018 beverly@umich.edu Office: (734) 647-2219 -------------------------------- End of nih-image-d Digest V98 Issue #76 *************************************** From nih-image-request@io.ece.drexel.edu Fri Oct 2 12:56 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08290; Fri, 2 Oct 1998 12:56:25 -0400 (EDT) Resent-Date: Fri, 2 Oct 1998 12:56:25 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Fri, 2 Oct 1998 12:41:13 +0100 To: nih-image@io.ece.drexel.edu From: Julian Smith III Subject: Re: Help with Frame Grabber Resent-Message-ID: <"bGJHe1.0.Tj1.F7G5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/436 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1599 Beverly: I've used a MacIIcx and a Scion LG-3 frame grabber for monochrome video capture for several years now. It works fine. You are correct that the computer has only NuBus slots. You may have a little trouble finding a Nubus Scion card, though. Scion may have discontinued them, since all of the new macs have PCI. I would give them a call and see. HTH Julian >We are interested in using the NIH Image program to help us count crystals >through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light >microscope. We have an old Mac IIcx that we would like to use as computer >to control the program. However, I can't seem to find a Frame Grabber >Card that I can use on an older mac. If memory serves correctly, it is >only equipped with NuBus slots. According to the NIH Image manual, the >VG-5 is a NuBus Card (Appendix B of the manual) however according to the >tech support specs at the SCION website, this card is PCI only. > >Where can I find a NuBus card that we can use in this Mac? Would this mac >have sufficient computing power to run the program affectively. We don't >need to capture live video just still images. > >Thanks for any support you can provide. I have copied this message to both >Sales and Tech Support because I'm not sure who would be the best group to >talk to about this. > >Thanks again > >Beverly C. Langevin R.Ph., M.S. > >University of Michigan >College of Pharmacy, Room 3018 >beverly@umich.edu >Office: (734) 647-2219 Julian P.S. Smith III Biology Winthrop University Rock Hill, SC 29733 803-323-2111 x6427 (vox) 803-323-2246 (fax) From nih-image-d-request@io.ece.drexel.edu Sat Oct 3 06:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA00956; Sat, 3 Oct 1998 06:10:41 -0400 (EDT) Date: Sat, 3 Oct 1998 06:10:41 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810031010.GAA00956@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #77 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/77 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2192 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 77 Today's Topics: Re: Help with Frame Grabber [ Julian Smith III To: nih-image@io.ece.drexel.edu Subject: Re: Help with Frame Grabber Message-Id: Content-Type: text/plain; charset="us-ascii" Beverly: I've used a MacIIcx and a Scion LG-3 frame grabber for monochrome video capture for several years now. It works fine. You are correct that the computer has only NuBus slots. You may have a little trouble finding a Nubus Scion card, though. Scion may have discontinued them, since all of the new macs have PCI. I would give them a call and see. HTH Julian >We are interested in using the NIH Image program to help us count crystals >through a CCD camera (Panasonic CCD WV-CL300) attached to an optical light >microscope. We have an old Mac IIcx that we would like to use as computer >to control the program. However, I can't seem to find a Frame Grabber >Card that I can use on an older mac. If memory serves correctly, it is >only equipped with NuBus slots. According to the NIH Image manual, the >VG-5 is a NuBus Card (Appendix B of the manual) however according to the >tech support specs at the SCION website, this card is PCI only. > >Where can I find a NuBus card that we can use in this Mac? Would this mac >have sufficient computing power to run the program affectively. We don't >need to capture live video just still images. > >Thanks for any support you can provide. I have copied this message to both >Sales and Tech Support because I'm not sure who would be the best group to >talk to about this. > >Thanks again > >Beverly C. Langevin R.Ph., M.S. > >University of Michigan >College of Pharmacy, Room 3018 >beverly@umich.edu >Office: (734) 647-2219 Julian P.S. Smith III Biology Winthrop University Rock Hill, SC 29733 803-323-2111 x6427 (vox) 803-323-2246 (fax) -------------------------------- End of nih-image-d Digest V98 Issue #77 *************************************** From nih-image-request@io.ece.drexel.edu Sat Oct 3 12:04 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00142; Sat, 3 Oct 1998 12:04:30 -0400 (EDT) Resent-Date: Sat, 3 Oct 1998 12:04:30 -0400 (EDT) Message-Id: In-Reply-To: References: Mime-Version: 1.0 Date: Sat, 3 Oct 1998 11:54:04 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: NIH'er moving on Resent-Message-ID: <"LNqPv.0.y27.xWa5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/437 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1232 Dear fellow NIH Imagers, October 9, 1998 will be my last day at NIH. I have over the years enjoyed being very active on this listserv and in applying NIH Image to many campus research matters in my work at NIH. I am moving on to Miami, FL where my wife is doing her fellowship (neuro-ophthalmology) at the Bascom Palmer Eye Institute/University of Miami. Although I will be signing off from this account and will remove myself from the listserv under this NIH email account I have resubscribed under my new email, which is for now: mvivino@rocketmail.com As of this time I am looking for consulting, biomedical engineering, or development work. In these capacities I would be interested in doing some of the many things I did here at NIH. Among these are, applying NIH Image & doing modifications to the package, data acquisition, other imaging, LabView, various collaborative biomedical research & development projects, and certainly a variety of other things. I am willing to do these via remote and various on sites and perhaps full time in the Miami area. Should any of you be interested in contacting me please feel free to do so at my rocketmail account or my NIH account in the near future. Sincerely, Mark A. Vivino From nih-image-request@io.ece.drexel.edu Sat Oct 3 16:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19239; Sat, 3 Oct 1998 16:00:56 -0400 (EDT) Resent-Date: Sat, 3 Oct 1998 16:00:56 -0400 (EDT) X-Authentication-Warning: maryann.eng.umd.edu: cgw owned process doing -bs Date: Sat, 3 Oct 1998 15:49:18 -0400 (EDT) From: Corey Washington X-Sender: cgw@maryann.eng.umd.edu To: nih-image@io.ece.drexel.edu Subject: Re: NIH'er moving on In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"J828l1.0.rQ4.E_d5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/438 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 377 Could you please remove my name from the listserv. cgw _______________________________________________________________________ Corey Washington (301) 405-5710 my office Dept. of Philosophy (301) 405-5689 main office 1123 Skinner Bldg. University of Maryland College Park, MD 20742-7615 _______________________________________________________________________ From nih-image-request@io.ece.drexel.edu Sat Oct 3 16:27 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA21507; Sat, 3 Oct 1998 16:27:38 -0400 (EDT) Resent-Date: Sat, 3 Oct 1998 16:27:38 -0400 (EDT) Message-Id: In-Reply-To: References: Mime-Version: 1.0 Date: Sat, 3 Oct 1998 16:17:51 -0500 To: nih-image@io.ece.drexel.edu From: Mark A Vivino Subject: how to (un)subscribe & list info Resent-Message-ID: <"txEdp2.0.6_4.FOe5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/439 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2478 e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. 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As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* Mark From nih-image-request@io.ece.drexel.edu Sat Oct 3 18:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA00138; Sat, 3 Oct 1998 18:09:59 -0400 (EDT) Resent-Date: Sat, 3 Oct 1998 18:09:59 -0400 (EDT) Message-ID: <3616A03A.CA77596D@howard.edu> Date: Sat, 03 Oct 1998 15:07:55 -0700 From: Bill Eckberg X-Mailer: Mozilla 4.5b1 (Macintosh; I; PPC) X-Accept-Language: English [en] MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: frame grabber available References: <199810031009.GAA00837@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"bdMxs.0.s57.gwf5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/440 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 174 If anyone needs a NuBus frame grabber, I have Scion VG-5 available. I've gotten a new G3 and had to order a PCI board. Send responses to me, not to the list. Bill Eckberg From nih-image-d-request@io.ece.drexel.edu Sun Oct 4 06:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23258; Sun, 4 Oct 1998 06:12:41 -0400 (EDT) Date: Sun, 4 Oct 1998 06:12:41 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810041012.GAA23258@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #78 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/78 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6009 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 78 Today's Topics: NIH'er moving on [ Mark A Vivino ] how to (un)subscribe & list info [ Mark A Vivino ] ------------------------------ Date: Sat, 3 Oct 1998 11:54:04 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: NIH'er moving on Message-Id: Content-Type: text/plain; charset="us-ascii" Dear fellow NIH Imagers, October 9, 1998 will be my last day at NIH. I have over the years enjoyed being very active on this listserv and in applying NIH Image to many campus research matters in my work at NIH. I am moving on to Miami, FL where my wife is doing her fellowship (neuro-ophthalmology) at the Bascom Palmer Eye Institute/University of Miami. Although I will be signing off from this account and will remove myself from the listserv under this NIH email account I have resubscribed under my new email, which is for now: mvivino@rocketmail.com As of this time I am looking for consulting, biomedical engineering, or development work. In these capacities I would be interested in doing some of the many things I did here at NIH. Among these are, applying NIH Image & doing modifications to the package, data acquisition, other imaging, LabView, various collaborative biomedical research & development projects, and certainly a variety of other things. I am willing to do these via remote and various on sites and perhaps full time in the Miami area. Should any of you be interested in contacting me please feel free to do so at my rocketmail account or my NIH account in the near future. Sincerely, Mark A. Vivino ------------------------------ Date: Sat, 3 Oct 1998 15:49:18 -0400 (EDT) From: Corey Washington To: nih-image@io.ece.drexel.edu Subject: Re: NIH'er moving on Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Could you please remove my name from the listserv. cgw _______________________________________________________________________ Corey Washington (301) 405-5710 my office Dept. of Philosophy (301) 405-5689 main office 1123 Skinner Bldg. University of Maryland College Park, MD 20742-7615 _______________________________________________________________________ ------------------------------ Date: Sat, 3 Oct 1998 16:17:51 -0500 From: Mark A Vivino To: nih-image@io.ece.drexel.edu Subject: how to (un)subscribe & list info Message-Id: Content-Type: text/plain; charset="us-ascii" e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". 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As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* Mark ------------------------------ Date: Sat, 03 Oct 1998 15:07:55 -0700 From: Bill Eckberg To: nih-image@io.ece.drexel.edu Subject: frame grabber available Message-ID: <3616A03A.CA77596D@howard.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit If anyone needs a NuBus frame grabber, I have Scion VG-5 available. I've gotten a new G3 and had to order a PCI board. Send responses to me, not to the list. Bill Eckberg -------------------------------- End of nih-image-d Digest V98 Issue #78 *************************************** From nih-image-request@io.ece.drexel.edu Sun Oct 4 16:51 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10131; Sun, 4 Oct 1998 16:51:18 -0400 (EDT) Resent-Date: Sun, 4 Oct 1998 16:51:18 -0400 (EDT) From: cadence@imap3.asu.edu Date: Sun, 04 Oct 1998 13:32:46 -0700 (MST) Subject: Fixing colors X-Sender: cadence@general4.asu.edu To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"sTPV01.0.F62.hkz5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/441 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 597 Hi, I'm fairly new to NIH. I've been importing Leica confocal data into NIH Image. My problem is the brightest points if the stained cells (single fluorescent stain) I'm looking at appear black when I initially import the data. I can solve the problem using the command "Fix Colors", but I have to ddo that for each data slice and it gets a little time consuming to do that for 500 or so slices. Is there a way to automate the process using a macro or can I fix the problem by changing some value? Karen Fisher Arizona State University Department of Plant Biology cadence@imap3.asu.edu From nih-image-request@io.ece.drexel.edu Sun Oct 4 19:16 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA21785; Sun, 4 Oct 1998 19:15:35 -0400 (EDT) Resent-Date: Sun, 4 Oct 1998 19:15:35 -0400 (EDT) Message-Id: <3.0.5.32.19981004190558.007f8d10@codon.nih.gov> X-Sender: wayne@codon.nih.gov X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sun, 04 Oct 1998 19:05:58 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Fixing colors In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"I0gXA.0.Q_4.6w_5s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/442 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 717 At 01:32 PM 10/4/98 -0700, you wrote: > Hi, > I'm fairly new to NIH. I've been importing Leica confocal data into >NIH Image. My problem is the brightest points if the stained cells (single >fluorescent stain) I'm looking at appear black when I initially import the >data. I can solve the problem using the command "Fix Colors", but I have to >ddo that for each data slice and it gets a little time consuming to do that >for 500 or so slices. Is there a way to automate the process using a macro or >can I fix the problem by changing some value? This macro should be equivalent to the "Fix Colors" command: macro 'Fix Colors'; begin ChangeValues(0,0,1); ChangeValues(255,255,254); end; -wayne From nih-image-request@io.ece.drexel.edu Mon Oct 5 02:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA27663; Mon, 5 Oct 1998 02:22:14 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 02:22:14 -0400 (EDT) Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST) Message-Id: <199810050231.MAA06943@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: Macro output Resent-Message-ID: <"MUzie2.0.gQ6.l966s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/443 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 731 Hi imagers, forgive me for being thicker than the offspring of a village idiot but I am currently trying to use a macro which is supposed to return a message with calculations in it. Unfortunately it does not appear to be doing this and since I am fairly new to NIH I am not exactly sure where this message is supposed to be. Is it supposed to be in the info box? The message goes along the lines of: Write('The answer is',answer); I have tried replacing Write with Putmessage and Showmessage but still no message appears and I am positive that the program is otherwise working properly. Can anyone shed some light on this for me? Thanx in advance, Cormac McCann Final year mechanical eng. student, CQU, Aust. From nih-image-request@io.ece.drexel.edu Mon Oct 5 03:03 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA01467; Mon, 5 Oct 1998 03:03:21 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 03:03:21 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: <199810050231.MAA06943@topaz.cqu.edu.au> Mime-Version: 1.0 Date: Mon, 5 Oct 1998 08:51:38 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: Macro output Resent-Message-ID: <"iFIEr.0.b3.tn66s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/444 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 958 > >The message goes along the lines of: > >Write('The answer is',answer); > >I have tried replacing Write with Putmessage and Showmessage but still no >message appears and I am positive that the program is otherwise working >properly. >Can anyone shed some light on this for me? > Write(message); will print the message in an active text window PutMessage(message); will display a dialog box with the message ShowMessage(message); will show the message in the info-window +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Oct 5 03:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA03036; Mon, 5 Oct 1998 03:18:47 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 03:18:47 -0400 (EDT) X-Sender: zuppinge@baba.ethz.ch Message-Id: Mime-Version: 1.0 Date: Mon, 5 Oct 1998 09:05:17 +0200 To: nih-image@io.ece.drexel.edu From: Christian Zuppinger Subject: Re: Fixing colors for Leica Resent-Message-ID: <"sl5AO.0.sQ.P_66s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/445 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 562 Hi, Leica tif-stacks can be color-fixed within seconds with one of the functions in the macro 'stacks' that comes with NIH Image. This macro does the same operation as Wayne suggested just in a loop for an entire stack. C. Zuppinger Dipl Biol Christian Zuppinger ETH Hoenggerberg Institut fuer Zellbiologie, HPM F27 CH-8093 Zurich Switzerland Tel: + 441 1 633 33 54 Fax: + 441 1 633 10 69 Email: zuppinge@cell.biol.ethz.ch or czuppinger@access.ch WWW: Institute http://www.cell.biol.ethz.ch/ private http://www.access.ch/whoswho/showwho?czuppinger From nih-image-request@io.ece.drexel.edu Mon Oct 5 05:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA12595; Mon, 5 Oct 1998 05:08:06 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 05:08:06 -0400 (EDT) X-Sender: sdb@pop1.liv.ac.uk Message-Id: In-Reply-To: <199810021535.LAA00818@io.ece.drexel.edu> Mime-Version: 1.0 Date: Mon, 5 Oct 1998 09:56:52 +0100 To: nih-image@io.ece.drexel.edu From: Steve Barrett Subject: Re: Help with Frame Grabber Cc: beverly@umich.edu Resent-Message-ID: <"wgxsh.0.5l2.yb86s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/446 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 731 >Where can I find a NuBus card that we can use in... >an old Mac IIcx? In the past, we have used ScreenMachine framegrabbers in a Mac IIx and a Mac IIfx. They worked well for grabbing single images. The speed of the Macs was not a problem for us - we only needed one frame every few seconds. It was distributed by ProficomP GmbH, but I'm afraid I don't have a web or email address to hand. ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ From nih-image-request@io.ece.drexel.edu Mon Oct 5 06:40 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA21272; Mon, 5 Oct 1998 06:40:10 -0400 (EDT) <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> Resent-Date: Mon, 5 Oct 1998 06:40:10 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: <9D916278299FD111A7E100805FA7C2BA4B9FC7@cheetah.uits.iupui.edu> Mime-Version: 1.0 Date: Mon, 5 Oct 1998 12:27:44 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: Meridian InSIGHT and MAC Resent-Message-ID: <"EijMn3.0.io4.Ry96s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/447 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2047 > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be used, >I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin >out seems to be different and it is not sending the data (using the >openserial( ) command), to change the filters etc. Apple said that I have to >become a developer to get this info., and cannot help. It seems simple, has >anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. > >Todd Kirk >Indiana University Medical Center The Mac interfaces to most RS232 compatible devices without any problem. A standard modem cable (DIN 8 to DB 25) plus a standard DB25 to DB 8 adapter has always worked fine for me. Buy the modem cable in a Mac shop and the adapter in a PC shop. There might be some magic inside these adapters; I remember an instance where we were unable to wire DIN 8 to DB 8 directly, but it worked fine with the DIN 8 to DB 25 plus adapter. Your problems may be because you are using some unstandard cabling. The pin outs for the Mac modem port is documented in the Inside Mac: Devices document. You can download it as a PDF file from Apple. There was a useful document explaining how to properly wire RS232 to RS422 (Mac serial) posted to this list many years ago, I think I downloaded it from Zippy. I can have a look in my old file archives and post it to you if you can't find it. If not I have a print-out somewhere and can fax it to you. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Mon Oct 5 08:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00356; Mon, 5 Oct 1998 08:22:19 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 08:22:19 -0400 (EDT) Date: Mon, 5 Oct 1998 13:12:21 +0100 (BST) From: Stamatis Pagakis To: nih-image@io.ece.drexel.edu Subject: Re: Fixing colors In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"GM0P1.0.P17.sQB6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/448 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1436 On Sun, 4 Oct 1998 cadence@imap3.asu.edu wrote: > Hi, > I'm fairly new to NIH. I've been importing Leica confocal data into > NIH Image. My problem is the brightest points if the stained cells (single > fluorescent stain) I'm looking at appear black when I initially import the > data. I can solve the problem using the command "Fix Colors", but I have to > ddo that for each data slice and it gets a little time consuming to do that > for 500 or so slices. Is there a way to automate the process using a macro or > can I fix the problem by changing some value? > Hi If you want to avoid the problem altogether, do not use the "Glowover" LUT on the confocal. The black spots appear where the "Glowover" LUT puts blue color to indicate PMT saturation. Use the "Glow" LUT instead or (if you really like to see the blue) change the LUT to another one just before saving the image. Regards, *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Division of Membrane Biology Switchboard: 0181 9593666 x2621 < >National Institute for Medical Research Message: x2219, x2622 < >The Ridgeway, Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < > Mobile: 0370 654288 < From nih-image-d-request@io.ece.drexel.edu Mon Oct 5 08:27 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00930; Mon, 5 Oct 1998 08:27:16 -0400 (EDT) Date: Mon, 5 Oct 1998 08:27:16 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810051227.IAA00930@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #79 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/79 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10906 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 79 Today's Topics: Fixing colors [ cadence@imap3.asu.edu ] Re: Fixing colors [ Wayne Rasband ] Macro output [ Cormac ] Re: Macro output [ Stein Roervik Content-type: TEXT/PLAIN; charset=US-ASCII Hi, I'm fairly new to NIH. I've been importing Leica confocal data into NIH Image. My problem is the brightest points if the stained cells (single fluorescent stain) I'm looking at appear black when I initially import the data. I can solve the problem using the command "Fix Colors", but I have to ddo that for each data slice and it gets a little time consuming to do that for 500 or so slices. Is there a way to automate the process using a macro or can I fix the problem by changing some value? Karen Fisher Arizona State University Department of Plant Biology cadence@imap3.asu.edu ------------------------------ Date: Sun, 04 Oct 1998 19:05:58 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Fixing colors Message-Id: <3.0.5.32.19981004190558.007f8d10@codon.nih.gov> Content-Type: text/plain; charset="us-ascii" At 01:32 PM 10/4/98 -0700, you wrote: > Hi, > I'm fairly new to NIH. I've been importing Leica confocal data into >NIH Image. My problem is the brightest points if the stained cells (single >fluorescent stain) I'm looking at appear black when I initially import the >data. I can solve the problem using the command "Fix Colors", but I have to >ddo that for each data slice and it gets a little time consuming to do that >for 500 or so slices. Is there a way to automate the process using a macro or >can I fix the problem by changing some value? This macro should be equivalent to the "Fix Colors" command: macro 'Fix Colors'; begin ChangeValues(0,0,1); ChangeValues(255,255,254); end; -wayne ------------------------------ Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: Macro output Message-Id: <199810050231.MAA06943@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" Hi imagers, forgive me for being thicker than the offspring of a village idiot but I am currently trying to use a macro which is supposed to return a message with calculations in it. Unfortunately it does not appear to be doing this and since I am fairly new to NIH I am not exactly sure where this message is supposed to be. Is it supposed to be in the info box? The message goes along the lines of: Write('The answer is',answer); I have tried replacing Write with Putmessage and Showmessage but still no message appears and I am positive that the program is otherwise working properly. Can anyone shed some light on this for me? Thanx in advance, Cormac McCann Final year mechanical eng. student, CQU, Aust. ------------------------------ Date: Mon, 5 Oct 1998 08:51:38 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: Macro output Message-Id: Content-Type: text/plain; charset="us-ascii" > >The message goes along the lines of: > >Write('The answer is',answer); > >I have tried replacing Write with Putmessage and Showmessage but still no >message appears and I am positive that the program is otherwise working >properly. >Can anyone shed some light on this for me? > Write(message); will print the message in an active text window PutMessage(message); will display a dialog box with the message ShowMessage(message); will show the message in the info-window +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Mon, 5 Oct 1998 09:05:17 +0200 From: Christian Zuppinger To: nih-image@io.ece.drexel.edu Subject: Re: Fixing colors for Leica Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, Leica tif-stacks can be color-fixed within seconds with one of the functions in the macro 'stacks' that comes with NIH Image. This macro does the same operation as Wayne suggested just in a loop for an entire stack. C. Zuppinger Dipl Biol Christian Zuppinger ETH Hoenggerberg Institut fuer Zellbiologie, HPM F27 CH-8093 Zurich Switzerland Tel: + 441 1 633 33 54 Fax: + 441 1 633 10 69 Email: zuppinge@cell.biol.ethz.ch or czuppinger@access.ch WWW: Institute http://www.cell.biol.ethz.ch/ private http://www.access.ch/whoswho/showwho?czuppinger ------------------------------ Date: Mon, 5 Oct 1998 09:56:52 +0100 From: Steve Barrett To: nih-image@io.ece.drexel.edu Cc: beverly@umich.edu Subject: Re: Help with Frame Grabber Message-Id: Content-Type: text/plain; charset="us-ascii" >Where can I find a NuBus card that we can use in... >an old Mac IIcx? In the past, we have used ScreenMachine framegrabbers in a Mac IIx and a Mac IIfx. They worked well for grabbing single images. The speed of the Macs was not a problem for us - we only needed one frame every few seconds. It was distributed by ProficomP GmbH, but I'm afraid I don't have a web or email address to hand. ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ ------------------------------ Date: Mon, 5 Oct 1998 12:27:44 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: Meridian InSIGHT and MAC Message-Id: Content-Type: text/plain; charset="us-ascii" > Has anyone connected a Mac to a Merdian Insight plus? We had a PC >connected to it, now we have a Mac. We used the serial port on the PC to >change filters, open the shutter etc. Now that the Mac is going to be used, >I cannot get a cable (mini din 8 to a DB 9 RS232), I have one but the pin >out seems to be different and it is not sending the data (using the >openserial( ) command), to change the filters etc. Apple said that I have to >become a developer to get this info., and cannot help. It seems simple, has >anyone used a "regular" (DB25 pinout) modem on an apple? Thanks. > >Todd Kirk >Indiana University Medical Center The Mac interfaces to most RS232 compatible devices without any problem. A standard modem cable (DIN 8 to DB 25) plus a standard DB25 to DB 8 adapter has always worked fine for me. Buy the modem cable in a Mac shop and the adapter in a PC shop. There might be some magic inside these adapters; I remember an instance where we were unable to wire DIN 8 to DB 8 directly, but it worked fine with the DIN 8 to DB 25 plus adapter. Your problems may be because you are using some unstandard cabling. The pin outs for the Mac modem port is documented in the Inside Mac: Devices document. You can download it as a PDF file from Apple. There was a useful document explaining how to properly wire RS232 to RS422 (Mac serial) posted to this list many years ago, I think I downloaded it from Zippy. I can have a look in my old file archives and post it to you if you can't find it. If not I have a print-out somewhere and can fax it to you. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Mon, 5 Oct 1998 13:12:21 +0100 (BST) From: Stamatis Pagakis To: nih-image@io.ece.drexel.edu Subject: Re: Fixing colors Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 4 Oct 1998 cadence@imap3.asu.edu wrote: > Hi, > I'm fairly new to NIH. I've been importing Leica confocal data into > NIH Image. My problem is the brightest points if the stained cells (single > fluorescent stain) I'm looking at appear black when I initially import the > data. I can solve the problem using the command "Fix Colors", but I have to > ddo that for each data slice and it gets a little time consuming to do that > for 500 or so slices. Is there a way to automate the process using a macro or > can I fix the problem by changing some value? > Hi If you want to avoid the problem altogether, do not use the "Glowover" LUT on the confocal. The black spots appear where the "Glowover" LUT puts blue color to indicate PMT saturation. Use the "Glow" LUT instead or (if you really like to see the blue) change the LUT to another one just before saving the image. Regards, *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Division of Membrane Biology Switchboard: 0181 9593666 x2621 < >National Institute for Medical Research Message: x2219, x2622 < >The Ridgeway, Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < > Mobile: 0370 654288 < -------------------------------- End of nih-image-d Digest V98 Issue #79 *************************************** From nih-image-request@io.ece.drexel.edu Mon Oct 5 08:57 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA03901; Mon, 5 Oct 1998 08:57:02 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 08:57:02 -0400 (EDT) Message-ID: <3618C032.994F05B6@soton.ac.uk> Date: Mon, 05 Oct 1998 13:48:45 +0100 From: Ashley Pringle Organization: Clinical Neurological Sciences X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Help with Frame Grabber References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"w-baP.0.Ff.9-B6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/449 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 468 We have been quite happily using a MacIIsi for capturing single images with NIH Image for many years using the Data Translation Quickcapture frame grabber. This board is still available and all the detail can be found on this web page: http://www.datatranslation.com/products/imaging/qc/qc.html Dr Ashley Pringle Dept Clinical Neurological Sciences University of Southampton Southampton General Hospital Tremona Rd, Southampton SO16 6YD UK email: akp1@soton.ac.uk From nih-image-request@io.ece.drexel.edu Mon Oct 5 10:25 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA12307; Mon, 5 Oct 1998 10:25:43 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 10:25:43 -0400 (EDT) Date: Mon, 5 Oct 1998 15:08:02 +0100 (BST) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: cell clusters Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"tVnxL2.0.xe2.tBD6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/450 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 368 Hi imagers, I heard about a macro that analyses cells in cell clusters by Chris Coulon in a newsgroup but I couldn't find it (not knowing its name). Any pointers? Thanks, Jan. Jan Kreft Phone +44 (0)1222 874000 ext. 6036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK From nih-image-request@io.ece.drexel.edu Mon Oct 5 11:48 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA20811; Mon, 5 Oct 1998 11:47:59 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 11:47:59 -0400 (EDT) From: SCHRANK@TIGGER.STCLOUDSTATE.EDU Date: Mon, 05 Oct 1998 10:24:35 -0600 (CST) Subject: Re: nih-image-d Digest V98 #79 To: nih-image@io.ece.drexel.edu Message-id: <01J2LWOGNRGI005G4E@TIGGER.STCLOUDSTATE.EDU> X-VMS-To: IN%"nih-image@io.ece.drexel.edu" X-VMS-Cc: SCHRANK MIME-version: 1.0 Resent-Message-ID: <"9R-DL3.0.9R4.sHE6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/451 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 74 Good - will be interesting to see how the cuttings or whatever work out. From nih-image-request@io.ece.drexel.edu Mon Oct 5 15:43 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA21934; Mon, 5 Oct 1998 15:43:04 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 15:43:04 -0400 (EDT) Message-ID: From: "Harrison, Janine" To: "'Multiple recipients of list'" Subject: Calcium ratio imaging experiments Date: Mon, 5 Oct 1998 12:23:03 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"eeu_k2.0.uh3.9lH6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/452 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 924 Hello All- We have users in our facility who would like to undertake calcium ratio imaging experiments. Does anyone have specific recommendations for filter sets (i.e. from Chroma) for the fura-2/indo-1 class of compounds? Can NIH-Image be used fairly easily for quantitating ratiometric data? Or would a commercial analysis package (such as Metamoph, Axon Inst) be better suited for extensive experiments? Responses can be sent directly to me, or the group - - whichever is the most suitable. Thanks for any helpful information. Regards, Janine ********************************************************************** Janine Harrison Manager, Image Analysis Facility ICOS Corporation 22021 20th Avenue S.E. Bothell WA 98021 1-425-485-1900 ext 2318 1-425-485-1961 FAX jharrison@icos.com ********************************************************************** From nih-image-request@io.ece.drexel.edu Mon Oct 5 18:25 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03370; Mon, 5 Oct 1998 18:24:43 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 18:24:43 -0400 (EDT) Date: Mon, 5 Oct 1998 16:03:00 -0600 (MDT) From: christopher helt To: nih-image@io.ece.drexel.edu Subject: Error 2208 Where is the solution Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"UvRN42.0.-m6.a6K6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/453 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 455 I have just downloaded the power PC version of NIH Image and I seem to be having a problem with it. When I try click on "start capturing" I get error number 2208. I have tried to turn off virtual memory but the problem persists. Turning off the ATI video memory extension results in a message of "unable to load VDIG" in the info box. Where is the solution to this problem? My hardware consists of a power PC macintosh G3 Thanks, Chris Helt From nih-image-request@io.ece.drexel.edu Mon Oct 5 20:29 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA09548; Mon, 5 Oct 1998 20:29:07 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 20:29:07 -0400 (EDT) X-Sender: ad1054@unix.worldpath.net Message-Id: Mime-Version: 1.0 Date: Mon, 5 Oct 1998 20:04:05 -0500 To: nih-image@io.ece.drexel.edu From: ad1054@worldpath.net (Dr. Christopher Coulon) Subject: Re: cell clusters Resent-Message-ID: <"ELDNw1.0.mG.uvL6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/454 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1082 Hi Jan, What is it you need? I have been working on all sorts of problems utilizing NIH Image for automating image analysis, grain counting among them. I have discovered that every problem is different and requires at least a modification of an existing macro if not a totally new start. Please let me know if I can be of help. Please contact me off list at ad1054@worldpath.net. Chris >Hi imagers, > >I heard about a macro that analyses cells in cell clusters by Chris >Coulon in a newsgroup but I couldn't find it (not knowing its name). > >Any pointers? > >Thanks, > >Jan. > >Jan Kreft Phone +44 (0)1222 874000 ext. 6036 >Cardiff School of Biosciences Fax +44 (0)1222 874305 >Cardiff University E-mail Kreft@cardiff.ac.uk >PO Box 915, Cardiff CF1 3TL, UK * * * * * * * * * * * * * * * * * * * Dr. Christopher Hunt Coulon * * The GAIA Group * * 40 Chick Road * * Wolfeboro, New Hampshire 03894 * * 603 569-0028 * * * * * * * * * * * * * * * * * * * From nih-image-request@io.ece.drexel.edu Mon Oct 5 20:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA16749; Mon, 5 Oct 1998 20:53:40 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 20:53:40 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu Date: Tue, 6 Oct 1998 10:39:03 GMT+1000 Subject: Re: Seed Fill plug-in ? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"Svpbw3.0.yw2.IPM6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/455 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1309 >Date: Fri, 02 Oct 1998 14:09:15 +0000 >From: MARMOTTANT Philippe >To: nih-image@io.ece.drexel.edu >Subject: Re: Seed Fill plug-in ? Philippe, Thankyou for taking the trouble to further explain your technique. I had mistakenly read "To eliminate discontinous edges, resulting from image anaysis of water drops" as implying that you somehow used Seedfill to close (ie complete) the discontinous edges. I understand now that you use Seedfill to remove those distcontinuous structures from the analysis. The Seedfill macro available in Object-Image will indeed serve your purpose but, particularly as you have skeletonised, the ratio of perimeter to area (including enclosed hole) would allow you to disqualify open circles from your results table if you wanted to stay with the orginal NIH-Image. You might also be interested in another extended version of NIH-Image which has implemented a Hough transform which allows detection/measurement of circular objects with indistinct or incomplete boundaries. ie Image SXM bt Steve Barrett which should be available at http://reg.ssci.liv.ac.uk/ Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Mon Oct 5 21:37 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA28855; Mon, 5 Oct 1998 21:36:54 -0400 (EDT) Resent-Date: Mon, 5 Oct 1998 21:36:54 -0400 (EDT) From: SolamereTG@aol.com Message-ID: <95c6545.36196ea6@aol.com> Date: Mon, 5 Oct 1998 21:13:10 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Calcium ratio imaging experiments Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"s8_IB3.0.hX5.YyM6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/456 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2289 to Janine Harrison Manager, Image Analysis Facility ICOS Corporation 22021 20th Avenue S.E. Bothell WA 98021 1-425-485-1900 ext 2318 1-425-485-1961 FAX jharrison@icos.comt We have experience using NIH to measure calcium, Na+, and pH in Lymphocytes, cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My recommendation is to spend the money on the front end of the measuring system (Camera, PMT system, illumination control) and start with NIH Image. You can always spend more on commercial software if NIH (with the appropriate macros) can't do what you need. I would be happy to discuss with you your groups proposed work.However I will be out of my office beginning Wednesday 10/7/98 (morning) but back by next Monday. Please feel free to call tomorrow or after 10/11/98. sincerely yours, George A. Peeters M.D. Pres. Solamere Technology Group Salt Lake City, UT 84103 801 322-2645 In a message dated 98-10-05 15:31:55 EDT, you write: << Does anyone have specific recommendations for filter sets (i.e. from Chroma) for the fura-2/indo-1 class of compounds? >> This will depend on the experiment. For example, Fura-2 is the most often used probe for ratio Ca 2+ imaging. This probe will require illumination waveband switching for each ratio pair and if you wish to collect 15 ratio pairs per second you will need a progressive scan sensor (not an interlaced detector). Flo3, and Flo4 are easier to use but not ratioed. Indo-1 is faster, but would require splitting the detector or an emission wave band switcher. We have both imaging and photometric equipment used for Ca2+ measurement at both Genentech, Squibb, Soanes, as well as academic institutions world wide. << Can NIH-Image be used fairly easily for quantitating ratiometric data? Or would a commercial analysis package (such as Metamoph, Axon Inst) be better suited for extensive experiments?>> Yes, we have Macros to ratio of images acquired at video rates (30 fps). A suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as little as $2500. This system can control waveband switchers (ours or others), filter wheels, shutters, electro-physiology, etc. We also have the macros that control these devices. From nih-image-d-request@io.ece.drexel.edu Tue Oct 6 01:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA29740; Tue, 6 Oct 1998 01:17:52 -0400 (EDT) Date: Tue, 6 Oct 1998 01:17:52 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810060517.BAA29740@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #80 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/80 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 12152 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 80 Today's Topics: Re: Help with Frame Grabber [ Ashley Pringle ] cell clusters [ Jan Kreft ] Re: nih-image-d Digest V98 #79 [ SCHRANK@TIGGER.STCLOUDSTATE.EDU ] Calcium ratio imaging experiments [ "Harrison, Janine" To: nih-image@io.ece.drexel.edu Subject: Re: Help with Frame Grabber Message-ID: <3618C032.994F05B6@soton.ac.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit We have been quite happily using a MacIIsi for capturing single images with NIH Image for many years using the Data Translation Quickcapture frame grabber. This board is still available and all the detail can be found on this web page: http://www.datatranslation.com/products/imaging/qc/qc.html Dr Ashley Pringle Dept Clinical Neurological Sciences University of Southampton Southampton General Hospital Tremona Rd, Southampton SO16 6YD UK email: akp1@soton.ac.uk ------------------------------ Date: Mon, 5 Oct 1998 15:08:02 +0100 (BST) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: cell clusters Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi imagers, I heard about a macro that analyses cells in cell clusters by Chris Coulon in a newsgroup but I couldn't find it (not knowing its name). Any pointers? Thanks, Jan. Jan Kreft Phone +44 (0)1222 874000 ext. 6036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK ------------------------------ Date: Mon, 05 Oct 1998 10:24:35 -0600 (CST) From: SCHRANK@TIGGER.STCLOUDSTATE.EDU To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #79 Message-id: <01J2LWOGNRGI005G4E@TIGGER.STCLOUDSTATE.EDU> Content-type: TEXT/PLAIN; CHARSET=US-ASCII Good - will be interesting to see how the cuttings or whatever work out. ------------------------------ Date: Mon, 5 Oct 1998 12:23:03 -0700 From: "Harrison, Janine" To: "'Multiple recipients of list'" Subject: Calcium ratio imaging experiments Message-ID: Content-Type: text/plain Hello All- We have users in our facility who would like to undertake calcium ratio imaging experiments. Does anyone have specific recommendations for filter sets (i.e. from Chroma) for the fura-2/indo-1 class of compounds? Can NIH-Image be used fairly easily for quantitating ratiometric data? Or would a commercial analysis package (such as Metamoph, Axon Inst) be better suited for extensive experiments? Responses can be sent directly to me, or the group - - whichever is the most suitable. Thanks for any helpful information. Regards, Janine ********************************************************************** Janine Harrison Manager, Image Analysis Facility ICOS Corporation 22021 20th Avenue S.E. Bothell WA 98021 1-425-485-1900 ext 2318 1-425-485-1961 FAX jharrison@icos.com ********************************************************************** ------------------------------ Date: Mon, 5 Oct 1998 16:03:00 -0600 (MDT) From: christopher helt To: nih-image@io.ece.drexel.edu Subject: Error 2208 Where is the solution Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I have just downloaded the power PC version of NIH Image and I seem to be having a problem with it. When I try click on "start capturing" I get error number 2208. I have tried to turn off virtual memory but the problem persists. Turning off the ATI video memory extension results in a message of "unable to load VDIG" in the info box. Where is the solution to this problem? My hardware consists of a power PC macintosh G3 Thanks, Chris Helt ------------------------------ Date: Mon, 5 Oct 1998 20:04:05 -0500 From: ad1054@worldpath.net (Dr. Christopher Coulon) To: nih-image@io.ece.drexel.edu Subject: Re: cell clusters Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Jan, What is it you need? I have been working on all sorts of problems utilizing NIH Image for automating image analysis, grain counting among them. I have discovered that every problem is different and requires at least a modification of an existing macro if not a totally new start. Please let me know if I can be of help. Please contact me off list at ad1054@worldpath.net. Chris >Hi imagers, > >I heard about a macro that analyses cells in cell clusters by Chris >Coulon in a newsgroup but I couldn't find it (not knowing its name). > >Any pointers? > >Thanks, > >Jan. > >Jan Kreft Phone +44 (0)1222 874000 ext. 6036 >Cardiff School of Biosciences Fax +44 (0)1222 874305 >Cardiff University E-mail Kreft@cardiff.ac.uk >PO Box 915, Cardiff CF1 3TL, UK * * * * * * * * * * * * * * * * * * * Dr. Christopher Hunt Coulon * * The GAIA Group * * 40 Chick Road * * Wolfeboro, New Hampshire 03894 * * 603 569-0028 * * * * * * * * * * * * * * * * * * * ------------------------------ Date: Tue, 6 Oct 1998 10:39:03 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: marmotta@hmg.inpg.fr, nih-image@io.ece.drexel.edu Subject: Re: Seed Fill plug-in ? Message-ID: >Date: Fri, 02 Oct 1998 14:09:15 +0000 >From: MARMOTTANT Philippe >To: nih-image@io.ece.drexel.edu >Subject: Re: Seed Fill plug-in ? Philippe, Thankyou for taking the trouble to further explain your technique. I had mistakenly read "To eliminate discontinous edges, resulting from image anaysis of water drops" as implying that you somehow used Seedfill to close (ie complete) the discontinous edges. I understand now that you use Seedfill to remove those distcontinuous structures from the analysis. The Seedfill macro available in Object-Image will indeed serve your purpose but, particularly as you have skeletonised, the ratio of perimeter to area (including enclosed hole) would allow you to disqualify open circles from your results table if you wanted to stay with the orginal NIH-Image. You might also be interested in another extended version of NIH-Image which has implemented a Hough transform which allows detection/measurement of circular objects with indistinct or incomplete boundaries. ie Image SXM bt Steve Barrett which should be available at http://reg.ssci.liv.ac.uk/ Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Mon, 5 Oct 1998 21:13:10 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Calcium ratio imaging experiments Message-ID: <95c6545.36196ea6@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit to Janine Harrison Manager, Image Analysis Facility ICOS Corporation 22021 20th Avenue S.E. Bothell WA 98021 1-425-485-1900 ext 2318 1-425-485-1961 FAX jharrison@icos.comt We have experience using NIH to measure calcium, Na+, and pH in Lymphocytes, cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My recommendation is to spend the money on the front end of the measuring system (Camera, PMT system, illumination control) and start with NIH Image. You can always spend more on commercial software if NIH (with the appropriate macros) can't do what you need. I would be happy to discuss with you your groups proposed work.However I will be out of my office beginning Wednesday 10/7/98 (morning) but back by next Monday. Please feel free to call tomorrow or after 10/11/98. sincerely yours, George A. Peeters M.D. Pres. Solamere Technology Group Salt Lake City, UT 84103 801 322-2645 In a message dated 98-10-05 15:31:55 EDT, you write: << Does anyone have specific recommendations for filter sets (i.e. from Chroma) for the fura-2/indo-1 class of compounds? >> This will depend on the experiment. For example, Fura-2 is the most often used probe for ratio Ca 2+ imaging. This probe will require illumination waveband switching for each ratio pair and if you wish to collect 15 ratio pairs per second you will need a progressive scan sensor (not an interlaced detector). Flo3, and Flo4 are easier to use but not ratioed. Indo-1 is faster, but would require splitting the detector or an emission wave band switcher. We have both imaging and photometric equipment used for Ca2+ measurement at both Genentech, Squibb, Soanes, as well as academic institutions world wide. << Can NIH-Image be used fairly easily for quantitating ratiometric data? Or would a commercial analysis package (such as Metamoph, Axon Inst) be better suited for extensive experiments?>> Yes, we have Macros to ratio of images acquired at video rates (30 fps). A suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as little as $2500. This system can control waveband switchers (ours or others), filter wheels, shutters, electro-physiology, etc. We also have the macros that control these devices. ------------------------------ Date: Tue, 6 Oct 1998 14:53:18 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu Subject: Re: Macro output Message-ID: >Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST) >To: nih-image@io.ece.drexel.edu >From: Cormac >Subject: Macro output >Hi imagers, > forgive me for being thicker than the offspring of a village >idiot but I am currently trying to use a macro which is supposed to return a >message with calculations in it. Unfortunately it does not appear to be >doing this and since I am fairly new to NIH I am not exactly sure where this >message is supposed to be. Is it supposed to be in the info box? > >The message goes along the lines of: > >Write('The answer is',answer); > >I have tried replacing Write with Putmessage and Showmessage but still no >message appears and I am positive that the program is otherwise working >properly. >Can anyone shed some light on this for me? > >Thanx in advance, > >Cormac McCann >Final year mechanical eng. student, CQU, Aust. As one of the other villagers, I thought I should add to Steinr's response: If the current window is an image window, "write(message);" will output the message string at the "current" position which can be controlled by moveTo(x,y); { so top left of image would be (0,5) if font is size 9 with "align left"} note: setForeGround(0);{255} and SetText(string); {'With Background' etc} If current window is a text window, then cursor will be : 1. where the user last left it 2. at the begining if an existing or new text file is opened 3. at the end if you "selectAll;" with text file the current file. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #80 *************************************** From nih-image-request@io.ece.drexel.edu Tue Oct 6 01:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA00025; Tue, 6 Oct 1998 01:18:40 -0400 (EDT) Resent-Date: Tue, 6 Oct 1998 01:18:40 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu Date: Tue, 6 Oct 1998 14:53:18 GMT+1000 Subject: Re: Macro output Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"DmBVS3.0.2A6.oIQ6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/457 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1681 >Date: Mon, 5 Oct 1998 12:31:22 +1000 (EST) >To: nih-image@io.ece.drexel.edu >From: Cormac >Subject: Macro output >Hi imagers, > forgive me for being thicker than the offspring of a village >idiot but I am currently trying to use a macro which is supposed to return a >message with calculations in it. Unfortunately it does not appear to be >doing this and since I am fairly new to NIH I am not exactly sure where this >message is supposed to be. Is it supposed to be in the info box? > >The message goes along the lines of: > >Write('The answer is',answer); > >I have tried replacing Write with Putmessage and Showmessage but still no >message appears and I am positive that the program is otherwise working >properly. >Can anyone shed some light on this for me? > >Thanx in advance, > >Cormac McCann >Final year mechanical eng. student, CQU, Aust. As one of the other villagers, I thought I should add to Steinr's response: If the current window is an image window, "write(message);" will output the message string at the "current" position which can be controlled by moveTo(x,y); { so top left of image would be (0,5) if font is size 9 with "align left"} note: setForeGround(0);{255} and SetText(string); {'With Background' etc} If current window is a text window, then cursor will be : 1. where the user last left it 2. at the begining if an existing or new text file is opened 3. at the end if you "selectAll;" with text file the current file. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Oct 6 08:58 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27845; Tue, 6 Oct 1998 08:58:27 -0400 (EDT) Resent-Date: Tue, 6 Oct 1998 08:58:27 -0400 (EDT) Message-Id: <199810061235.OAA15085@pinus.slu.se> X-Sender: jorgenh@pinus.slu.se Mime-Version: 1.0 Date: Tue, 6 Oct 1998 14:42:32 +0100 To: nih-image@io.ece.drexel.edu From: Jorgen.Henriksson@farmtox.slu.se ( =?iso-8859-1?Q?J=F6rgen?= Henriksson) Subject: Scanner and "Save Blank Field" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id IAA25332 Resent-Message-ID: <"WTmVS2.0.yB6.jwW6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/458 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 422 Dear listmembers, I'm new to NIH-Image so I hope that You will forgive me for asking a question that may have been asked before. I will be using a scanner to capture my images, and my question is how to proceed if I would like to correct the images captured by the scanner in the same way as the function "Save Blank Field" corrects images captured with a camera. Thank You very much for Your help. Sincerely, Jrgen From nih-image-d-request@io.ece.drexel.edu Wed Oct 7 04:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA25130; Wed, 7 Oct 1998 04:53:12 -0400 (EDT) Date: Wed, 7 Oct 1998 04:53:12 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810070853.EAA25130@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #81 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/81 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2229 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 81 Today's Topics: Scanner and "Save Blank Field" [ Jorgen.Henriksson@farmtox.slu.se ( ] Unwanted Noise in Image [ Cormac ] ------------------------------ Date: Tue, 6 Oct 1998 14:42:32 +0100 From: Jorgen.Henriksson@farmtox.slu.se ( =?iso-8859-1?Q?J=F6rgen?= Henriksson) To: nih-image@io.ece.drexel.edu Subject: Scanner and "Save Blank Field" Message-Id: <199810061235.OAA15085@pinus.slu.se> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Dear listmembers, I'm new to NIH-Image so I hope that You will forgive me for asking a question that may have been asked before. I will be using a scanner to capture my images, and my question is how to proceed if I would like to correct the images captured by the scanner in the same way as the function "Save Blank Field" corrects images captured with a camera. Thank You very much for Your help. Sincerely, Jrgen ------------------------------ Date: Wed, 7 Oct 1998 18:36:00 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: Unwanted Noise in Image Message-Id: <199810070836.SAA23944@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" Greetings once again Imagers, At the moment I am capturing microscopic images on the 1.61/PPC version of NIH (I'm unsure as to the type of frame grabber card that's installed) and while that is working fine, I am getting some unwanted noise (distortion) down the left hand side of the image. The distortion is not there in the 'live' image, only in the captured (saved) images. I would like to know how to remove this noise as it is affecting my analysis. I am using density slicing and then particle analysis and this noise is being counted as one of the particles and throwing out my results. Is there any way of removing it from the image for good? Thanks again for any help you can give, Cormac McCann Final year mechanical eng. student, CQU, Aust. -------------------------------- End of nih-image-d Digest V98 Issue #81 *************************************** From nih-image-request@io.ece.drexel.edu Wed Oct 7 04:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA24997; Wed, 7 Oct 1998 04:53:05 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 04:53:05 -0400 (EDT) Date: Wed, 7 Oct 1998 18:36:00 +1000 (EST) Message-Id: <199810070836.SAA23944@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: Unwanted Noise in Image Resent-Message-ID: <"2LpRl2.0.PP2.yVo6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/459 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 790 Greetings once again Imagers, At the moment I am capturing microscopic images on the 1.61/PPC version of NIH (I'm unsure as to the type of frame grabber card that's installed) and while that is working fine, I am getting some unwanted noise (distortion) down the left hand side of the image. The distortion is not there in the 'live' image, only in the captured (saved) images. I would like to know how to remove this noise as it is affecting my analysis. I am using density slicing and then particle analysis and this noise is being counted as one of the particles and throwing out my results. Is there any way of removing it from the image for good? Thanks again for any help you can give, Cormac McCann Final year mechanical eng. student, CQU, Aust. From nih-image-request@io.ece.drexel.edu Wed Oct 7 09:06 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA18885; Wed, 7 Oct 1998 09:06:15 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 09:06:15 -0400 (EDT) Message-ID: <361BAB6B.3A9@pro.via-rs.com.br> Date: Wed, 07 Oct 1998 09:57:00 -0800 From: Luthero Martins Reply-To: luthero@pro.via-rs.com.br X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: question Content-Transfer-Encoding: 7bit Resent-Message-ID: <"cAXyk.0.NB4.JCs6s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/460 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 198 Please! I need to know if there are somebody that work with NIH's software, here in Brazil. And if somebody knows some course of NIH. Thanks Luthero Martins http://www.oftlamologia-digital.com From nih-image-request@io.ece.drexel.edu Wed Oct 7 11:21 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA01192; Wed, 7 Oct 1998 11:20:57 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 11:20:57 -0400 (EDT) Message-Id: <199810071455.KAA28776@io.ECE.Drexel.EDU> From: Chris Liner Subject: Donation To: nih-image@io.ece.drexel.edu Date: Wed, 7 Oct 98 10:19:46 CDT Cc: cll@utulsa.edu (Chris Liner) Mailer: Elm [revision: 70.85] Resent-Message-ID: <"DokWy.0.n17.f3u6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/461 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1221 I have developed a commercial seismic interpretation system around NIH-Image. The system is called Cubic and consists of macros, external utility applications and documentation for applying NIH-Image to visualize and interpret geophysical data. Cubic includes an external gridding program that makes it useful for many kinds of geophysical data (gravity, mag, conductivity, etc.) as well as subsurface geology (structure maps, isopachs, etc.). We use the system at U. of Tulsa to teach the fundamentals of 3D seismic interpretation, including tracking, depth conversion, and rock property estimation from seismic amplitude. Cubic currently in use by universities in Arkansas, Texas and California. I am interested in additional donations to a U.S. universities before the end of the year. If anyone on the NIH-Image mail list is interested, please contact me directly via email. Information about Cubic can be found at my web site listed below. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] From nih-image-request@io.ece.drexel.edu Wed Oct 7 12:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05427; Wed, 7 Oct 1998 12:08:27 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 12:08:27 -0400 (EDT) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: video capture Message-ID: Date: Wed, 7 Oct 1998 16:55:28 +0100 (BST) Delivery-Receipt-To: "j.gregory" Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"3aIXf1.0.6_.hwu6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/462 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 585 Hi, I was wondering if any more experienced imagers could help us, We are writing a grant application and looking to include video capture equipment for use with a PC & Scion image. We need a field of view (approx 5mm) and a resolution of at least 5 microns. We are measuring changes over a period of 2-3 seconds. If anyone could suggest useful equipment, methods or other information, it would be a great help. Thanks in advance, Jenny Gregory ---------------------- Jenny Gregory Department of Orthopaedics University of Aberdeen Aberdeen Scotland j.gregory@abdn.ac.uk From nih-image-request@io.ece.drexel.edu Wed Oct 7 13:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA21561; Wed, 7 Oct 1998 13:09:46 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 13:09:46 -0400 (EDT) From: frautsch@ucla.edu X-Sender: frautsch@pop.ben2.ucla.edu Message-Id: In-Reply-To: <199810070836.SAA23944@topaz.cqu.edu.au> Mime-Version: 1.0 Date: Wed, 7 Oct 1998 09:59:52 -0700 To: nih-image@io.ece.drexel.edu Subject: area of irregularly shaped ROI Resent-Message-ID: <"721F2.0.U53.Lnv6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/463 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 173 i have macros that compute # and size of cells per unit area using oval or rectangular ROIs. If i draw an irregularly shaped ROI. How do i compute the ROI area? Sally From nih-image-request@io.ece.drexel.edu Wed Oct 7 14:15 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA08533; Wed, 7 Oct 1998 14:14:55 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 14:14:55 -0400 (EDT) Message-Id: <361BAEAE.25CDBCE8@purdue.edu> Date: Wed, 07 Oct 1998 13:10:54 -0500 From: Kris Jorgensen Reply-To: kris@purdue.edu Organization: Purdue University X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Setting the Z-value in Object Image References: <199810071455.KAA28776@io.ECE.Drexel.EDU> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"SDUtm3.0.cn6.Cmw6s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/464 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 800 Hi all: Is it possible to set the Z value in Object Image? I would like to use the export XYZ data and make use of the Z value. I have thought of making all the images into a stack, but the distribution of the Z value is not uniform between images. To make matters worse, it is actually a heat transfer coefficient and computed from input provided by the user and so is not know before hand. Also, making each image into a stack with a single image seems a little cumbersome. If someone has another way of writing to a file the X and Y locations along with one or more computed values for each point in an object I could use that instead. Thanks Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris From nih-image-request@io.ece.drexel.edu Wed Oct 7 19:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA16980; Wed, 7 Oct 1998 19:11:46 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 19:11:46 -0400 (EDT) Date: Wed, 7 Oct 1998 18:48:36 -0400 (EDT) From: Cengizhan Ozturk X-Sender: cozturk@henryv To: frautsch@ucla.edu cc: nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"bv6Xp.0.1_.M_-6s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/465 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1188 Hi, There may be quick ways of doing it at image resolution. Roughly, open your ROI in an empty image. Fill your ROI with index 1, get its integrated density. Mathematically: You can find the centroid (C), calculate the area by summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) as you travel along the perimeter. This will handle even if the shape is irregular, if you watch the signs. ( Do not forget to divide everything by 2 at the end). One word of caution, the coordinates that you get from NIH-Image ROI might be off by 1 pixel at some locations. Please refer to earlier discussions about ROI X-Y coordinate corrections. Good Luck. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Wed, 7 Oct 1998 frautsch@ucla.edu wrote: > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > > From nih-image-request@io.ece.drexel.edu Wed Oct 7 21:11 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA22661; Wed, 7 Oct 1998 21:11:05 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 21:11:05 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: frautsch@ucla.edu, nih-image@io.ece.drexel.edu Date: Thu, 8 Oct 1998 10:28:00 GMT+1000 Subject: Re: area of irregularly shaped ROI Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"3tNaF2.0.WL2.Fk07s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/466 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1031 >From: frautsch@ucla.edu >Date: Wed, 7 Oct 1998 09:59:52 -0700 >To: nih-image@io.ece.drexel.edu > >i have macros that compute # and size of cells per unit area using oval or >rectangular ROIs. > >If i draw an irregularly shaped ROI. How do i compute the ROI area? > Sally, The answer is much simpler than you or Cengizhan's response would imply. A simple 'measure(Analyse menu' will place the area and the coordinates of the centroid of the current ROI (including a compound ROI created using option/control keys) in both the 'Info' window and the Results Table. (It is easy enough to check by using 'fill' to make a binary image to allow 'manual' verification of simple or geometric cases. You can rely on Image's accuracy within the accuracy of the image pixels. The variation in the xycoordinates list wont affect these results.) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Wed Oct 7 23:02 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA06113; Wed, 7 Oct 1998 22:32:12 -0400 (EDT) Resent-Date: Wed, 7 Oct 1998 22:32:12 -0400 (EDT) Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) Message-Id: <199810080122.LAA32197@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au (Unverified) X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: Macro error message Resent-Message-ID: <"DtWHs1.0.377.kF17s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/467 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 636 Hello again imagers, I am trying to incorporate the line 'Undo EditMenu' into my Macro program. When I run the macro, I get an error message saying that I an "end" or ";" is expected in the Undo EditMenu line. I have checked and tried to use the advised corrections but I still recieve the same error message. I should note that the macro still actually carries out the Undo edit function but the rest of the program is halted because of the error message. Can anyone out there shed some light on this small but annoying problem? Thanx in advance, Cormac McCann Final year mechanical eng. student, CQU, Aust. From nih-image-request@io.ece.drexel.edu Thu Oct 8 01:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23155; Thu, 8 Oct 1998 01:00:15 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 01:00:15 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu Date: Thu, 8 Oct 1998 14:10:47 GMT+1000 Subject: Re: Macro error message Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"dA0261.0.894.3H47s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/469 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1331 >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) >>To: nih-image@io.ece.drexel.edu >From: Cormac >Subject: Macro error message >> >Hello again imagers, > > I am trying to incorporate the line 'Undo EditMenu' into >my Macro program. When I run the macro, I get an error message saying that >I an "end" or ";" is expected in the Undo EditMenu line. I have checked and >tried to use the advised corrections but I still recieve the same error >message. I should note that the macro still actually carries out the Undo >edit function but the rest of the program is halted because of the error >message. > >Can anyone out there shed some light on this small but annoying problem? >Thanx in advance, > >Cormac McCann >Final year mechanical eng. student, CQU, Aust. :-) You are missing a statement end ie ";" or "end" (presumablly soon after the "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro program", it should be just " Undo; " not ! " Undo EditMenu; " If you want someone to make inteligent comment, it would be better to paste macro into email query (or maillist post). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Oct 8 01:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23062; Thu, 8 Oct 1998 01:00:06 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 01:00:06 -0400 (EDT) Message-ID: <361C2D4C.5CA0@earthlink.net> Date: Wed, 07 Oct 1998 20:11:08 -0700 From: Shawn Makanvand Reply-To: shawnmak@earthlink.net X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Plugins References: <199809241015.GAA26131@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"391bS.0.-64.wG47s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/468 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 630 Hi folks, I am new to the Image program and need help creating a plugin project. I would like to create a plugin using CodeWarrior Pro 2 and am uncertain as to how to set up the project parameters. Does anyone have a blank or basic project which would work on Code Warrior Pro 2? I tried downloading and reading the existing projects from the NIH web site but was unable to open any of them using the tools I have. They are written either in Think C or older versions of Code Warrior and I have not been able to convert any of them. Any help to get me started would be appreciated. Thanks. Shawn M. shawnmak@earthlink.net From nih-image-d-request@io.ece.drexel.edu Thu Oct 8 01:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA23384; Thu, 8 Oct 1998 01:00:40 -0400 (EDT) Date: Thu, 8 Oct 1998 01:00:40 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810080500.BAA23384@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #82 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/82 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9877 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 82 Today's Topics: question [ Luthero Martins ] area of irregularly shaped ROI [ frautsch@ucla.edu ] Setting the Z-value in Object Image [ Kris Jorgensen ] Re: area of irregularly shaped ROI [ Cengizhan Ozturk ] Plugins [ Shawn Makanvand To: nih-image@io.ece.drexel.edu Subject: question Message-ID: <361BAB6B.3A9@pro.via-rs.com.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please! I need to know if there are somebody that work with NIH's software, here in Brazil. And if somebody knows some course of NIH. Thanks Luthero Martins http://www.oftlamologia-digital.com ------------------------------ Date: Wed, 7 Oct 98 10:19:46 CDT From: Chris Liner To: nih-image@io.ece.drexel.edu Cc: cll@utulsa.edu (Chris Liner) Subject: Donation Message-Id: <199810071455.KAA28776@io.ECE.Drexel.EDU> I have developed a commercial seismic interpretation system around NIH-Image. The system is called Cubic and consists of macros, external utility applications and documentation for applying NIH-Image to visualize and interpret geophysical data. Cubic includes an external gridding program that makes it useful for many kinds of geophysical data (gravity, mag, conductivity, etc.) as well as subsurface geology (structure maps, isopachs, etc.). We use the system at U. of Tulsa to teach the fundamentals of 3D seismic interpretation, including tracking, depth conversion, and rock property estimation from seismic amplitude. Cubic currently in use by universities in Arkansas, Texas and California. I am interested in additional donations to a U.S. universities before the end of the year. If anyone on the NIH-Image mail list is interested, please contact me directly via email. Information about Cubic can be found at my web site listed below. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] ------------------------------ Date: Wed, 7 Oct 1998 16:55:28 +0100 (BST) From: "j.gregory" To: nih-image@io.ece.drexel.edu Subject: video capture Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hi, I was wondering if any more experienced imagers could help us, We are writing a grant application and looking to include video capture equipment for use with a PC & Scion image. We need a field of view (approx 5mm) and a resolution of at least 5 microns. We are measuring changes over a period of 2-3 seconds. If anyone could suggest useful equipment, methods or other information, it would be a great help. Thanks in advance, Jenny Gregory ---------------------- Jenny Gregory Department of Orthopaedics University of Aberdeen Aberdeen Scotland j.gregory@abdn.ac.uk ------------------------------ Date: Wed, 7 Oct 1998 09:59:52 -0700 From: frautsch@ucla.edu To: nih-image@io.ece.drexel.edu Subject: area of irregularly shaped ROI Message-Id: Content-Type: text/plain; charset="us-ascii" i have macros that compute # and size of cells per unit area using oval or rectangular ROIs. If i draw an irregularly shaped ROI. How do i compute the ROI area? Sally ------------------------------ Date: Wed, 07 Oct 1998 13:10:54 -0500 From: Kris Jorgensen To: nih-image@io.ece.drexel.edu Subject: Setting the Z-value in Object Image Message-Id: <361BAEAE.25CDBCE8@purdue.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all: Is it possible to set the Z value in Object Image? I would like to use the export XYZ data and make use of the Z value. I have thought of making all the images into a stack, but the distribution of the Z value is not uniform between images. To make matters worse, it is actually a heat transfer coefficient and computed from input provided by the user and so is not know before hand. Also, making each image into a stack with a single image seems a little cumbersome. If someone has another way of writing to a file the X and Y locations along with one or more computed values for each point in an object I could use that instead. Thanks Kris -- Kris L. Jorgensen Office: ME 183 Phone: (765) 494-8585 Email: kris@purdue.edu WWW: http://www.ecn.purdue.edu/~kris ------------------------------ Date: Wed, 7 Oct 1998 18:48:36 -0400 (EDT) From: Cengizhan Ozturk To: frautsch@ucla.edu cc: nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, There may be quick ways of doing it at image resolution. Roughly, open your ROI in an empty image. Fill your ROI with index 1, get its integrated density. Mathematically: You can find the centroid (C), calculate the area by summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) as you travel along the perimeter. This will handle even if the shape is irregular, if you watch the signs. ( Do not forget to divide everything by 2 at the end). One word of caution, the coordinates that you get from NIH-Image ROI might be off by 1 pixel at some locations. Please refer to earlier discussions about ROI X-Y coordinate corrections. Good Luck. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Wed, 7 Oct 1998 frautsch@ucla.edu wrote: > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > > ------------------------------ Date: Thu, 8 Oct 1998 10:28:00 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: frautsch@ucla.edu, nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI Message-ID: >From: frautsch@ucla.edu >Date: Wed, 7 Oct 1998 09:59:52 -0700 >To: nih-image@io.ece.drexel.edu > >i have macros that compute # and size of cells per unit area using oval or >rectangular ROIs. > >If i draw an irregularly shaped ROI. How do i compute the ROI area? > Sally, The answer is much simpler than you or Cengizhan's response would imply. A simple 'measure(Analyse menu' will place the area and the coordinates of the centroid of the current ROI (including a compound ROI created using option/control keys) in both the 'Info' window and the Results Table. (It is easy enough to check by using 'fill' to make a binary image to allow 'manual' verification of simple or geometric cases. You can rely on Image's accuracy within the accuracy of the image pixels. The variation in the xycoordinates list wont affect these results.) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: Macro error message Message-Id: <199810080122.LAA32197@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" Hello again imagers, I am trying to incorporate the line 'Undo EditMenu' into my Macro program. When I run the macro, I get an error message saying that I an "end" or ";" is expected in the Undo EditMenu line. I have checked and tried to use the advised corrections but I still recieve the same error message. I should note that the macro still actually carries out the Undo edit function but the rest of the program is halted because of the error message. Can anyone out there shed some light on this small but annoying problem? Thanx in advance, Cormac McCann Final year mechanical eng. student, CQU, Aust. ------------------------------ Date: Wed, 07 Oct 1998 20:11:08 -0700 From: Shawn Makanvand To: nih-image@io.ece.drexel.edu Subject: Plugins Message-ID: <361C2D4C.5CA0@earthlink.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi folks, I am new to the Image program and need help creating a plugin project. I would like to create a plugin using CodeWarrior Pro 2 and am uncertain as to how to set up the project parameters. Does anyone have a blank or basic project which would work on Code Warrior Pro 2? I tried downloading and reading the existing projects from the NIH web site but was unable to open any of them using the tools I have. They are written either in Think C or older versions of Code Warrior and I have not been able to convert any of them. Any help to get me started would be appreciated. Thanks. Shawn M. shawnmak@earthlink.net -------------------------------- End of nih-image-d Digest V98 Issue #82 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 8 01:33 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA10359; Thu, 8 Oct 1998 01:33:20 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 01:33:20 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: kris@purdue.edu, nih-image@io.ece.drexel.edu Date: Thu, 8 Oct 1998 13:05:54 GMT+1000 Subject: Re: Setting the Z-value in Object Image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"MMzcY1.0.QI1.Wn47s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/470 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3135 >Date: Wed, 07 Oct 1998 13:10:54 -0500 >From: Kris Jorgensen >Subject: Setting the Z-value in Object Image >Resent-From: nih-image@io.ece.drexel.edu > >Hi all: > >Is it possible to set the Z value in Object Image? I would like to use >the export XYZ data and make use of the Z value. I have thought of >making all the images into a stack, but the distribution of the Z value >is not uniform between images. To make matters worse, it is actually a >heat transfer coefficient and computed from input provided by the user >and so is not know before hand. Also, making each image into a stack >with a single image seems a little cumbersome. > >If someone has another way of writing to a file the X and Y locations >along with one or more computed values for each point in an object I >could use that instead. > >Thanks >Kris Kris, I hope I haven't misread you this time :-) For a 3D object to be associated with an image in Object-Image, it is not necessary for the image to be a stack. However, to introduce a Z measurement "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by sliceSpacing which again requires that the underlying image be a stack. If you have a single frame stack, then -0.50.5 pixels and scaled by sliceSpacing (can be set to arbitary scaling value). If you use the mouse to set x,y points you will be unable to speciy z manually without a multiframe stack but you have pointed out that Z values are computed. You may have a 2D object on which you wish to impose the Z dimension or you may be also computing the xy coords to go with the Z. In the first case, you can merge the Z dimension in by transcribing the original 2D object to a new 3D object using SwitchToObject and a setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. In the second case, you supply all three dimensions in the setMarker(x,y,x) loop which creates the object. While "making each image into a stack with a single image seems a little cumbersome", it is not expensive to getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose; makeNewStack(title);paste; It is not really necessary to save as stack. If you are only after exporting the 3D object dimensions for visualisation via Rotator or some such program, you could create a dummy stack onto which you transcribe the 3D objects from their source 2D object & image as you merge the Z dimension. Perhaps the most straightforward approach is "writing to a file the X and Y locations along with one or more computed values for each point in an object" to your own textfile with tab delimeters, headings etc. (but you lose some advantages of storing processed data in objects). Readily done with: var tab:string;i:ineteger; tab:=chr(9); newTextFile('xyz'); writeln('heading'); for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other); Hope this makes a little sense and helps. :-) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Oct 8 10:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA08620; Thu, 8 Oct 1998 10:21:43 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 10:21:43 -0400 (EDT) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 8 Oct 1998 10:05:05 -0400 To: nih-image@io.ece.drexel.edu From: Marc Steed Subject: Re: area of irregularly shaped ROI Resent-Message-ID: <"48VNY3.0.va6.KMC7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/471 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1581 On a related note: Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to a certain percentage of the original, while maintaining the original center point? TIA >>From: frautsch@ucla.edu >>Date: Wed, 7 Oct 1998 09:59:52 -0700 >>To: nih-image@io.ece.drexel.edu >> >>i have macros that compute # and size of cells per unit area using oval or >>rectangular ROIs. >> >>If i draw an irregularly shaped ROI. How do i compute the ROI area? >> >Sally, > >The answer is much simpler than you or Cengizhan's response would imply. > >A simple 'measure(Analyse menu' will place the area and the coordinates of >the >centroid of the current ROI (including a compound ROI created using >option/control keys) in both the 'Info' window and the Results Table. > >(It is easy enough to check by using 'fill' to make a binary image to allow >'manual' verification of simple or geometric cases. You can rely on Image's >accuracy within the accuracy of the image pixels. The variation in the >xycoordinates list wont affect these results.) > > > >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia ........................................................................... Marc A. Steed, M.S. Department of Psychology 513-556-1615 (West Campus) University of Cincinnati 513-558-5113 (East Campus) 429 Dyer Hall 513-556-1904 (fax) Cincinnati, OH 45221-0376 ........................................................................... From nih-image-request@io.ece.drexel.edu Thu Oct 8 12:52 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12169; Thu, 8 Oct 1998 12:51:31 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 12:51:31 -0400 (EDT) Message-ID: From: "Harrison, Janine" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Calcium ratio imaging experiments Date: Thu, 8 Oct 1998 09:34:26 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"ttaXH2.0.b71.TZE7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/472 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 3306 Hi Dr. Peeters- I appreciate your response. I am aware of some of the macros that are available in Image. My facility is so busy, however, that we cannot take on the added responsibility of programming to try and get the entire system to work. I was very interested in your comment regarding camera & etc. Would you be able to make a recommendation on types of cameras that are best suited for these ratioing experiments? We currently are using a one-chip Dage and we have it cooled to -35degC. We also use the Dage DSP2000 digital processor to integrate those samples whose light intensities are very low. Thanks for your suggestions, Regards, Janine > -----Original Message----- > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com] > Sent: Monday, October 05, 1998 6:13 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Calcium ratio imaging experiments > > to Janine Harrison > Manager, Image Analysis Facility > ICOS Corporation > 22021 20th Avenue S.E. > Bothell WA 98021 > > 1-425-485-1900 ext 2318 > 1-425-485-1961 FAX > jharrison@icos.comt > > > We have experience using NIH to measure calcium, Na+, and pH in > Lymphocytes, > cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My > recommendation is to spend the money on the front end of the measuring > system > (Camera, PMT system, illumination control) and start with NIH Image. You > can > always spend more on commercial software if NIH (with the appropriate > macros) > can't do what you need. I would be happy to discuss with you your groups > proposed work.However I will be out of my office beginning Wednesday > 10/7/98 > (morning) but back by next Monday. Please feel free to call tomorrow or > after > 10/11/98. > > sincerely yours, > > George A. Peeters M.D. > Pres. Solamere Technology Group > Salt Lake City, UT 84103 > > 801 322-2645 > > In a message dated 98-10-05 15:31:55 EDT, you write: > > << > > Does anyone have specific recommendations for filter sets (i.e. from > Chroma) > for the fura-2/indo-1 > class of compounds? >> > > This will depend on the experiment. For example, Fura-2 is the most often > used > probe for ratio Ca 2+ imaging. This probe will require illumination > waveband > switching for each ratio pair and if you wish to collect 15 ratio pairs > per > second you will need a progressive scan sensor (not an interlaced > detector). > Flo3, and Flo4 are easier to use but not ratioed. > Indo-1 is faster, but would require splitting the detector or an emission > wave > band switcher. > We have both imaging and photometric equipment used for Ca2+ measurement > at > both Genentech, Squibb, Soanes, as well as academic institutions world > wide. > > << Can NIH-Image be used fairly easily for quantitating ratiometric data? > Or > would a commercial analysis package (such as Metamoph, Axon Inst) be > better > suited for extensive experiments?>> > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A > suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as > little as $2500. This system can control waveband switchers (ours or > others), > filter wheels, shutters, electro-physiology, etc. We also have the macros > that > control these devices. From nih-image-request@io.ece.drexel.edu Thu Oct 8 18:31 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03520; Thu, 8 Oct 1998 18:31:13 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 18:31:13 -0400 (EDT) Message-Id: <199810082215.TAA18877@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: area of irregularly shaped ROI Date: Thu, 8 Oct 1998 19:11:42 -0300 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"G1nL01.0.hW.ofJ7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/474 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 550 Dear Sally, Could you send to me the macros that compute # and size of cells per unit area? Thanks in advance. Rejane Galindo Universidade Federal Rural de Pernambuco Morfologia e Anatomia Vegetal ---------- > From: frautsch@ucla.edu > To: nih-image@io.ece.drexel.edu > Subject: area of irregularly shaped ROI > Date: Quarta-feira, 07 Outubro, 1998 13:59 > > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > From nih-image-request@io.ece.drexel.edu Thu Oct 8 18:31 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03522; Thu, 8 Oct 1998 18:31:15 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 18:31:15 -0400 (EDT) Message-Id: <199810082215.TAA12014@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Donation Date: Thu, 8 Oct 1998 19:06:05 -0300 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"vF_DC3.0.jV.gfJ7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/473 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 1720 Dear Chris, I'm interested to receive more informations about this system, specially about conductivity. What exactly it does? Thanks in advance, Rejane Galindo Universidade Federal Rural de Pernambuco Morfologia e Anatomia Vegetal ---------- > From: Chris Liner > To: nih-image@io.ece.drexel.edu > Cc: Chris Liner > Subject: Donation > Date: Quarta-feira, 07 Outubro, 1998 12:19 > > > > I have developed a commercial seismic interpretation system > around NIH-Image. The system is called Cubic and consists of > macros, external utility applications and documentation for > applying NIH-Image to visualize and interpret geophysical data. > Cubic includes an external gridding program that makes it useful > for many kinds of geophysical data (gravity, mag, conductivity, etc.) > as well as subsurface geology (structure maps, isopachs, etc.). > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic > interpretation, including tracking, depth conversion, and > rock property estimation from seismic amplitude. > > Cubic currently in use by universities in Arkansas, Texas > and California. I am interested in additional donations to a > U.S. universities before the end of the year. > > If anyone on the NIH-Image mail list is interested, please contact > me directly via email. > > Information about Cubic can be found at my web site listed below. > > > Dr. Christopher L. Liner > Associate Professor > Department of Geoscience > University of Tulsa > 600 S. College Ave > Tulsa, OK 74104-3189 > --------------------------- > cll@utulsa.edu > http://douze.utulsa.edu/~cll/ChrisLiner.html > 918-631-3028 [phone] > 918-631-2091 [fax] > From nih-image-d-request@io.ece.drexel.edu Thu Oct 8 18:36 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA04039; Thu, 8 Oct 1998 18:36:07 -0400 (EDT) Date: Thu, 8 Oct 1998 18:36:07 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810082236.SAA04039@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #83 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/83 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 13150 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 83 Today's Topics: Re: Macro error message [ GJOSS@rna.bio.mq.edu.au ] Re: Setting the Z-value in Object Im [ GJOSS@rna.bio.mq.edu.au ] Re: area of irregularly shaped ROI [ Marc Steed ] RE: Calcium ratio imaging experiment [ "Harrison, Janine" >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) >>To: nih-image@io.ece.drexel.edu >From: Cormac >Subject: Macro error message >> >Hello again imagers, > > I am trying to incorporate the line 'Undo EditMenu' into >my Macro program. When I run the macro, I get an error message saying that >I an "end" or ";" is expected in the Undo EditMenu line. I have checked and >tried to use the advised corrections but I still recieve the same error >message. I should note that the macro still actually carries out the Undo >edit function but the rest of the program is halted because of the error >message. > >Can anyone out there shed some light on this small but annoying problem? >Thanx in advance, > >Cormac McCann >Final year mechanical eng. student, CQU, Aust. :-) You are missing a statement end ie ";" or "end" (presumablly soon after the "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro program", it should be just " Undo; " not ! " Undo EditMenu; " If you want someone to make inteligent comment, it would be better to paste macro into email query (or maillist post). Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 8 Oct 1998 13:05:54 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: kris@purdue.edu, nih-image@io.ece.drexel.edu Subject: Re: Setting the Z-value in Object Image Message-ID: >Date: Wed, 07 Oct 1998 13:10:54 -0500 >From: Kris Jorgensen >Subject: Setting the Z-value in Object Image >Resent-From: nih-image@io.ece.drexel.edu > >Hi all: > >Is it possible to set the Z value in Object Image? I would like to use >the export XYZ data and make use of the Z value. I have thought of >making all the images into a stack, but the distribution of the Z value >is not uniform between images. To make matters worse, it is actually a >heat transfer coefficient and computed from input provided by the user >and so is not know before hand. Also, making each image into a stack >with a single image seems a little cumbersome. > >If someone has another way of writing to a file the X and Y locations >along with one or more computed values for each point in an object I >could use that instead. > >Thanks >Kris Kris, I hope I haven't misread you this time :-) For a 3D object to be associated with an image in Object-Image, it is not necessary for the image to be a stack. However, to introduce a Z measurement "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by sliceSpacing which again requires that the underlying image be a stack. If you have a single frame stack, then -0.50.5 pixels and scaled by sliceSpacing (can be set to arbitary scaling value). If you use the mouse to set x,y points you will be unable to speciy z manually without a multiframe stack but you have pointed out that Z values are computed. You may have a 2D object on which you wish to impose the Z dimension or you may be also computing the xy coords to go with the Z. In the first case, you can merge the Z dimension in by transcribing the original 2D object to a new 3D object using SwitchToObject and a setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. In the second case, you supply all three dimensions in the setMarker(x,y,x) loop which creates the object. While "making each image into a stack with a single image seems a little cumbersome", it is not expensive to getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose; makeNewStack(title);paste; It is not really necessary to save as stack. If you are only after exporting the 3D object dimensions for visualisation via Rotator or some such program, you could create a dummy stack onto which you transcribe the 3D objects from their source 2D object & image as you merge the Z dimension. Perhaps the most straightforward approach is "writing to a file the X and Y locations along with one or more computed values for each point in an object" to your own textfile with tab delimeters, headings etc. (but you lose some advantages of storing processed data in objects). Readily done with: var tab:string;i:ineteger; tab:=chr(9); newTextFile('xyz'); writeln('heading'); for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other); Hope this makes a little sense and helps. :-) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 8 Oct 1998 10:05:05 -0400 From: Marc Steed To: nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI Message-Id: Content-Type: text/plain; charset="us-ascii" On a related note: Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to a certain percentage of the original, while maintaining the original center point? TIA >>From: frautsch@ucla.edu >>Date: Wed, 7 Oct 1998 09:59:52 -0700 >>To: nih-image@io.ece.drexel.edu >> >>i have macros that compute # and size of cells per unit area using oval or >>rectangular ROIs. >> >>If i draw an irregularly shaped ROI. How do i compute the ROI area? >> >Sally, > >The answer is much simpler than you or Cengizhan's response would imply. > >A simple 'measure(Analyse menu' will place the area and the coordinates of >the >centroid of the current ROI (including a compound ROI created using >option/control keys) in both the 'Info' window and the Results Table. > >(It is easy enough to check by using 'fill' to make a binary image to allow >'manual' verification of simple or geometric cases. You can rely on Image's >accuracy within the accuracy of the image pixels. The variation in the >xycoordinates list wont affect these results.) > > > >Greg Joss, >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 >Macquarie University, Email gjoss@rna.bio.mq.edu.au >North Ryde, (Sydney,) NSW 2109, Australia ........................................................................... Marc A. Steed, M.S. Department of Psychology 513-556-1615 (West Campus) University of Cincinnati 513-558-5113 (East Campus) 429 Dyer Hall 513-556-1904 (fax) Cincinnati, OH 45221-0376 ........................................................................... ------------------------------ Date: Thu, 8 Oct 1998 09:34:26 -0700 From: "Harrison, Janine" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Calcium ratio imaging experiments Message-ID: Content-Type: text/plain Hi Dr. Peeters- I appreciate your response. I am aware of some of the macros that are available in Image. My facility is so busy, however, that we cannot take on the added responsibility of programming to try and get the entire system to work. I was very interested in your comment regarding camera & etc. Would you be able to make a recommendation on types of cameras that are best suited for these ratioing experiments? We currently are using a one-chip Dage and we have it cooled to -35degC. We also use the Dage DSP2000 digital processor to integrate those samples whose light intensities are very low. Thanks for your suggestions, Regards, Janine > -----Original Message----- > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com] > Sent: Monday, October 05, 1998 6:13 PM > To: nih-image@io.ece.drexel.edu > Subject: Re: Calcium ratio imaging experiments > > to Janine Harrison > Manager, Image Analysis Facility > ICOS Corporation > 22021 20th Avenue S.E. > Bothell WA 98021 > > 1-425-485-1900 ext 2318 > 1-425-485-1961 FAX > jharrison@icos.comt > > > We have experience using NIH to measure calcium, Na+, and pH in > Lymphocytes, > cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My > recommendation is to spend the money on the front end of the measuring > system > (Camera, PMT system, illumination control) and start with NIH Image. You > can > always spend more on commercial software if NIH (with the appropriate > macros) > can't do what you need. I would be happy to discuss with you your groups > proposed work.However I will be out of my office beginning Wednesday > 10/7/98 > (morning) but back by next Monday. Please feel free to call tomorrow or > after > 10/11/98. > > sincerely yours, > > George A. Peeters M.D. > Pres. Solamere Technology Group > Salt Lake City, UT 84103 > > 801 322-2645 > > In a message dated 98-10-05 15:31:55 EDT, you write: > > << > > Does anyone have specific recommendations for filter sets (i.e. from > Chroma) > for the fura-2/indo-1 > class of compounds? >> > > This will depend on the experiment. For example, Fura-2 is the most often > used > probe for ratio Ca 2+ imaging. This probe will require illumination > waveband > switching for each ratio pair and if you wish to collect 15 ratio pairs > per > second you will need a progressive scan sensor (not an interlaced > detector). > Flo3, and Flo4 are easier to use but not ratioed. > Indo-1 is faster, but would require splitting the detector or an emission > wave > band switcher. > We have both imaging and photometric equipment used for Ca2+ measurement > at > both Genentech, Squibb, Soanes, as well as academic institutions world > wide. > > << Can NIH-Image be used fairly easily for quantitating ratiometric data? > Or > would a commercial analysis package (such as Metamoph, Axon Inst) be > better > suited for extensive experiments?>> > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A > suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as > little as $2500. This system can control waveband switchers (ours or > others), > filter wheels, shutters, electro-physiology, etc. We also have the macros > that > control these devices. ------------------------------ Date: Thu, 8 Oct 1998 19:06:05 -0300 From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: Donation Message-Id: <199810082215.TAA12014@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Chris, I'm interested to receive more informations about this system, specially about conductivity. What exactly it does? Thanks in advance, Rejane Galindo Universidade Federal Rural de Pernambuco Morfologia e Anatomia Vegetal ---------- > From: Chris Liner > To: nih-image@io.ece.drexel.edu > Cc: Chris Liner > Subject: Donation > Date: Quarta-feira, 07 Outubro, 1998 12:19 > > > > I have developed a commercial seismic interpretation system > around NIH-Image. The system is called Cubic and consists of > macros, external utility applications and documentation for > applying NIH-Image to visualize and interpret geophysical data. > Cubic includes an external gridding program that makes it useful > for many kinds of geophysical data (gravity, mag, conductivity, etc.) > as well as subsurface geology (structure maps, isopachs, etc.). > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic > interpretation, including tracking, depth conversion, and > rock property estimation from seismic amplitude. > > Cubic currently in use by universities in Arkansas, Texas > and California. I am interested in additional donations to a > U.S. universities before the end of the year. > > If anyone on the NIH-Image mail list is interested, please contact > me directly via email. > > Information about Cubic can be found at my web site listed below. > > > Dr. Christopher L. Liner > Associate Professor > Department of Geoscience > University of Tulsa > 600 S. College Ave > Tulsa, OK 74104-3189 > --------------------------- > cll@utulsa.edu > http://douze.utulsa.edu/~cll/ChrisLiner.html > 918-631-3028 [phone] > 918-631-2091 [fax] > -------------------------------- End of nih-image-d Digest V98 Issue #83 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 8 20:15 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12553; Thu, 8 Oct 1998 20:14:03 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 20:14:03 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: steedma@email.uc.edu, nih-image@io.ece.drexel.edu Date: Fri, 9 Oct 1998 9:53:12 GMT+1000 Subject: Re: area of irregularly shaped ROI (reduction Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"RuTfz3.0.qS2.u_K7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/475 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1629 >Date: Thu, 8 Oct 1998 10:05:05 -0400 >To: nih-image@io.ece.drexel.edu >From: Marc Steed >Subject: Re: area of irregularly shaped ROI >.......... >Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to >a certain percentage of the original, while maintaining the original center >point? > >............. >Department of Psychology 513-556-1615 (West Campus) >University of Cincinnati 513-558-5113 (East Campus) >429 Dyer Hall 513-556-1904 (fax) >Cincinnati, OH 45221-0376 That is a strange operation(?) The irregular-shaped ROI needs to be a reasonable shape to avoid splitting to multiple parts eg a dumbbell could result in two circles. Out-of-balance dumbbell could migrate towards the image boundary causing failure of macro. The following will do what you ask: (It behaves reasonably for reasonable shapes :-) macro'[r]educe area, retain center of ROI'; var rp,r:real;x,y,w,h,pi:integer; begin getRoi(x,y,w,h); if w=0 then exit('make selection'); rp:=getNumber('%reduction',33);r:=1-rp/100; SetOptions('Area X-Y Center'); resetCounter; measure;pi:=rCount; while rArea[rCount]/rArea[pi]>r do begin insetRoi(1);measure; moveRoi(rX[pi]-rX[rCount],rY[pi]-rY[rCount]); end; measure; showResults; showMessage('reduced',rArea[pi]:6,'\to ',rArea[rCount]:6 ,'\',rArea[rCount]/rArea[pi]*100:4:2 ,'%\at (',rX[rCount]:3:1,',',rY[rCount]:3:1,')'); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Oct 8 20:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA12753; Thu, 8 Oct 1998 20:16:01 -0400 (EDT) Resent-Date: Thu, 8 Oct 1998 20:16:01 -0400 (EDT) Message-ID: <361CA8B9.F2F8402D@jingxian.xmu.edu.cn> Date: Thu, 08 Oct 1998 19:57:46 +0800 From: tianling zheng X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: remove References: <199810082219.SAA02082@io.ece.drexel.edu> Content-Transfer-Encoding: 8bit Resent-Message-ID: <"xE_GE1.0._c2.Y5L7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/476 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 13471 nih-image-d-request@io.ece.drexel.edu wrote: > Subject: > > nih-image-d Digest Volume 98 : Issue 83 > > Today's Topics: > Re: Macro error message [ GJOSS@rna.bio.mq.edu.au ] > Re: Setting the Z-value in Object Im [ GJOSS@rna.bio.mq.edu.au ] > Re: area of irregularly shaped ROI [ Marc Steed ] > RE: Calcium ratio imaging experiment [ "Harrison, Janine" Re: Donation [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ] > > ------------------------------------------------------------------------ > > Subject: Re: Macro error message > Date: Thu, 8 Oct 1998 14:10:47 GMT+1000 > From: GJOSS@rna.bio.mq.edu.au > To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu > > >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) > >>To: nih-image@io.ece.drexel.edu > >From: Cormac > >Subject: Macro error message > >> > >Hello again imagers, > > > > I am trying to incorporate the line 'Undo EditMenu' into > >my Macro program. When I run the macro, I get an error message saying that > >I an "end" or ";" is expected in the Undo EditMenu line. I have checked and > >tried to use the advised corrections but I still recieve the same error > >message. I should note that the macro still actually carries out the Undo > >edit function but the rest of the program is halted because of the error > >message. > > > >Can anyone out there shed some light on this small but annoying problem? > >Thanx in advance, > > > >Cormac McCann > >Final year mechanical eng. student, CQU, Aust. > > :-) You are missing a statement end ie ";" or "end" (presumablly soon after the > "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro > program", it should be just > " > Undo; > " > not ! > " > Undo EditMenu; > " > If you want someone to make inteligent comment, it would be better to paste > macro into email query (or maillist post). > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > > ------------------------------------------------------------------------ > > Subject: Re: Setting the Z-value in Object Image > Date: Thu, 8 Oct 1998 13:05:54 GMT+1000 > From: GJOSS@rna.bio.mq.edu.au > To: kris@purdue.edu, nih-image@io.ece.drexel.edu > > >Date: Wed, 07 Oct 1998 13:10:54 -0500 > >From: Kris Jorgensen > >Subject: Setting the Z-value in Object Image > >Resent-From: nih-image@io.ece.drexel.edu > > > >Hi all: > > > >Is it possible to set the Z value in Object Image? I would like to use > >the export XYZ data and make use of the Z value. I have thought of > >making all the images into a stack, but the distribution of the Z value > >is not uniform between images. To make matters worse, it is actually a > >heat transfer coefficient and computed from input provided by the user > >and so is not know before hand. Also, making each image into a stack > >with a single image seems a little cumbersome. > > > >If someone has another way of writing to a file the X and Y locations > >along with one or more computed values for each point in an object I > >could use that instead. > > > >Thanks > >Kris > > Kris, > > I hope I haven't misread you this time :-) > > For a 3D object to be associated with an image in Object-Image, it is not > necessary for the image to be a stack. However, to introduce a Z measurement > "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by > sliceSpacing which again requires that the underlying image be a stack. > If you have a single frame stack, then -0.50.5 pixels and scaled by > sliceSpacing (can be set to arbitary scaling value). > > If you use the mouse to set x,y points you will be unable to speciy z manually > without a multiframe stack but you have pointed out that Z values are computed. > You may have a 2D object on which you wish to impose the Z dimension or you may > be also computing the xy coords to go with the Z. > In the first case, you can merge the Z dimension in by transcribing the > original 2D object to a new 3D object using SwitchToObject and a > setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. > In the second case, you supply all three dimensions in the setMarker(x,y,x) > loop which creates the object. > > While "making each image into a stack with a single image seems a little > cumbersome", it is not expensive to > getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose; > makeNewStack(title);paste; > It is not really necessary to save as stack. > > If you are only after exporting the 3D object dimensions for visualisation via > Rotator or some such program, you could create a dummy stack onto which you > transcribe the 3D objects from their source 2D object & image as you merge the > Z dimension. > > Perhaps the most straightforward approach is "writing to a file the X and Y > locations along with one or more computed values for each point in an object" > to your own textfile with tab delimeters, headings etc. (but you lose some > advantages of storing processed data in objects). > Readily done with: > > var tab:string;i:ineteger; > tab:=chr(9); > newTextFile('xyz'); > writeln('heading'); > for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other); > > Hope this makes a little sense and helps. :-) > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > > ------------------------------------------------------------------------ > > Subject: Re: area of irregularly shaped ROI > Date: Thu, 8 Oct 1998 10:05:05 -0400 > From: Marc Steed > To: nih-image@io.ece.drexel.edu > > On a related note: > > Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to > a certain percentage of the original, while maintaining the original center > point? > > TIA > > >>From: frautsch@ucla.edu > >>Date: Wed, 7 Oct 1998 09:59:52 -0700 > >>To: nih-image@io.ece.drexel.edu > >> > >>i have macros that compute # and size of cells per unit area using oval or > >>rectangular ROIs. > >> > >>If i draw an irregularly shaped ROI. How do i compute the ROI area? > >> > >Sally, > > > >The answer is much simpler than you or Cengizhan's response would imply. > > > >A simple 'measure(Analyse menu' will place the area and the coordinates of > >the > >centroid of the current ROI (including a compound ROI created using > >option/control keys) in both the 'Info' window and the Results Table. > > > >(It is easy enough to check by using 'fill' to make a binary image to allow > >'manual' verification of simple or geometric cases. You can rely on Image's > >accuracy within the accuracy of the image pixels. The variation in the > >xycoordinates list wont affect these results.) > > > > > > > >Greg Joss, > >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > >Macquarie University, Email gjoss@rna.bio.mq.edu.au > >North Ryde, (Sydney,) NSW 2109, Australia > > ........................................................................... > Marc A. Steed, M.S. > Department of Psychology 513-556-1615 (West Campus) > University of Cincinnati 513-558-5113 (East Campus) > 429 Dyer Hall 513-556-1904 (fax) > Cincinnati, OH 45221-0376 > ........................................................................... > > ------------------------------------------------------------------------ > > Subject: RE: Calcium ratio imaging experiments > Date: Thu, 8 Oct 1998 09:34:26 -0700 > From: "Harrison, Janine" > To: "'nih-image@io.ece.drexel.edu'" > > Hi Dr. Peeters- > > I appreciate your response. I am aware of some of the macros that are > available in Image. My facility is so busy, however, that we cannot take on > the added responsibility of programming to try and get the entire system to > work. > > I was very interested in your comment regarding camera & etc. Would you be > able to make a recommendation on types of cameras that are best suited for > these ratioing experiments? We currently are using a one-chip Dage and we > have it cooled to -35degC. We also use the Dage DSP2000 digital processor > to integrate those samples whose light intensities are very low. > > Thanks for your suggestions, > > Regards, > > Janine > > > -----Original Message----- > > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com] > > Sent: Monday, October 05, 1998 6:13 PM > > To: nih-image@io.ece.drexel.edu > > Subject: Re: Calcium ratio imaging experiments > > > > to Janine Harrison > > Manager, Image Analysis Facility > > ICOS Corporation > > 22021 20th Avenue S.E. > > Bothell WA 98021 > > > > 1-425-485-1900 ext 2318 > > 1-425-485-1961 FAX > > jharrison@icos.comt > > > > > > We have experience using NIH to measure calcium, Na+, and pH in > > Lymphocytes, > > cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My > > recommendation is to spend the money on the front end of the measuring > > system > > (Camera, PMT system, illumination control) and start with NIH Image. You > > can > > always spend more on commercial software if NIH (with the appropriate > > macros) > > can't do what you need. I would be happy to discuss with you your groups > > proposed work.However I will be out of my office beginning Wednesday > > 10/7/98 > > (morning) but back by next Monday. Please feel free to call tomorrow or > > after > > 10/11/98. > > > > sincerely yours, > > > > George A. Peeters M.D. > > Pres. Solamere Technology Group > > Salt Lake City, UT 84103 > > > > 801 322-2645 > > > > In a message dated 98-10-05 15:31:55 EDT, you write: > > > > << > > > > Does anyone have specific recommendations for filter sets (i.e. from > > Chroma) > > for the fura-2/indo-1 > > class of compounds? >> > > > > This will depend on the experiment. For example, Fura-2 is the most often > > used > > probe for ratio Ca 2+ imaging. This probe will require illumination > > waveband > > switching for each ratio pair and if you wish to collect 15 ratio pairs > > per > > second you will need a progressive scan sensor (not an interlaced > > detector). > > Flo3, and Flo4 are easier to use but not ratioed. > > Indo-1 is faster, but would require splitting the detector or an emission > > wave > > band switcher. > > We have both imaging and photometric equipment used for Ca2+ measurement > > at > > both Genentech, Squibb, Soanes, as well as academic institutions world > > wide. > > > > << Can NIH-Image be used fairly easily for quantitating ratiometric data? > > Or > > would a commercial analysis package (such as Metamoph, Axon Inst) be > > better > > suited for extensive experiments?>> > > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A > > suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as > > little as $2500. This system can control waveband switchers (ours or > > others), > > filter wheels, shutters, electro-physiology, etc. We also have the macros > > that > > control these devices. > > ------------------------------------------------------------------------ > > Subject: Re: Donation > Date: Thu, 8 Oct 1998 19:06:05 -0300 > From: "Rejane Magalhes Pimentel Galindo" > To: > > Dear Chris, > I'm interested to receive more informations about this system, specially > about conductivity. What exactly it does? > Thanks in advance, > Rejane Galindo > Universidade Federal Rural de Pernambuco > Morfologia e Anatomia Vegetal > > ---------- > > From: Chris Liner > > To: nih-image@io.ece.drexel.edu > > Cc: Chris Liner > > Subject: Donation > > Date: Quarta-feira, 07 Outubro, 1998 12:19 > > > > > > > > I have developed a commercial seismic interpretation system > > around NIH-Image. The system is called Cubic and consists of > > macros, external utility applications and documentation for > > applying NIH-Image to visualize and interpret geophysical data. > > Cubic includes an external gridding program that makes it useful > > for many kinds of geophysical data (gravity, mag, conductivity, etc.) > > as well as subsurface geology (structure maps, isopachs, etc.). > > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic > > interpretation, including tracking, depth conversion, and > > rock property estimation from seismic amplitude. > > > > Cubic currently in use by universities in Arkansas, Texas > > and California. I am interested in additional donations to a > > U.S. universities before the end of the year. > > > > If anyone on the NIH-Image mail list is interested, please contact > > me directly via email. > > > > Information about Cubic can be found at my web site listed below. > > > > > > Dr. Christopher L. Liner > > Associate Professor > > Department of Geoscience > > University of Tulsa > > 600 S. College Ave > > Tulsa, OK 74104-3189 > > --------------------------- > > cll@utulsa.edu > > http://douze.utulsa.edu/~cll/ChrisLiner.html > > 918-631-3028 [phone] > > 918-631-2091 [fax] > > From nih-image-request@io.ece.drexel.edu Fri Oct 9 01:35 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA13879; Fri, 9 Oct 1998 01:34:23 -0400 (EDT) Resent-Date: Fri, 9 Oct 1998 01:34:23 -0400 (EDT) References: TVWTICHR, Company Limited by Guarantee, ACN 009 278 755 Mime-Version: 1.0 Message-Id: In-Reply-To: <199810070836.SAA23944@topaz.cqu.edu.au> X-Mailer: Eudora Pro 4.01 for the Mac. Date: Fri, 9 Oct 1998 13:19:56 +0800 To: nih-image@io.ece.drexel.edu From: Mike Schon-Hegrad Subject: G3 Upgrade conflict with LG 3?? Cc: karenw@ichr.uwa.edu.au Resent-Message-ID: <"ofYLl1.0.0_2.OqP7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/477 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 753 Hi all, We've been running a successful project using NIH Image on an 8100/80AV PowerMac with a Scion LG 3 card. We'd like to upgrade the 8100/80AV to a G3 processor and are looking at the MAXpower G3 cards for the 8100 from Newertech. I'm just wondering if anyone else has done this, or if anyone can forsee any problems with the Scion LG 3 card and this G3 configuration. Thanks in advance, Mike ------------------------------------------------- Mike Schon-Hegrad (Macintosh Administrator) Central IT Services TVW Telethon Institute for Child Health Research Perth, Western Australia Company limited by guarantee Phone 61 8 9340 7072 Fax 61 8 9388 3414 WWW: http://www.ichr.uwa.edu.au ------------------------------------------------- From nih-image-request@io.ece.drexel.edu Fri Oct 9 10:44 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA11389; Fri, 9 Oct 1998 10:44:15 -0400 (EDT) Resent-Date: Fri, 9 Oct 1998 10:44:15 -0400 (EDT) From: MASandberg@aol.com Message-ID: <86dd0702.361e1b22@aol.com> Date: Fri, 9 Oct 1998 10:18:10 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Sprintscan plug-in error. Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"qSHTc2.0.n62.8jX7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/478 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 294 With NIH Image 1.62b and a G3 Powerbook with 192 RAM I can scan one slide with a Sprintscan 35 plug-in but get an "out of memory" error message when I try to do a second scan. If I quit and reopen NIH Image, I can then do the second scan. Any advice on how to fix this problem? Thanks, MAS From nih-image-d-request@io.ece.drexel.edu Fri Oct 9 10:49 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA12089; Fri, 9 Oct 1998 10:49:54 -0400 (EDT) Date: Fri, 9 Oct 1998 10:49:54 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810091449.KAA12089@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #84 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/84 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 18826 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 84 Today's Topics: Re: area of irregularly shaped ROI [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ] Re: area of irregularly shaped ROI ( [ GJOSS@rna.bio.mq.edu.au ] remove [ tianling zheng To: Subject: Re: area of irregularly shaped ROI Message-Id: <199810082215.TAA18877@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Sally, Could you send to me the macros that compute # and size of cells per unit area? Thanks in advance. Rejane Galindo Universidade Federal Rural de Pernambuco Morfologia e Anatomia Vegetal ---------- > From: frautsch@ucla.edu > To: nih-image@io.ece.drexel.edu > Subject: area of irregularly shaped ROI > Date: Quarta-feira, 07 Outubro, 1998 13:59 > > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > ------------------------------ Date: Fri, 9 Oct 1998 9:53:12 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: steedma@email.uc.edu, nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI (reduction Message-ID: >Date: Thu, 8 Oct 1998 10:05:05 -0400 >To: nih-image@io.ece.drexel.edu >From: Marc Steed >Subject: Re: area of irregularly shaped ROI >.......... >Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to >a certain percentage of the original, while maintaining the original center >point? > >............. >Department of Psychology 513-556-1615 (West Campus) >University of Cincinnati 513-558-5113 (East Campus) >429 Dyer Hall 513-556-1904 (fax) >Cincinnati, OH 45221-0376 That is a strange operation(?) The irregular-shaped ROI needs to be a reasonable shape to avoid splitting to multiple parts eg a dumbbell could result in two circles. Out-of-balance dumbbell could migrate towards the image boundary causing failure of macro. The following will do what you ask: (It behaves reasonably for reasonable shapes :-) macro'[r]educe area, retain center of ROI'; var rp,r:real;x,y,w,h,pi:integer; begin getRoi(x,y,w,h); if w=0 then exit('make selection'); rp:=getNumber('%reduction',33);r:=1-rp/100; SetOptions('Area X-Y Center'); resetCounter; measure;pi:=rCount; while rArea[rCount]/rArea[pi]>r do begin insetRoi(1);measure; moveRoi(rX[pi]-rX[rCount],rY[pi]-rY[rCount]); end; measure; showResults; showMessage('reduced',rArea[pi]:6,'\to ',rArea[rCount]:6 ,'\',rArea[rCount]/rArea[pi]*100:4:2 ,'%\at (',rX[rCount]:3:1,',',rY[rCount]:3:1,')'); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 08 Oct 1998 19:57:46 +0800 From: tianling zheng To: nih-image@io.ece.drexel.edu Subject: remove Message-ID: <361CA8B9.F2F8402D@jingxian.xmu.edu.cn> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit nih-image-d-request@io.ece.drexel.edu wrote: > Subject: > > nih-image-d Digest Volume 98 : Issue 83 > > Today's Topics: > Re: Macro error message [ GJOSS@rna.bio.mq.edu.au ] > Re: Setting the Z-value in Object Im [ GJOSS@rna.bio.mq.edu.au ] > Re: area of irregularly shaped ROI [ Marc Steed ] > RE: Calcium ratio imaging experiment [ "Harrison, Janine" Re: Donation [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ] > > ------------------------------------------------------------------------ > > Subject: Re: Macro error message > Date: Thu, 8 Oct 1998 14:10:47 GMT+1000 > From: GJOSS@rna.bio.mq.edu.au > To: mccannc@topaz.cqu.edu.au, nih-image@io.ece.drexel.edu > > >Date: Thu, 8 Oct 1998 11:22:27 +1000 (EST) > >>To: nih-image@io.ece.drexel.edu > >From: Cormac > >Subject: Macro error message > >> > >Hello again imagers, > > > > I am trying to incorporate the line 'Undo EditMenu' into > >my Macro program. When I run the macro, I get an error message saying that > >I an "end" or ";" is expected in the Undo EditMenu line. I have checked and > >tried to use the advised corrections but I still recieve the same error > >message. I should note that the macro still actually carries out the Undo > >edit function but the rest of the program is halted because of the error > >message. > > > >Can anyone out there shed some light on this small but annoying problem? > >Thanx in advance, > > > >Cormac McCann > >Final year mechanical eng. student, CQU, Aust. > > :-) You are missing a statement end ie ";" or "end" (presumablly soon after the > "Undo". Note that if you have "the line 'Undo EditMenu' in(to my/your) Macro > program", it should be just > " > Undo; > " > not ! > " > Undo EditMenu; > " > If you want someone to make inteligent comment, it would be better to paste > macro into email query (or maillist post). > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > > ------------------------------------------------------------------------ > > Subject: Re: Setting the Z-value in Object Image > Date: Thu, 8 Oct 1998 13:05:54 GMT+1000 > From: GJOSS@rna.bio.mq.edu.au > To: kris@purdue.edu, nih-image@io.ece.drexel.edu > > >Date: Wed, 07 Oct 1998 13:10:54 -0500 > >From: Kris Jorgensen > >Subject: Setting the Z-value in Object Image > >Resent-From: nih-image@io.ece.drexel.edu > > > >Hi all: > > > >Is it possible to set the Z value in Object Image? I would like to use > >the export XYZ data and make use of the Z value. I have thought of > >making all the images into a stack, but the distribution of the Z value > >is not uniform between images. To make matters worse, it is actually a > >heat transfer coefficient and computed from input provided by the user > >and so is not know before hand. Also, making each image into a stack > >with a single image seems a little cumbersome. > > > >If someone has another way of writing to a file the X and Y locations > >along with one or more computed values for each point in an object I > >could use that instead. > > > >Thanks > >Kris > > Kris, > > I hope I haven't misread you this time :-) > > For a 3D object to be associated with an image in Object-Image, it is not > necessary for the image to be a stack. However, to introduce a Z measurement > "Z must be between 1 and nSlices (+/-0.5)". It (the Z dimension) is scaled by > sliceSpacing which again requires that the underlying image be a stack. > If you have a single frame stack, then -0.50.5 pixels and scaled by > sliceSpacing (can be set to arbitary scaling value). > > If you use the mouse to set x,y points you will be unable to speciy z manually > without a multiframe stack but you have pointed out that Z values are computed. > You may have a 2D object on which you wish to impose the Z dimension or you may > be also computing the xy coords to go with the Z. > In the first case, you can merge the Z dimension in by transcribing the > original 2D object to a new 3D object using SwitchToObject and a > setMarker(xpos(i),ypos(i),z); looping through npoints of the selectedCell. > In the second case, you supply all three dimensions in the setMarker(x,y,x) > loop which creates the object. > > While "making each image into a stack with a single image seems a little > cumbersome", it is not expensive to > getPicsize(w,h);setNewSize(w,h);selectAll;copy;title:=windowTitle;dispose; > makeNewStack(title);paste; > It is not really necessary to save as stack. > > If you are only after exporting the 3D object dimensions for visualisation via > Rotator or some such program, you could create a dummy stack onto which you > transcribe the 3D objects from their source 2D object & image as you merge the > Z dimension. > > Perhaps the most straightforward approach is "writing to a file the X and Y > locations along with one or more computed values for each point in an object" > to your own textfile with tab delimeters, headings etc. (but you lose some > advantages of storing processed data in objects). > Readily done with: > > var tab:string;i:ineteger; > tab:=chr(9); > newTextFile('xyz'); > writeln('heading'); > for i:=1 to npoints do writeln(xpos(i),tab,ypos(i),tab,z,tab,other); > > Hope this makes a little sense and helps. :-) > > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > > ------------------------------------------------------------------------ > > Subject: Re: area of irregularly shaped ROI > Date: Thu, 8 Oct 1998 10:05:05 -0400 > From: Marc Steed > To: nih-image@io.ece.drexel.edu > > On a related note: > > Is it possible to then scale down (i.e., erode) an irregular-shaped ROI to > a certain percentage of the original, while maintaining the original center > point? > > TIA > > >>From: frautsch@ucla.edu > >>Date: Wed, 7 Oct 1998 09:59:52 -0700 > >>To: nih-image@io.ece.drexel.edu > >> > >>i have macros that compute # and size of cells per unit area using oval or > >>rectangular ROIs. > >> > >>If i draw an irregularly shaped ROI. How do i compute the ROI area? > >> > >Sally, > > > >The answer is much simpler than you or Cengizhan's response would imply. > > > >A simple 'measure(Analyse menu' will place the area and the coordinates of > >the > >centroid of the current ROI (including a compound ROI created using > >option/control keys) in both the 'Info' window and the Results Table. > > > >(It is easy enough to check by using 'fill' to make a binary image to allow > >'manual' verification of simple or geometric cases. You can rely on Image's > >accuracy within the accuracy of the image pixels. The variation in the > >xycoordinates list wont affect these results.) > > > > > > > >Greg Joss, > >School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > >Macquarie University, Email gjoss@rna.bio.mq.edu.au > >North Ryde, (Sydney,) NSW 2109, Australia > > ........................................................................... > Marc A. Steed, M.S. > Department of Psychology 513-556-1615 (West Campus) > University of Cincinnati 513-558-5113 (East Campus) > 429 Dyer Hall 513-556-1904 (fax) > Cincinnati, OH 45221-0376 > ........................................................................... > > ------------------------------------------------------------------------ > > Subject: RE: Calcium ratio imaging experiments > Date: Thu, 8 Oct 1998 09:34:26 -0700 > From: "Harrison, Janine" > To: "'nih-image@io.ece.drexel.edu'" > > Hi Dr. Peeters- > > I appreciate your response. I am aware of some of the macros that are > available in Image. My facility is so busy, however, that we cannot take on > the added responsibility of programming to try and get the entire system to > work. > > I was very interested in your comment regarding camera & etc. Would you be > able to make a recommendation on types of cameras that are best suited for > these ratioing experiments? We currently are using a one-chip Dage and we > have it cooled to -35degC. We also use the Dage DSP2000 digital processor > to integrate those samples whose light intensities are very low. > > Thanks for your suggestions, > > Regards, > > Janine > > > -----Original Message----- > > From: SolamereTG@aol.com [SMTP:SolamereTG@aol.com] > > Sent: Monday, October 05, 1998 6:13 PM > > To: nih-image@io.ece.drexel.edu > > Subject: Re: Calcium ratio imaging experiments > > > > to Janine Harrison > > Manager, Image Analysis Facility > > ICOS Corporation > > 22021 20th Avenue S.E. > > Bothell WA 98021 > > > > 1-425-485-1900 ext 2318 > > 1-425-485-1961 FAX > > jharrison@icos.comt > > > > > > We have experience using NIH to measure calcium, Na+, and pH in > > Lymphocytes, > > cardiac myocytes, vascular smooth muscle cells, and endothelial cells. My > > recommendation is to spend the money on the front end of the measuring > > system > > (Camera, PMT system, illumination control) and start with NIH Image. You > > can > > always spend more on commercial software if NIH (with the appropriate > > macros) > > can't do what you need. I would be happy to discuss with you your groups > > proposed work.However I will be out of my office beginning Wednesday > > 10/7/98 > > (morning) but back by next Monday. Please feel free to call tomorrow or > > after > > 10/11/98. > > > > sincerely yours, > > > > George A. Peeters M.D. > > Pres. Solamere Technology Group > > Salt Lake City, UT 84103 > > > > 801 322-2645 > > > > In a message dated 98-10-05 15:31:55 EDT, you write: > > > > << > > > > Does anyone have specific recommendations for filter sets (i.e. from > > Chroma) > > for the fura-2/indo-1 > > class of compounds? >> > > > > This will depend on the experiment. For example, Fura-2 is the most often > > used > > probe for ratio Ca 2+ imaging. This probe will require illumination > > waveband > > switching for each ratio pair and if you wish to collect 15 ratio pairs > > per > > second you will need a progressive scan sensor (not an interlaced > > detector). > > Flo3, and Flo4 are easier to use but not ratioed. > > Indo-1 is faster, but would require splitting the detector or an emission > > wave > > band switcher. > > We have both imaging and photometric equipment used for Ca2+ measurement > > at > > both Genentech, Squibb, Soanes, as well as academic institutions world > > wide. > > > > << Can NIH-Image be used fairly easily for quantitating ratiometric data? > > Or > > would a commercial analysis package (such as Metamoph, Axon Inst) be > > better > > suited for extensive experiments?>> > > Yes, we have Macros to ratio of images acquired at video rates (30 fps). A > > suitable G-3 platform, 64MB RAM, LG-3 frame grabber, software can run as > > little as $2500. This system can control waveband switchers (ours or > > others), > > filter wheels, shutters, electro-physiology, etc. We also have the macros > > that > > control these devices. > > ------------------------------------------------------------------------ > > Subject: Re: Donation > Date: Thu, 8 Oct 1998 19:06:05 -0300 > From: "Rejane Magalhes Pimentel Galindo" > To: > > Dear Chris, > I'm interested to receive more informations about this system, specially > about conductivity. What exactly it does? > Thanks in advance, > Rejane Galindo > Universidade Federal Rural de Pernambuco > Morfologia e Anatomia Vegetal > > ---------- > > From: Chris Liner > > To: nih-image@io.ece.drexel.edu > > Cc: Chris Liner > > Subject: Donation > > Date: Quarta-feira, 07 Outubro, 1998 12:19 > > > > > > > > I have developed a commercial seismic interpretation system > > around NIH-Image. The system is called Cubic and consists of > > macros, external utility applications and documentation for > > applying NIH-Image to visualize and interpret geophysical data. > > Cubic includes an external gridding program that makes it useful > > for many kinds of geophysical data (gravity, mag, conductivity, etc.) > > as well as subsurface geology (structure maps, isopachs, etc.). > > We use the system at U. of Tulsa to teach the fundamentals of 3D seismic > > interpretation, including tracking, depth conversion, and > > rock property estimation from seismic amplitude. > > > > Cubic currently in use by universities in Arkansas, Texas > > and California. I am interested in additional donations to a > > U.S. universities before the end of the year. > > > > If anyone on the NIH-Image mail list is interested, please contact > > me directly via email. > > > > Information about Cubic can be found at my web site listed below. > > > > > > Dr. Christopher L. Liner > > Associate Professor > > Department of Geoscience > > University of Tulsa > > 600 S. College Ave > > Tulsa, OK 74104-3189 > > --------------------------- > > cll@utulsa.edu > > http://douze.utulsa.edu/~cll/ChrisLiner.html > > 918-631-3028 [phone] > > 918-631-2091 [fax] > > ------------------------------ Date: Fri, 9 Oct 1998 13:19:56 +0800 From: Mike Schon-Hegrad To: nih-image@io.ece.drexel.edu Cc: karenw@ichr.uwa.edu.au Subject: G3 Upgrade conflict with LG 3?? Message-Id: Content-Type: text/plain; charset="us-ascii" Hi all, We've been running a successful project using NIH Image on an 8100/80AV PowerMac with a Scion LG 3 card. We'd like to upgrade the 8100/80AV to a G3 processor and are looking at the MAXpower G3 cards for the 8100 from Newertech. I'm just wondering if anyone else has done this, or if anyone can forsee any problems with the Scion LG 3 card and this G3 configuration. Thanks in advance, Mike ------------------------------------------------- Mike Schon-Hegrad (Macintosh Administrator) Central IT Services TVW Telethon Institute for Child Health Research Perth, Western Australia Company limited by guarantee Phone 61 8 9340 7072 Fax 61 8 9388 3414 WWW: http://www.ichr.uwa.edu.au ------------------------------------------------- ------------------------------ Date: Fri, 9 Oct 1998 10:18:10 EDT From: MASandberg@aol.com To: nih-image@io.ece.drexel.edu Subject: Sprintscan plug-in error. Message-ID: <86dd0702.361e1b22@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit With NIH Image 1.62b and a G3 Powerbook with 192 RAM I can scan one slide with a Sprintscan 35 plug-in but get an "out of memory" error message when I try to do a second scan. If I quit and reopen NIH Image, I can then do the second scan. Any advice on how to fix this problem? Thanks, MAS -------------------------------- End of nih-image-d Digest V98 Issue #84 *************************************** From nih-image-request@io.ece.drexel.edu Fri Oct 9 12:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA20912; Fri, 9 Oct 1998 12:09:23 -0400 (EDT) Resent-Date: Fri, 9 Oct 1998 12:09:23 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Fri, 9 Oct 1998 08:35:59 -0700 To: schlu@alpha.bio.nat.tu-bs.de From: constance j temm Subject: Re: area of irregularly shaped ROI Cc: nih-image@io.ece.drexel.edu Resent-Message-ID: <"9nKKs2.0.yc4.o2Z7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/479 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1365 Hi, There may be quick ways of doing it at image resolution. Roughly, open your ROI in an empty image. Fill your ROI with index 1, get its integrated density. Mathematically: You can find the centroid (C), calculate the area by summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) as you travel along the perimeter. This will handle even if the shape is irregular, if you watch the signs. ( Do not forget to divide everything by 2 at the end). One word of caution, the coordinates that you get from NIH-Image ROI might be off by 1 pixel at some locations. Please refer to earlier discussions about ROI X-Y coordinate corrections. Good Luck. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Wed, 7 Oct 1998 frautsch@ucla.edu wrote: > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > > Constance J. Temm, Ph.D. University of Arizona Tel.: (520) 621-8643 Nutritional Sciences Dept. Fax: 520 621 1396 632 Shantz Building Tucson, AZ 85721 USA From nih-image-request@io.ece.drexel.edu Fri Oct 9 12:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA25063; Fri, 9 Oct 1998 12:53:23 -0400 (EDT) Resent-Date: Fri, 9 Oct 1998 12:53:23 -0400 (EDT) Message-Id: <199810091634.MAA25321@codon.nih.gov> X-Sender: tsuyoshi@codon.nih.gov (Unverified) X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Date: Fri, 9 Oct 1998 12:36:21 -0400 To: nih-image@io.ece.drexel.edu From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) Subject: 1.62b30 and QT frame Grabber Resent-Message-ID: <"rGHGw.0.dj5.gkZ7s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/480 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="ISO-2022-JP" Content-Length: 940 Hi, I am using powerbookG3 and QuickTime compatible frame grabber, PicPomZV. When I was using NIH Image 1.61, I could not do 'start capturing' because of the -2208 error. In version 1.62b30, 'start capturing' works, the live images are perfectly displayed, but 'make movie' does not work well. That is, when I run 'make movie', blank rectangles are displayed while capturing, and relulting stack only contains completely black slices. Has anyone expericed this kind of problem with PicPomZV, or other frame grabbers, using 1.62b30? If yes, any solutions ? Thanks. Tsuyoshi ________________________________________ Tsuyoshi Miyakawa, Ph. D. Section on Behavioral Neuropharmacology Experimental Therapeutics Branch National Institute of Mental Health Building 10 Room 4D11 Bethesda, MD 20892-1375 Lab phone#: 301-496-4838 or 301-496-4839 Lab fax#: 301-480-1164 E-mail tsuyoshi@codon.nih.gov ________________________________________ From nih-image-d-request@io.ece.drexel.edu Sat Oct 10 06:14 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17136; Sat, 10 Oct 1998 06:14:18 -0400 (EDT) Date: Sat, 10 Oct 1998 06:14:18 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810101014.GAA17136@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #85 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/85 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3302 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 85 Today's Topics: Re: area of irregularly shaped ROI [ constance j temm To: schlu@alpha.bio.nat.tu-bs.de Cc: nih-image@io.ece.drexel.edu Subject: Re: area of irregularly shaped ROI Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, There may be quick ways of doing it at image resolution. Roughly, open your ROI in an empty image. Fill your ROI with index 1, get its integrated density. Mathematically: You can find the centroid (C), calculate the area by summing all the triangles ( cross product CP(i) and CP(i+1) i from 1 to N) as you travel along the perimeter. This will handle even if the shape is irregular, if you watch the signs. ( Do not forget to divide everything by 2 at the end). One word of caution, the coordinates that you get from NIH-Image ROI might be off by 1 pixel at some locations. Please refer to earlier discussions about ROI X-Y coordinate corrections. Good Luck. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- On Wed, 7 Oct 1998 frautsch@ucla.edu wrote: > i have macros that compute # and size of cells per unit area using oval or > rectangular ROIs. > > If i draw an irregularly shaped ROI. How do i compute the ROI area? > > Sally > > > Constance J. Temm, Ph.D. University of Arizona Tel.: (520) 621-8643 Nutritional Sciences Dept. Fax: 520 621 1396 632 Shantz Building Tucson, AZ 85721 USA ------------------------------ Date: Fri, 9 Oct 1998 12:36:21 -0400 From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) To: nih-image@io.ece.drexel.edu Subject: 1.62b30 and QT frame Grabber Message-Id: <199810091634.MAA25321@codon.nih.gov> Content-Type: text/plain; charset="ISO-2022-JP" Hi, I am using powerbookG3 and QuickTime compatible frame grabber, PicPomZV. When I was using NIH Image 1.61, I could not do 'start capturing' because of the -2208 error. In version 1.62b30, 'start capturing' works, the live images are perfectly displayed, but 'make movie' does not work well. That is, when I run 'make movie', blank rectangles are displayed while capturing, and relulting stack only contains completely black slices. Has anyone expericed this kind of problem with PicPomZV, or other frame grabbers, using 1.62b30? If yes, any solutions ? Thanks. Tsuyoshi ________________________________________ Tsuyoshi Miyakawa, Ph. D. Section on Behavioral Neuropharmacology Experimental Therapeutics Branch National Institute of Mental Health Building 10 Room 4D11 Bethesda, MD 20892-1375 Lab phone#: 301-496-4838 or 301-496-4839 Lab fax#: 301-480-1164 E-mail tsuyoshi@codon.nih.gov ________________________________________ -------------------------------- End of nih-image-d Digest V98 Issue #85 *************************************** From nih-image-request@io.ece.drexel.edu Mon Oct 12 08:57 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA21587; Mon, 12 Oct 1998 08:57:28 -0400 (EDT) Resent-Date: Mon, 12 Oct 1998 08:57:28 -0400 (EDT) From: srb22@hermes.cam.ac.uk Date: Mon, 12 Oct 1998 13:46:53 +0000 To: nih-image@io.ece.drexel.edu Subject: PCR band quantitation Message-ID: <724841.3117188813@md8mac01.medschl.cam.ac.uk> X-Mailer: Mulberry (MacOS) [1.3.2.2, s/n S-100001] X-Authenticated: srb22 by imap.hermes.cam.ac.uk X-Licensed-To: University of Cambridge MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"AHGIf.0.cc3.PZV8s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/481 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 560 I was hoping someone could tell me how, after obtaining densitometry values for PCR bands using NIH image (eth.bromide gels), I use this information to compare the levels of PCR product between different samples. I wish to first adjust the PCR band densities for the band densities of a housekeeping gene amplified in the same tube. I'm sampling the reaction at 5 different cycles, so both products will have timepoints in the linear range. Thank you very much for any help Yours sincerely Sian Beavan Research Associate Dept Medicine Cambridge University From nih-image-request@io.ece.drexel.edu Mon Oct 12 17:48 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA02463; Mon, 12 Oct 1998 17:48:19 -0400 (EDT) Resent-Date: Mon, 12 Oct 1998 17:48:19 -0400 (EDT) X-Authentication-Warning: phoenix.princeton.edu: huntley owned process doing -bs Date: Mon, 12 Oct 1998 17:31:22 -0400 (EDT) From: "Mark B. Huntley" To: nih-image@io.ece.drexel.edu Subject: Need NUBUS Frame Grabber Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"FQjmo1.0.KU6.7Ld8s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/482 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 181 Looking for NUBUS frame grabber for Mac 8100 (Scion LG-3 or VG-5?). If you have one available, let me know (huntley@princeton.edu) and we'll negotiate a price. Thanks. -Mark From nih-image-d-request@io.ece.drexel.edu Tue Oct 13 06:14 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10814; Tue, 13 Oct 1998 06:14:48 -0400 (EDT) Date: Tue, 13 Oct 1998 06:14:48 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810131014.GAA10814@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #86 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/86 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1733 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 86 Today's Topics: PCR band quantitation [ srb22@hermes.cam.ac.uk ] Need NUBUS Frame Grabber [ "Mark B. Huntley" Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I was hoping someone could tell me how, after obtaining densitometry values for PCR bands using NIH image (eth.bromide gels), I use this information to compare the levels of PCR product between different samples. I wish to first adjust the PCR band densities for the band densities of a housekeeping gene amplified in the same tube. I'm sampling the reaction at 5 different cycles, so both products will have timepoints in the linear range. Thank you very much for any help Yours sincerely Sian Beavan Research Associate Dept Medicine Cambridge University ------------------------------ Date: Mon, 12 Oct 1998 17:31:22 -0400 (EDT) From: "Mark B. Huntley" To: nih-image@io.ece.drexel.edu Subject: Need NUBUS Frame Grabber Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Looking for NUBUS frame grabber for Mac 8100 (Scion LG-3 or VG-5?). If you have one available, let me know (huntley@princeton.edu) and we'll negotiate a price. Thanks. -Mark -------------------------------- End of nih-image-d Digest V98 Issue #86 *************************************** From nih-image-request@io.ece.drexel.edu Tue Oct 13 10:01 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04833; Tue, 13 Oct 1998 10:01:07 -0400 (EDT) Resent-Date: Tue, 13 Oct 1998 10:01:07 -0400 (EDT) Message-Id: In-Reply-To: <199810131015.GAA11106@io.ece.drexel.edu> Mime-Version: 1.0 Date: Tue, 13 Oct 1998 09:43:18 +0300 To: nih-image@io.ece.drexel.edu From: Al Lyckman Subject: unsubscribe me Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA27547 Resent-Message-ID: <"ydecq1.0.vk6.RYr8s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/483 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 378 unsubscribe ...... '''''''''' || || || || || || |||||||||||||||||||||||||||||||||||||||||||||| Alvin W. Lyckman, Ph.D. Massachusetts Institute of Technology Department of Brain & Cognitive Sciences Building E25, Room 235 Cambridge, MA 02139 617.253.8785 lyckman@mit.edu -- Tous je sais sur la moralit et nos devoirs vient du foot, A. Camus -- From nih-image-request@io.ece.drexel.edu Tue Oct 13 11:48 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA14549; Tue, 13 Oct 1998 11:48:10 -0400 (EDT) Resent-Date: Tue, 13 Oct 1998 11:48:10 -0400 (EDT) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Tue, 13 Oct 1998 10:26:23 -0500 From: "Bob Cormier" To: nih-image@io.ece.drexel.edu Subject: LUT Scaling Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA06287 Resent-Message-ID: <"x96AM1.0.dY1.a4t8s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/484 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 361 Hi, Does anyone have any ideas of how to set the lower and upper limits (calibrated values) for a LUT using macro commands. For example, I have a series of real value images that have values ranging from .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another. How can I set the range of the LUT to .1 to 2 with macro commands? Thanks, Bob From nih-image-request@io.ece.drexel.edu Tue Oct 13 15:18 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA04336; Tue, 13 Oct 1998 15:17:58 -0400 (EDT) Resent-Date: Tue, 13 Oct 1998 15:17:58 -0400 (EDT) From: "Andreas Becker" Organization: =?ISO-8859-1?Q?Inst._f._Pharma./_Tox.;_Universit=E4t;_Marbur?= To: nih-image@io.ece.drexel.edu Date: Tue, 13 Oct 1998 20:51:37 +0200 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: confocal laser scanning microscope Reply-to: becker@ps1515.chemie.uni-marburg.de Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.01b) Message-ID: <919F76267@ps1515.chemie.uni-marburg.de> Resent-Message-ID: <"xZgzE2.0.q86.V6w8s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/485 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 334 Our institut is looking for a confocal laser scanning microscope with a UV-laser. Do you now any enterprises which distribute this kind of device. Do you already have any experience with a certain device. Please do not reply to the list. Send email to : becker@ps1515.chemie.uni-marburg.de Thanks for your help Andreas Becker From nih-image-request@io.ece.drexel.edu Wed Oct 14 04:41 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA15493; Wed, 14 Oct 1998 04:41:05 -0400 (EDT) Resent-Date: Wed, 14 Oct 1998 04:41:05 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: cormierb@psychiatry.wustl.edu, nih-image@io.ece.drexel.edu Date: Wed, 14 Oct 1998 18:29:52 GMT+1000 Subject: Re: LUT Scaling Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"lq43H3.0.PU2.a169s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/486 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 5180 >Date: Tue, 13 Oct 1998 10:26:23 -0500 >From: "Bob Cormier" >To: nih-image@io.ece.drexel.edu >Subject: LUT Scaling > >Hi, >Does anyone have any ideas of how to set the lower and upper limits >(calibrated values) for a LUT using macro commands. For example, I have a >series of real value images that have values ranging fr >m .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another. >How can I set the range of the LUT to .1 to 2 with macro commands? >Thanks, >Bob > Bob, Calibration sets the transformation used to convert pixel value to some external unit value. It doesn't directly affect the LUT. macro'calibrate image';var desMax,desMin,min,max:real; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); measure; max:=rMax[rCount];min:=rMin[rCount]; calibrate('Straight', 'xxx',0,desmin,255,desMax); showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax); end will cause the end of the LUT corresponding to pixel value 255 to be desMax external units and 0 end to be desMin external units with linear interpolation. If applied to a REAL-Value image, the real-value maximum and minimum as shown in the Info window or histogram will be calibrated or transformed to the values set by calibration, changing all real values read. For your REAL-Value images, I expect that what you want to achieve is to have the same LUT for each of the images with a common minimum/maximum range. My understanding of NIH-Image support for REAL-Value images is that it doesn't extend that far. NIH-Image carries a REAL-Value image in memory (resulting from image-math etc) and displays an integer version of the real image the LUT of which is scaled so that min<>max = 0<>255. There are some limitations with LUT modifications which arise because 0,255 are used for min/maximum rather than 1,254. (0,255 are reserved for many LUT operations). You can do quite a bit of processing with the real-value image using NIH-Image imageMath and inspect values via Info window and Histogram, save, save as text etc but the visual presentation is actually an integer proxy. 'Duplicate' makes a copy of the scaled integer proxy, so, for intensity-scaled presentation, you could make the integer version of each real by 'duplicate' and then scale the presented intensity by scaling the pixel values of each image. ie multiply by ratio of actual range:desired range; add scaled offset. macro'real image to scaled integer intensity'; var desMax,desMin,min,max:real; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); measure; max:=rMax[rCount];min:=rMin[rCount]; duplicate(windowTitle,'.scaled'); multiplyByConstant((max-min)/(desMax-desMin)); addConstant((min-desMin)/(desMax-desMin)*255); showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax); end Although you would then have the intensities scaled to the real-value of the coresponding real pixel, the image would be a separated integer image proxy and the real-values would not be displayed when you inspect the image by cursor. Another approach which would be better, if processing accomodates it, would be to include (generate) pixels of the desired maximum/minimum in each real image so that the real image and its proxy integer presentation are scaled desirably. eg ensure topleft and adjacent pixels are the desired maximum/minimum real values. This involves the detail of the real image generation. As far as I know, there is no simple way of grafting such values into an existing real image eg by putPixel or paste etc. so that the appropriate values would need to be inserted in processing. The following is more of a sledgehammer approach but achieves the desired result at the expense of some time and 2 pixels of the real image. (provided desMax/desMin are at least equal to max/min). It inserts the desired maximum/minimum real values into the two topleft and adjacent pixels by using masks and scaling via imagemath. macro'scale real image'; var desMax,desMin:real;w,h,p,t,m:integer; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); p:=pidNumber; getPicSize(w,h);setNewSize(w,h); setBackGround(1); makeNewWindow('temp');t:=pidNumber; putPixel(0,0,0); putPixel(1,0,0); imageMath('copy real',t,t,1,0,'mask');m:=pidNumber; imageMath('mul real',p,m,1,0,p); {clears topleft and adjacent pixels} selectPic(t);setBackGround(0);clear;putPixel(0,0,1); imageMath('copy real',t,t,desMax,0,m); imageMath('add real',p,m,1,0,p); {inserts desMax in topleft} if desMin<>0.0 then begin selectPic(t);putPixel(0,0,0);putPixel(1,0,1); imageMath('copy real',t,t,desMin,0,m); imageMath('add real',p,m,1,0,p); {inserts desMin in adjacent topleft} end; selectPic(t);dispose;selectPic(m);dispose;selectPic(p); showMessage('scaled to\',desMin,'<>',desMax); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Wed Oct 14 04:44 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA16824; Wed, 14 Oct 1998 04:44:35 -0400 (EDT) Date: Wed, 14 Oct 1998 04:44:35 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810140844.EAA16824@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #87 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/87 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7992 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 87 Today's Topics: unsubscribe me [ Al Lyckman ] LUT Scaling [ "Bob Cormier" To: nih-image@io.ece.drexel.edu Subject: unsubscribe me Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit unsubscribe ...... '''''''''' || || || || || || |||||||||||||||||||||||||||||||||||||||||||||| Alvin W. Lyckman, Ph.D. Massachusetts Institute of Technology Department of Brain & Cognitive Sciences Building E25, Room 235 Cambridge, MA 02139 617.253.8785 lyckman@mit.edu -- Tous je sais sur la moralit et nos devoirs vient du foot, A. Camus -- ------------------------------ Date: Tue, 13 Oct 1998 10:26:23 -0500 From: "Bob Cormier" To: nih-image@io.ece.drexel.edu Subject: LUT Scaling Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit Hi, Does anyone have any ideas of how to set the lower and upper limits (calibrated values) for a LUT using macro commands. For example, I have a series of real value images that have values ranging from .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another. How can I set the range of the LUT to .1 to 2 with macro commands? Thanks, Bob ------------------------------ Date: Tue, 13 Oct 1998 20:51:37 +0200 From: "Andreas Becker" To: nih-image@io.ece.drexel.edu Subject: confocal laser scanning microscope Message-ID: <919F76267@ps1515.chemie.uni-marburg.de> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Our institut is looking for a confocal laser scanning microscope with a UV-laser. Do you now any enterprises which distribute this kind of device. Do you already have any experience with a certain device. Please do not reply to the list. Send email to : becker@ps1515.chemie.uni-marburg.de Thanks for your help Andreas Becker ------------------------------ Date: Wed, 14 Oct 1998 18:29:52 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: cormierb@psychiatry.wustl.edu, nih-image@io.ece.drexel.edu Subject: Re: LUT Scaling Message-ID: >Date: Tue, 13 Oct 1998 10:26:23 -0500 >From: "Bob Cormier" >To: nih-image@io.ece.drexel.edu >Subject: LUT Scaling > >Hi, >Does anyone have any ideas of how to set the lower and upper limits >(calibrated values) for a LUT using macro commands. For example, I have a >series of real value images that have values ranging fr >m .1 to 1.5 in one image, .2 to 2 in another image, and .18 to 1 in another. >How can I set the range of the LUT to .1 to 2 with macro commands? >Thanks, >Bob > Bob, Calibration sets the transformation used to convert pixel value to some external unit value. It doesn't directly affect the LUT. macro'calibrate image';var desMax,desMin,min,max:real; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); measure; max:=rMax[rCount];min:=rMin[rCount]; calibrate('Straight', 'xxx',0,desmin,255,desMax); showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax); end will cause the end of the LUT corresponding to pixel value 255 to be desMax external units and 0 end to be desMin external units with linear interpolation. If applied to a REAL-Value image, the real-value maximum and minimum as shown in the Info window or histogram will be calibrated or transformed to the values set by calibration, changing all real values read. For your REAL-Value images, I expect that what you want to achieve is to have the same LUT for each of the images with a common minimum/maximum range. My understanding of NIH-Image support for REAL-Value images is that it doesn't extend that far. NIH-Image carries a REAL-Value image in memory (resulting from image-math etc) and displays an integer version of the real image the LUT of which is scaled so that min<>max = 0<>255. There are some limitations with LUT modifications which arise because 0,255 are used for min/maximum rather than 1,254. (0,255 are reserved for many LUT operations). You can do quite a bit of processing with the real-value image using NIH-Image imageMath and inspect values via Info window and Histogram, save, save as text etc but the visual presentation is actually an integer proxy. 'Duplicate' makes a copy of the scaled integer proxy, so, for intensity-scaled presentation, you could make the integer version of each real by 'duplicate' and then scale the presented intensity by scaling the pixel values of each image. ie multiply by ratio of actual range:desired range; add scaled offset. macro'real image to scaled integer intensity'; var desMax,desMin,min,max:real; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); measure; max:=rMax[rCount];min:=rMin[rCount]; duplicate(windowTitle,'.scaled'); multiplyByConstant((max-min)/(desMax-desMin)); addConstant((min-desMin)/(desMax-desMin)*255); showMessage(min,'<>',max,'\scaled to\',desMin,'<>',desMax); end Although you would then have the intensities scaled to the real-value of the coresponding real pixel, the image would be a separated integer image proxy and the real-values would not be displayed when you inspect the image by cursor. Another approach which would be better, if processing accomodates it, would be to include (generate) pixels of the desired maximum/minimum in each real image so that the real image and its proxy integer presentation are scaled desirably. eg ensure topleft and adjacent pixels are the desired maximum/minimum real values. This involves the detail of the real image generation. As far as I know, there is no simple way of grafting such values into an existing real image eg by putPixel or paste etc. so that the appropriate values would need to be inserted in processing. The following is more of a sledgehammer approach but achieves the desired result at the expense of some time and 2 pixels of the real image. (provided desMax/desMin are at least equal to max/min). It inserts the desired maximum/minimum real values into the two topleft and adjacent pixels by using masks and scaling via imagemath. macro'scale real image'; var desMax,desMin:real;w,h,p,t,m:integer; begin desMax:=2; desMin:=.1; desMax:=getNumber('desired Maximum',desMax); desMin:=getNumber('desired Minimum',desMin); p:=pidNumber; getPicSize(w,h);setNewSize(w,h); setBackGround(1); makeNewWindow('temp');t:=pidNumber; putPixel(0,0,0); putPixel(1,0,0); imageMath('copy real',t,t,1,0,'mask');m:=pidNumber; imageMath('mul real',p,m,1,0,p); {clears topleft and adjacent pixels} selectPic(t);setBackGround(0);clear;putPixel(0,0,1); imageMath('copy real',t,t,desMax,0,m); imageMath('add real',p,m,1,0,p); {inserts desMax in topleft} if desMin<>0.0 then begin selectPic(t);putPixel(0,0,0);putPixel(1,0,1); imageMath('copy real',t,t,desMin,0,m); imageMath('add real',p,m,1,0,p); {inserts desMin in adjacent topleft} end; selectPic(t);dispose;selectPic(m);dispose;selectPic(p); showMessage('scaled to\',desMin,'<>',desMax); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #87 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 15 03:50 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09974; Thu, 15 Oct 1998 03:50:23 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 03:50:23 -0400 (EDT) Mime-Version: 1.0 X-Sender: mantv@alf.uib.no Message-Id: Date: Thu, 15 Oct 1998 09:36:38 +0100 To: nih-image@io.ece.drexel.edu From: Therese Visted Subject: nih-image Resent-Message-ID: <"ZscgU3.0.201.ZMQ9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/487 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 215 My efforts in trying to find the latest version of nih-image has not succeeded. Could you please help me in getting that information? Also, how do I get the latest version of nih-image (what url/http/ftp adress)? From nih-image-request@io.ece.drexel.edu Thu Oct 15 03:50 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09948; Thu, 15 Oct 1998 03:50:20 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 03:50:20 -0400 (EDT) Mime-Version: 1.0 X-Sender: mantv@alf.uib.no (Unverified) Message-Id: Date: Thu, 15 Oct 1998 09:41:00 +0100 To: nih-image@io.ece.drexel.edu From: Therese Visted Subject: nih-image Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id DAA05640 Resent-Message-ID: <"zaJvJ3.0.TO1.ZQQ9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/488 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 370 My efforts in trying to find the latest version of nih-image has not succeeded. Could you please help me in getting that information? Also, how do I get the latest version of nih-image (what url/http/ftp adress)? Thank you! Therese Visted Institutt for Anatomi og Cellebiologi rstadveien 19 5009 Bergen tlf:55-586373 fax:55-586360 e-mail:therese.visted@pki.uib.no From nih-image-request@io.ece.drexel.edu Thu Oct 15 05:23 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13636; Thu, 15 Oct 1998 05:23:32 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 05:23:32 -0400 (EDT) Message-Id: <199810150906.GAA02006@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: nih-image Date: Thu, 15 Oct 1998 06:10:26 -0300 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Resent-Message-ID: <"dlbfe2.0.862.5mR9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/489 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 692 Dear Therese, you can find ScionImage (NIH) in this adress: http//:www.scioncorp.com I hope this help Regards, Rejane ---------- > De: Therese Visted > Para: nih-image@io.ece.drexel.edu > Assunto: nih-image > Data: Quinta-feira, 15 de Outubro de 1998 05:41 > > > My efforts in trying to find the latest version of nih-image has not succeeded. > Could you please help me in getting that information? > Also, how do I get the latest version of nih-image (what url/http/ftp adress)? > Thank you! > Therese Visted > > Institutt for Anatomi og Cellebiologi > rstadveien 19 > 5009 Bergen > > tlf:55-586373 > fax:55-586360 > > e-mail:therese.visted@pki.uib.no > From nih-image-request@io.ece.drexel.edu Thu Oct 15 05:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA24669; Thu, 15 Oct 1998 05:53:45 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 05:53:45 -0400 (EDT) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 15 Oct 1998 11:41:41 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: nih-image Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id FAA19966 Resent-Message-ID: <"Ra2AB2.0.Nu4.1DS9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/490 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1055 >My efforts in trying to find the latest version of nih-image has not >succeeded. >Could you please help me in getting that information? >Also, how do I get the latest version of nih-image (what url/http/ftp adress)? >Thank you! >Therese Visted > >Institutt for Anatomi og Cellebiologi >rstadveien 19 >5009 Bergen > >tlf:55-586373 >fax:55-586360 > >e-mail:therese.visted@pki.uib.no http://rsb.info.nih.gov/nih-image/ Jeg bruker programmet svrt mye s du kan ringe eller maile om det er noe du lurer p. Jeg bruker Mac versjonen. PC versjonen er full av feil og bugs. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Thu Oct 15 12:03 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA05877; Thu, 15 Oct 1998 12:02:40 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 12:02:40 -0400 (EDT) Date: Thu, 15 Oct 1998 16:32:15 +0100 From: Ranjan Kumar Patro Subject: DT- Image In-reply-to: X-Sender: 9698842p@bodkin.ucg.ie (Unverified) To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 References: Resent-Message-ID: <"5VKk71.0.Ll6.TSX9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/491 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 772 Hello Every body!! I am trying to capture the image by DT board. Does any body know, where can I get the DT-IMAGE software from internt or by FTP. Thank you in advance. Ranjan ***************************************************** *Ranjan Kumar Patro * *Dept. Of Oceanography * *Martin Ryan Institute of Marine Sciences * *National University of Ireland, Galway * *Ireland. * * Voic: ++353 91 524411, Xt: 3208 * * Fax: ++353 91 528302 * *E-mail: ranjan.patro@ucg.ie * * Web: http://www.angelfire.com/ri/rpatro* ******************************************************* From nih-image-request@io.ece.drexel.edu Thu Oct 15 17:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03052; Thu, 15 Oct 1998 17:09:40 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 17:09:40 -0400 (EDT) Subject: Frame Grabber Date: Thu, 15 Oct 98 16:49:02 -0400 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: "anyone" Mime-Version: 1.0 Message-ID: <2A4E40E154B@qc1.qc.edu> Resent-Message-ID: <"apETW1.0.wB.e_b9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/492 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 195 please give me name, address (snailmail or web), phone # of manufacturer of scion video card; also of other high resolution videocards. FOR MAC ONLY. many thanks in advance for information. From nih-image-request@io.ece.drexel.edu Thu Oct 15 17:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03305; Thu, 15 Oct 1998 17:10:45 -0400 (EDT) Resent-Date: Thu, 15 Oct 1998 17:10:45 -0400 (EDT) Subject: Re: Need NUBUS Frame Grabber Date: Thu, 15 Oct 98 16:50:31 -0400 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: "anyone" Mime-Version: 1.0 Message-ID: <2A4EA244E65@qc1.qc.edu> Resent-Message-ID: <"CiIXu.0.UE.p0c9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/493 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 55 please give me name,address,phone for manufacturer of From nih-image-d-request@io.ece.drexel.edu Fri Oct 16 06:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24499; Fri, 16 Oct 1998 06:22:06 -0400 (EDT) Date: Fri, 16 Oct 1998 06:22:06 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810161022.GAA24499@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #88 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/88 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6174 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 88 Today's Topics: nih-image [ Therese Visted To: nih-image@io.ece.drexel.edu Subject: nih-image Message-Id: Content-Type: text/plain; charset="us-ascii" My efforts in trying to find the latest version of nih-image has not succeeded. Could you please help me in getting that information? Also, how do I get the latest version of nih-image (what url/http/ftp adress)? ------------------------------ Date: Thu, 15 Oct 1998 09:41:00 +0100 From: Therese Visted To: nih-image@io.ece.drexel.edu Subject: nih-image Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit My efforts in trying to find the latest version of nih-image has not succeeded. Could you please help me in getting that information? Also, how do I get the latest version of nih-image (what url/http/ftp adress)? Thank you! Therese Visted Institutt for Anatomi og Cellebiologi rstadveien 19 5009 Bergen tlf:55-586373 fax:55-586360 e-mail:therese.visted@pki.uib.no ------------------------------ Date: Thu, 15 Oct 1998 06:10:26 -0300 From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: nih-image Message-Id: <199810150906.GAA02006@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear Therese, you can find ScionImage (NIH) in this adress: http//:www.scioncorp.com I hope this help Regards, Rejane ---------- > De: Therese Visted > Para: nih-image@io.ece.drexel.edu > Assunto: nih-image > Data: Quinta-feira, 15 de Outubro de 1998 05:41 > > > My efforts in trying to find the latest version of nih-image has not succeeded. > Could you please help me in getting that information? > Also, how do I get the latest version of nih-image (what url/http/ftp adress)? > Thank you! > Therese Visted > > Institutt for Anatomi og Cellebiologi > rstadveien 19 > 5009 Bergen > > tlf:55-586373 > fax:55-586360 > > e-mail:therese.visted@pki.uib.no > ------------------------------ Date: Thu, 15 Oct 1998 11:41:41 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: nih-image Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit >My efforts in trying to find the latest version of nih-image has not >succeeded. >Could you please help me in getting that information? >Also, how do I get the latest version of nih-image (what url/http/ftp adress)? >Thank you! >Therese Visted > >Institutt for Anatomi og Cellebiologi >rstadveien 19 >5009 Bergen > >tlf:55-586373 >fax:55-586360 > >e-mail:therese.visted@pki.uib.no http://rsb.info.nih.gov/nih-image/ Jeg bruker programmet svrt mye s du kan ringe eller maile om det er noe du lurer p. Jeg bruker Mac versjonen. PC versjonen er full av feil og bugs. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Thu, 15 Oct 1998 16:32:15 +0100 From: Ranjan Kumar Patro To: nih-image@io.ece.drexel.edu Subject: DT- Image Message-id: Content-type: text/plain; charset="us-ascii" Hello Every body!! I am trying to capture the image by DT board. Does any body know, where can I get the DT-IMAGE software from internt or by FTP. Thank you in advance. Ranjan ***************************************************** *Ranjan Kumar Patro * *Dept. Of Oceanography * *Martin Ryan Institute of Marine Sciences * *National University of Ireland, Galway * *Ireland. * * Voic: ++353 91 524411, Xt: 3208 * * Fax: ++353 91 528302 * *E-mail: ranjan.patro@ucg.ie * * Web: http://www.angelfire.com/ri/rpatro* ******************************************************* ------------------------------ Date: Thu, 15 Oct 98 16:49:02 -0400 From: "Jared L. Rifkin" To: "anyone" Subject: Frame Grabber Message-ID: <2A4E40E154B@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" please give me name, address (snailmail or web), phone # of manufacturer of scion video card; also of other high resolution videocards. FOR MAC ONLY. many thanks in advance for information. ------------------------------ Date: Thu, 15 Oct 98 16:50:31 -0400 From: "Jared L. Rifkin" To: "anyone" Subject: Re: Need NUBUS Frame Grabber Message-ID: <2A4EA244E65@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" please give me name,address,phone for manufacturer of -------------------------------- End of nih-image-d Digest V98 Issue #88 *************************************** From nih-image-request@io.ece.drexel.edu Fri Oct 16 06:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA01851; Fri, 16 Oct 1998 06:53:47 -0400 (EDT) Resent-Date: Fri, 16 Oct 1998 06:53:47 -0400 (EDT) Message-ID: <01BDF8F8.D61A2F20.t.morris@co.umist.ac.uk> From: Tim Morris Reply-To: "t.morris@co.umist.ac.uk" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: DT-Image Date: Fri, 16 Oct 1998 11:33:45 +0100 Organization: UMIST X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"29f-T2.0.tg6.Q4o9s"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/494 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 630 Ranjan, et al. I'm using the DT3155 at present. The useful software came with it. But we also had problems setting up the board correctly, our local distributors were very helpful (sending us updated software etc), and so was the DT website: www.datx.com Tim. --------------------------------------------------------------------------------- Dr Tim Morris Dept of Computation, UMIST, PO Box 88 Manchester, M60 1QD, UK tel: 0161 200 3376 fax: 0161 200 3300 http://www.ap.co.umist.ac.uk/~dtm/IP1.html --------------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Fri Oct 16 16:37 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19970; Fri, 16 Oct 1998 16:37:24 -0400 (EDT) Resent-Date: Fri, 16 Oct 1998 16:37:24 -0400 (EDT) X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs Date: Fri, 16 Oct 1998 16:11:34 -0400 (EDT) From: Randy Cutter To: nih-image@io.ece.drexel.edu cc: nih-image-d@io.ece.drexel.edu Subject: Object-Image: deleting objects, not entire cells In-Reply-To: <199810021551.LAA02635@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"4ZxNE2.0.C_1.TYw9s"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/495 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 621 When using Object-Image, is there a way to delete individual objects within a cell? There are macro commands SelectCell, SelectObject, DeleteCell, but apparently no DeleteObject. Is there a way around this, because if a cell contains multiple objects, and a mistake is made upon an object, once the cell is closed, apparently the whole cell must be deleted if only one object needs to be. Thanks, Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- From nih-image-d-request@io.ece.drexel.edu Sat Oct 17 06:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA18246; Sat, 17 Oct 1998 06:09:31 -0400 (EDT) Date: Sat, 17 Oct 1998 06:09:31 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810171009.GAA18246@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #89 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/89 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2326 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 89 Today's Topics: RE: DT-Image [ Tim Morris ] ------------------------------ Date: Fri, 16 Oct 1998 11:33:45 +0100 From: Tim Morris To: "'nih-image@io.ece.drexel.edu'" Subject: RE: DT-Image Message-ID: <01BDF8F8.D61A2F20.t.morris@co.umist.ac.uk> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Ranjan, et al. I'm using the DT3155 at present. The useful software came with it. But we also had problems setting up the board correctly, our local distributors were very helpful (sending us updated software etc), and so was the DT website: www.datx.com Tim. --------------------------------------------------------------------------------- Dr Tim Morris Dept of Computation, UMIST, PO Box 88 Manchester, M60 1QD, UK tel: 0161 200 3376 fax: 0161 200 3300 http://www.ap.co.umist.ac.uk/~dtm/IP1.html --------------------------------------------------------------------------------- ------------------------------ Date: Fri, 16 Oct 1998 16:11:34 -0400 (EDT) From: Randy Cutter To: nih-image@io.ece.drexel.edu cc: nih-image-d@io.ece.drexel.edu Subject: Object-Image: deleting objects, not entire cells Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII When using Object-Image, is there a way to delete individual objects within a cell? There are macro commands SelectCell, SelectObject, DeleteCell, but apparently no DeleteObject. Is there a way around this, because if a cell contains multiple objects, and a mistake is made upon an object, once the cell is closed, apparently the whole cell must be deleted if only one object needs to be. Thanks, Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- -------------------------------- End of nih-image-d Digest V98 Issue #89 *************************************** From nih-image-request@io.ece.drexel.edu Sat Oct 17 08:03 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA29593; Sat, 17 Oct 1998 08:03:02 -0400 (EDT) Resent-Date: Sat, 17 Oct 1998 08:03:02 -0400 (EDT) Date: Sat, 17 Oct 1998 08:50:00 -0300 (ADT) X-Sender: rhawkes@mailserv.mta.ca Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: rhawkes@mta.ca (Robert Hawkes) Subject: looking for fast 25 mm C mount lens Resent-Message-ID: <"mVOnM.0.B16.jH8As"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/496 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 647 I am sorry if this is not directly an NIH Image posting, but we desperately need to find a source of fast 25 mm C mount lens which can deliver in the next 10 days. Preferably, Fujinon C25L (25 mm /f0.85). All of our regular suppliers have these backordered by Fujinon for end November, and we need to ship them for use in a meteor field campaign in Mongolia much earlier than that. Any suggestions, those who might have one to sell, etc. directly to me at rhawkes@mta.ca would be appreciated. We certainly would consider used lenses, if in good condition. Bob Hawkes rhawkes@mta.ca Physics, Mount Allison University Sackville, NB Canada From nih-image-request@io.ece.drexel.edu Sat Oct 17 09:41 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA04997; Sat, 17 Oct 1998 09:41:05 -0400 (EDT) Resent-Date: Sat, 17 Oct 1998 09:41:05 -0400 (EDT) Message-ID: <3628A94B.D7A183D3@netmatters.co.uk> Date: Sat, 17 Oct 1998 14:27:30 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk Organization: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Advise on a commercial product References: Content-Transfer-Encoding: 8bit Resent-Message-ID: <"zfDtx3.0.G6.Lk9As"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/497 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1101 Hello all, Sorry to bother you with a non-Image related question but, Has anyone ever come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at the University here is considering purchasing a set-up from them (38 000: Camera, Z-Focus control, Mac, Software, No Microscope or objectives). Improvision are claiming that their software can produce con focal images from a standard fluorescent or white light source by mathematical de-convolution of a z series of standard images to discard the out of focus information in much the same way as the optics of a con focal would. To me it sounds possible, but I can not imagine that it would be as good as the real thing. They are not giving the module that performs this function away as a demo, for obvious reasons if it really works. Any thoughts on the plausibility of this? Many Thanks in advance, Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Sat Oct 17 16:47 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA27069; Sat, 17 Oct 1998 16:47:19 -0400 (EDT) Resent-Date: Sat, 17 Oct 1998 16:47:19 -0400 (EDT) Message-ID: <001f01bdfa0e$2263e4a0$LocalHost@MSN/rchristie> From: "rchristie" To: Subject: BioRad 1024 z-series Date: Sat, 17 Oct 1998 16:38:43 -0400 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2120.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 Resent-Message-ID: <"aIg_u1.0.WK5.6zFAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/498 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 418 I've been using NIH-image to manipulate stacks generated by a BioRad 1024 confocal system. They are easy enough to open up and play with, but I'm wondering if anyone has seen a macro to re-save the stack in the BioRad format, with the header appropriately modified. Any help would be appreciated, Rich Christie rchristie@msn.com Alzheimer's Research CNY 6320 Massachusetts General Hospital Charlestown, MA 02129 From nih-image-d-request@io.ece.drexel.edu Sun Oct 18 06:22 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA00210; Sun, 18 Oct 1998 06:22:11 -0400 (EDT) Date: Sun, 18 Oct 1998 06:22:11 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810181022.GAA00210@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #90 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/90 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3519 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 90 Today's Topics: looking for fast 25 mm C mount lens [ rhawkes@mta.ca (Robert Hawkes) ] Advise on a commercial product [ Jeremy Brown Content-Type: text/plain; charset="us-ascii" I am sorry if this is not directly an NIH Image posting, but we desperately need to find a source of fast 25 mm C mount lens which can deliver in the next 10 days. Preferably, Fujinon C25L (25 mm /f0.85). All of our regular suppliers have these backordered by Fujinon for end November, and we need to ship them for use in a meteor field campaign in Mongolia much earlier than that. Any suggestions, those who might have one to sell, etc. directly to me at rhawkes@mta.ca would be appreciated. We certainly would consider used lenses, if in good condition. Bob Hawkes rhawkes@mta.ca Physics, Mount Allison University Sackville, NB Canada ------------------------------ Date: Sat, 17 Oct 1998 14:27:30 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Advise on a commercial product Message-ID: <3628A94B.D7A183D3@netmatters.co.uk> Content-Type: text/plain; charset=iso-8859-1; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 8bit Hello all, Sorry to bother you with a non-Image related question but, Has anyone ever come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at the University here is considering purchasing a set-up from them (38 000: Camera, Z-Focus control, Mac, Software, No Microscope or objectives). Improvision are claiming that their software can produce con focal images from a standard fluorescent or white light source by mathematical de-convolution of a z series of standard images to discard the out of focus information in much the same way as the optics of a con focal would. To me it sounds possible, but I can not imagine that it would be as good as the real thing. They are not giving the module that performs this function away as a demo, for obvious reasons if it really works. Any thoughts on the plausibility of this? Many Thanks in advance, Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Sat, 17 Oct 1998 16:38:43 -0400 From: "rchristie" To: Subject: BioRad 1024 z-series Message-ID: <001f01bdfa0e$2263e4a0$LocalHost@MSN/rchristie> I've been using NIH-image to manipulate stacks generated by a BioRad 1024 confocal system. They are easy enough to open up and play with, but I'm wondering if anyone has seen a macro to re-save the stack in the BioRad format, with the header appropriately modified. Any help would be appreciated, Rich Christie rchristie@msn.com Alzheimer's Research CNY 6320 Massachusetts General Hospital Charlestown, MA 02129 -------------------------------- End of nih-image-d Digest V98 Issue #90 *************************************** From nih-image-request@io.ece.drexel.edu Sun Oct 18 08:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA08228; Sun, 18 Oct 1998 08:09:19 -0400 (EDT) Resent-Date: Sun, 18 Oct 1998 08:09:19 -0400 (EDT) Date: Sun, 18 Oct 1998 12:52:15 +0100 (BST) From: Jan Kreft X-Sender: sabjk@thor To: Jeremy Brown cc: nih-image@io.ece.drexel.edu Subject: Re: Advise on a commercial product In-Reply-To: <3628A94B.D7A183D3@netmatters.co.uk> Message-ID: X-MIME-Autoconverted: from 8bit to quoted-printable by thor.cf.ac.uk id MAA26117 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id HAA02239 Resent-Message-ID: <"GSKPH1.0.uZ.wQTAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/499 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/PLAIN; charset="ISO-8859-1" Content-Length: 1717 Dear Jeremy, I came across XCosm recently. It seems to do the same job and is for free (runs on XWindow under Unix/Linux). At least you can ask the developers of this software what they think about charging 38 000 pounds sterling for Open Lab. Have a look at: www.ibc.wustl.edu/bcl/xcosm Hope this helps, Jan. Dr. Jan-Ulrich Kreft Phone +44 (0)1222 874000 ext. 6036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Sat, 17 Oct 1998, Jeremy Brown wrote: > Hello all, > > Sorry to bother you with a non-Image related question but, Has anyone ever > come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at > the University here is considering purchasing a set-up from them (38 000: > Camera, Z-Focus control, Mac, Software, No Microscope or objectives). > Improvision are claiming that their software can produce con focal images from a > standard fluorescent or white light source by mathematical de-convolution of a z > series of standard images to discard the out of focus information in much the > same way as the optics of a con focal would. To me it sounds possible, but I can > not imagine that it would be as good as the real thing. They are not giving the > module that performs this function away as a demo, for obvious reasons if it > really works. Any > thoughts on the plausibility of this? > > Many Thanks in advance, > > Jeremy > > > > ************************************************ > Jeremy Brown > Edinburgh University/Moredun Research Institute > http://www.netmatters.co.uk/users/brownj/HomePage.html > ************************************************ > > > > > From nih-image-request@io.ece.drexel.edu Sun Oct 18 09:01 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27153; Sun, 18 Oct 1998 09:01:15 -0400 (EDT) Resent-Date: Sun, 18 Oct 1998 09:01:15 -0400 (EDT) Message-Id: <199810181241.JAA23172@ceiun01.elogica.com.br> From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: nih-image Date: Sun, 18 Oct 1998 09:17:48 -0200 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Resent-Message-ID: <"5gVxQ3.0.a85.DBUAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/500 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 644 Dear Therese, did you try http://www.scioncorp.com Good luck, Rejane ---------- > De: Therese Visted > Para: nih-image@io.ece.drexel.edu > Assunto: nih-image > Data: Quinta-feira, 15 de Outubro de 1998 06:41 > > > My efforts in trying to find the latest version of nih-image has not succeeded. > Could you please help me in getting that information? > Also, how do I get the latest version of nih-image (what url/http/ftp adress)? > Thank you! > Therese Visted > > Institutt for Anatomi og Cellebiologi > rstadveien 19 > 5009 Bergen > > tlf:55-586373 > fax:55-586360 > > e-mail:therese.visted@pki.uib.no > From nih-image-request@io.ece.drexel.edu Sun Oct 18 19:24 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA17207; Sun, 18 Oct 1998 19:24:39 -0400 (EDT) Resent-Date: Sun, 18 Oct 1998 19:24:39 -0400 (EDT) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Deleting Objects Date: Sun, 18 Oct 1998 23:07:59 +0000 Resent-Message-ID: <"TxxQ12.0.4U2.MJdAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/501 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1018 >When using Object-Image, is there a way to delete individual objects >within a cell? There are macro commands SelectCell, SelectObject, >DeleteCell, but apparently no DeleteObject. Is there a way around this, >because if a cell contains multiple objects, and a mistake is made upon an >object, once the cell is closed, apparently the whole cell must be deleted >if only one object needs to be. This is indeed something which needs to be improved in Object-Image. Meanwhile, you can use the macro command OpenCell(n), which opens the specified cell so you can add more markers, or delete them with the backspace key. However, you only can delete them sequentially from back to front. So you can highlight a cell with the select tool (Finger cursor, now on the extended part of the tools window) and then issue macro 'Open cell'; begin OpenCell(SelectedCell); ShowCell(SelectedCell); end; The cell number of the cell which is open appears in italic. Note that you need the newest version. Norbert Vischer From nih-image-d-request@io.ece.drexel.edu Mon Oct 19 06:17 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA22186; Mon, 19 Oct 1998 06:17:58 -0400 (EDT) Date: Mon, 19 Oct 1998 06:17:58 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810191017.GAA22186@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #91 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/91 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5236 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 91 Today's Topics: Re: Advise on a commercial product [ Jan Kreft ] Re: nih-image [ "=?ISO-8859-1?Q?Rejane_Magalh=E3es_ ] Re: Deleting Objects [ Norbert Vischer To: Jeremy Brown cc: nih-image@io.ece.drexel.edu Subject: Re: Advise on a commercial product Message-ID: Content-type: text/PLAIN; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear Jeremy, I came across XCosm recently. It seems to do the same job and is for free (runs on XWindow under Unix/Linux). At least you can ask the developers of this software what they think about charging 38 000 pounds sterling for Open Lab. Have a look at: www.ibc.wustl.edu/bcl/xcosm Hope this helps, Jan. Dr. Jan-Ulrich Kreft Phone +44 (0)1222 874000 ext. 6036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Sat, 17 Oct 1998, Jeremy Brown wrote: > Hello all, > > Sorry to bother you with a non-Image related question but, Has anyone ever > come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at > the University here is considering purchasing a set-up from them (38 000: > Camera, Z-Focus control, Mac, Software, No Microscope or objectives). > Improvision are claiming that their software can produce con focal images from a > standard fluorescent or white light source by mathematical de-convolution of a z > series of standard images to discard the out of focus information in much the > same way as the optics of a con focal would. To me it sounds possible, but I can > not imagine that it would be as good as the real thing. They are not giving the > module that performs this function away as a demo, for obvious reasons if it > really works. Any > thoughts on the plausibility of this? > > Many Thanks in advance, > > Jeremy > > > > ************************************************ > Jeremy Brown > Edinburgh University/Moredun Research Institute > http://www.netmatters.co.uk/users/brownj/HomePage.html > ************************************************ > > > > > ------------------------------ Date: Sun, 18 Oct 1998 09:17:48 -0200 From: "=?ISO-8859-1?Q?Rejane_Magalh=E3es_Pimentel_Galindo?=" To: Subject: Re: nih-image Message-Id: <199810181241.JAA23172@ceiun01.elogica.com.br> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear Therese, did you try http://www.scioncorp.com Good luck, Rejane ---------- > De: Therese Visted > Para: nih-image@io.ece.drexel.edu > Assunto: nih-image > Data: Quinta-feira, 15 de Outubro de 1998 06:41 > > > My efforts in trying to find the latest version of nih-image has not succeeded. > Could you please help me in getting that information? > Also, how do I get the latest version of nih-image (what url/http/ftp adress)? > Thank you! > Therese Visted > > Institutt for Anatomi og Cellebiologi > rstadveien 19 > 5009 Bergen > > tlf:55-586373 > fax:55-586360 > > e-mail:therese.visted@pki.uib.no > ------------------------------ Date: Sun, 18 Oct 1998 23:07:59 +0000 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Deleting Objects Message-Id: Content-Type: text/plain; charset="us-ascii" >When using Object-Image, is there a way to delete individual objects >within a cell? There are macro commands SelectCell, SelectObject, >DeleteCell, but apparently no DeleteObject. Is there a way around this, >because if a cell contains multiple objects, and a mistake is made upon an >object, once the cell is closed, apparently the whole cell must be deleted >if only one object needs to be. This is indeed something which needs to be improved in Object-Image. Meanwhile, you can use the macro command OpenCell(n), which opens the specified cell so you can add more markers, or delete them with the backspace key. However, you only can delete them sequentially from back to front. So you can highlight a cell with the select tool (Finger cursor, now on the extended part of the tools window) and then issue macro 'Open cell'; begin OpenCell(SelectedCell); ShowCell(SelectedCell); end; The cell number of the cell which is open appears in italic. Note that you need the newest version. Norbert Vischer ------------------------------ Date: Mon, 19 Oct 98 08:53:13 +0930 From: cbrown@medicine.adelaide.edu.au To: Subject: unsubscribe Message-Id: <9810199087.AA908754606@usbnt01.itd.adelaide.edu.au> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit unsubscribe -------------------------------- End of nih-image-d Digest V98 Issue #91 *************************************** From nih-image-request@io.ece.drexel.edu Mon Oct 19 08:37 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA10469; Mon, 19 Oct 1998 08:37:46 -0400 (EDT) Resent-Date: Mon, 19 Oct 1998 08:37:46 -0400 (EDT) Message-Id: <199810191215.HAA45524@mail1.doit.wisc.edu> X-Sender: kvogt@facstaff.wisc.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Date: Mon, 19 Oct 1998 07:11:07 -0500 To: nih-image@io.ece.drexel.edu From: Kevin Vogt Subject: Re: nih-image-d Digest V98 #88 Resent-Message-ID: <"HrJD11.0.sg.XroAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/502 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 185 Hello, I have been using gelReader with the nih-image and am having trouble generating a report when calibrating MW standards. Does anyone know how this can be fixed? Kevin From nih-image-request@io.ece.drexel.edu Mon Oct 19 11:26 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA06680; Mon, 19 Oct 1998 11:26:04 -0400 (EDT) Resent-Date: Mon, 19 Oct 1998 11:26:04 -0400 (EDT) Message-ID: <362B523A.6DF1D5CB@sdsc.edu> Date: Mon, 19 Oct 1998 07:52:42 -0700 From: "Harvey J. Karten" Reply-To: hjkarten@UCSD.EDU Organization: UCSD X-Mailer: Mozilla 4.04 [en] (Win95; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Advice on a Commercial Product References: <199810191015.GAA21214@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ebBDi1.0.sk6.kFrAs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/503 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2631 Jeremy Brown inquired about a deconvolution package for 38,000 English Pounds I estimate this to be equal to about $64,000 in U.S. dollars. This didn't include microscope, motorized stage z-axis, objectives, etc. Deconvolution is said to be a useful adjunct to confocal. But if you want a serious assessment, test out how long it would take to collect the data, then how long to process the data to generate a series of images. Ask about the flexibility of the system relative to confocal. Amongst other things, you will find that the time required to generate a deconvolution image can run to hours of time. This same information is rapidly available with confocal in a matter of seconds. Since the procedures are different, there is a different mix of acquisition time and processing time. There are a whole range of other issues, including the type of camera you use for acquiring the deconvolution images (8 bit, 12 bit or 16 bit?), the method of obtaining uniform illumination (scanning laser spot beats a mercury burner in every measure for uniformity, though can't give a real time image to the user. ) Finally, I suggest that you check out the Olympus Confocal microscope system. We recently have bought several of them at our university. The price, including microscope, objectives, fluorescent attachment, Nomarski optics, z-axis motor, computer, scanning module, control box, filter set, and computer, was about $100,000. We bought thelaser directly from Melles Griot for $8,300 (Argon-Krypton 50 RYB laser). You may be able to negotiate a still better deal, depending upon the effectiveness of your negotiating ability. I don't work for Olympus, but we use their equipment, and I strongly believe that a low price helps advance the technology. Their unit is equal in image quality to the very expensive Zeiss 510. Obviously, the Zeiss will give you more bells and whistles for $330,000, but I can whistle my own tune for $230,000 savings. Oh, another advantage - you can easily convert the Olympus to a two photon unit if you happen to have the money for the necessary laser. There are many benefits to the two photon imaging, which are simply completely unavailable if you have sunk all you money into a deconvolution system. Hope this helps. Harvey Karten -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org From nih-image-request@io.ece.drexel.edu Mon Oct 19 12:55 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06768; Mon, 19 Oct 1998 12:55:08 -0400 (EDT) Resent-Date: Mon, 19 Oct 1998 12:55:08 -0400 (EDT) From: SolamereTG@aol.com Message-ID: Date: Mon, 19 Oct 1998 12:24:06 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Advice on a Commercial Product Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"Ed2cN3.0._V6.wVsAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/504 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1108 I would like to re-iterate Dr. Karten's statement about speed but also mention another commercially available Confocal, CSU-100 Dual Nipkow Disk attachment that will work with any microscope, and works well with NIH image. (Yes, we do sell it in North America, Applied Imaging sells it in Europe). The image quality in tests at the City of Hope Medical Center showed the image quality is equal to those made by a Zeiss confocal. The speed is <4 msec per complete scan & can be sync'ed to video and used with any low light camera ICCD, cooled, integrating CCD. The confocal sells for $65,000 USD. If you have a microscope then you would need a laser ($6500 to 8500), and a camera ($3,500 to $26,750). A video rate confocal system that can run on NIH Image without the need of a full time staff would be under $96,000 and can be moved from microscope to microscope. I apologize to those who may view this as too commercial but we are discussing what the available alternatives are. Please respond to me directly at Solameretg@aol.com Dr. George A. Peeters Solamere Technology Group Salt Lake City, Utah From nih-image-request@io.ece.drexel.edu Mon Oct 19 14:19 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA05859; Mon, 19 Oct 1998 14:19:28 -0400 (EDT) Resent-Date: Mon, 19 Oct 1998 14:19:28 -0400 (EDT) Date: Mon, 19 Oct 1998 13:26:04 -0400 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Re: Advice on a Commercial Product (pseudoconfocal imaging) Resent-Message-ID: <"yD3UE3.0.3E7.butAs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/505 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1030 I think the method of reconstructing images by deconvolution is well accepted. The images are crisp and impressive. I'm less clear about how to be sure the parameters for deconvolution are properly set to be accurate at less than a micron resolution. Scanalytics' Cellscan (Windows) is a commercial package for pseudo-confocal imaging. A collaborator down the hall uses it and is satisfied. Image reconstruction takes a long time on fast computers (see Karten's email), but if it can be fit in between experiments, is "cheap". I'm told that the current version is packaged in IPLab. "Scanalytics, Inc.creates scientific image processing software and gel analysis systems for Apple Macintosh, Windows 95 and Windows NT 4.0 --http://www.iplab.com/" Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 From nih-image-d-request@io.ece.drexel.edu Tue Oct 20 06:16 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA16579; Tue, 20 Oct 1998 06:16:09 -0400 (EDT) Date: Tue, 20 Oct 1998 06:16:09 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810201016.GAA16579@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #92 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/92 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7228 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 92 Today's Topics: Unidentified subject! [ "Dan Frich" ] Re: nih-image-d Digest V98 #88 [ Kevin Vogt To: nih-image-d@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: <852566A2.003F1AF3.00@nsns-h01.arcochem.com> Content-type: text/plain; charset=us-ascii I was wondering if anyone had any idea how I could correct oversegmentation when using the watershed function in v 1.61? Thanks, Dan Frich cscdjf@arcochem.com ------------------------------ Date: Mon, 19 Oct 1998 07:11:07 -0500 From: Kevin Vogt To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #88 Message-Id: <199810191215.HAA45524@mail1.doit.wisc.edu> Content-Type: text/plain; charset="us-ascii" Hello, I have been using gelReader with the nih-image and am having trouble generating a report when calibrating MW standards. Does anyone know how this can be fixed? Kevin ------------------------------ Date: Mon, 19 Oct 1998 07:52:42 -0700 From: "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: Re: Advice on a Commercial Product Message-ID: <362B523A.6DF1D5CB@sdsc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jeremy Brown inquired about a deconvolution package for 38,000 English Pounds I estimate this to be equal to about $64,000 in U.S. dollars. This didn't include microscope, motorized stage z-axis, objectives, etc. Deconvolution is said to be a useful adjunct to confocal. But if you want a serious assessment, test out how long it would take to collect the data, then how long to process the data to generate a series of images. Ask about the flexibility of the system relative to confocal. Amongst other things, you will find that the time required to generate a deconvolution image can run to hours of time. This same information is rapidly available with confocal in a matter of seconds. Since the procedures are different, there is a different mix of acquisition time and processing time. There are a whole range of other issues, including the type of camera you use for acquiring the deconvolution images (8 bit, 12 bit or 16 bit?), the method of obtaining uniform illumination (scanning laser spot beats a mercury burner in every measure for uniformity, though can't give a real time image to the user. ) Finally, I suggest that you check out the Olympus Confocal microscope system. We recently have bought several of them at our university. The price, including microscope, objectives, fluorescent attachment, Nomarski optics, z-axis motor, computer, scanning module, control box, filter set, and computer, was about $100,000. We bought thelaser directly from Melles Griot for $8,300 (Argon-Krypton 50 RYB laser). You may be able to negotiate a still better deal, depending upon the effectiveness of your negotiating ability. I don't work for Olympus, but we use their equipment, and I strongly believe that a low price helps advance the technology. Their unit is equal in image quality to the very expensive Zeiss 510. Obviously, the Zeiss will give you more bells and whistles for $330,000, but I can whistle my own tune for $230,000 savings. Oh, another advantage - you can easily convert the Olympus to a two photon unit if you happen to have the money for the necessary laser. There are many benefits to the two photon imaging, which are simply completely unavailable if you have sunk all you money into a deconvolution system. Hope this helps. Harvey Karten -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org ------------------------------ Date: Mon, 19 Oct 1998 12:24:06 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Advice on a Commercial Product Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit I would like to re-iterate Dr. Karten's statement about speed but also mention another commercially available Confocal, CSU-100 Dual Nipkow Disk attachment that will work with any microscope, and works well with NIH image. (Yes, we do sell it in North America, Applied Imaging sells it in Europe). The image quality in tests at the City of Hope Medical Center showed the image quality is equal to those made by a Zeiss confocal. The speed is <4 msec per complete scan & can be sync'ed to video and used with any low light camera ICCD, cooled, integrating CCD. The confocal sells for $65,000 USD. If you have a microscope then you would need a laser ($6500 to 8500), and a camera ($3,500 to $26,750). A video rate confocal system that can run on NIH Image without the need of a full time staff would be under $96,000 and can be moved from microscope to microscope. I apologize to those who may view this as too commercial but we are discussing what the available alternatives are. Please respond to me directly at Solameretg@aol.com Dr. George A. Peeters Solamere Technology Group Salt Lake City, Utah ------------------------------ Date: Mon, 19 Oct 1998 13:26:04 -0400 From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Re: Advice on a Commercial Product (pseudoconfocal imaging) Message-Id: Content-Type: text/plain; charset="us-ascii" I think the method of reconstructing images by deconvolution is well accepted. The images are crisp and impressive. I'm less clear about how to be sure the parameters for deconvolution are properly set to be accurate at less than a micron resolution. Scanalytics' Cellscan (Windows) is a commercial package for pseudo-confocal imaging. A collaborator down the hall uses it and is satisfied. Image reconstruction takes a long time on fast computers (see Karten's email), but if it can be fit in between experiments, is "cheap". I'm told that the current version is packaged in IPLab. "Scanalytics, Inc.creates scientific image processing software and gel analysis systems for Apple Macintosh, Windows 95 and Windows NT 4.0 --http://www.iplab.com/" Henry M. Thomas, III MD (Harry) Professor of Clinical Medicine, Pulmonary and Critical Care Division Department of Medicine, Cornell Univ. Medical School Director, Pulmonary Research, Burke Rehabilitation Hospital 785 Mamaroneck Ave. White Plains, NY 10605 (914) 597-2141 -------------------------------- End of nih-image-d Digest V98 Issue #92 *************************************** From nih-image-request@io.ece.drexel.edu Tue Oct 20 08:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27212; Tue, 20 Oct 1998 08:12:11 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 08:12:11 -0400 (EDT) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: interior measurements Message-ID: Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"so6H3.0.kF5.8g7Bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/506 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 480 Whilst there are many automated procedures for measuring the size of an object and the space it takes up, does anyone have a macro or method for measuring the largest ellipse, rectangle or other regular object(not constrained to horizontal and vertical axis) that can fill the interior of an irregular ROI? Thanks in advance, Jenny Gregory ---------------------- Jenny Gregory Department of Orthopaedics University of Aberdeen Aberdeen Scotland j.gregory@abdn.ac.uk From nih-image-request@io.ece.drexel.edu Tue Oct 20 08:58 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA13075; Tue, 20 Oct 1998 08:58:45 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 08:58:45 -0400 (EDT) Message-ID: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1> From: "Baron, Paul A." To: "'nih-image@io.ece.drexel.edu'" Subject: Advise on a commercial product Date: Tue, 20 Oct 1998 08:39:58 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id IAA07023 Resent-Message-ID: <"pnQiC2.0.-j1.GJ8Bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/507 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1559 I looked at a similar product that appeared to work from a company called Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone 515 472 2227 Fax 515 472 8131. This was several years ago and I don't even know if they are still in business. Paul Baron NIOSH MS R7 4676 Columbia Parkway Cincinnati OH 45226 Phone: 513 841 4278 Fax: 513 841 4500 Email: pab2@cdc.gov Hello all, Sorry to bother you with a non-Image related question but, Has anyone ever come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at the University here is considering purchasing a set-up from them (38 000: Camera, Z-Focus control, Mac, Software, No Microscope or objectives). Improvision are claiming that their software can produce con focal images from a standard fluorescent or white light source by mathematical de-convolution of a z series of standard images to discard the out of focus information in much the same way as the optics of a con focal would. To me it sounds possible, but I can not imagine that it would be as good as the real thing. They are not giving the module that performs this function away as a demo, for obvious reasons if it really works. Any thoughts on the plausibility of this? Many Thanks in advance, Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ : Advise on a commercial product >> << Message: BioRad 1024 z-series >> From nih-image-request@io.ece.drexel.edu Tue Oct 20 10:00 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02817; Tue, 20 Oct 1998 10:00:01 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 10:00:01 -0400 (EDT) Date: Tue, 20 Oct 1998 07:41:53 -0600 (CST) From: "Geoffrey D. Guttmann" To: "'nih-image@io.ece.drexel.edu'" cc: Paul Baron Subject: Re: Advise on a commercial product In-Reply-To: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Xg445.0.wX6.cC9Bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/508 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1351 Hi folks >I looked at a similar product that appeared to work from a company called >Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone >515 472 2227 Fax 515 472 8131. This was several years ago and I don't even >know if they are still in business. > >Paul Baron The answer is Vaytek is very much alive. I just checked their website. Below is a contact and address: Chris MacLean, Ph.D. VayTek, Inc. 305 West. Lowe, Suite 109 P.O. Box 732 Fairfield, Iowa, 52556-0732 Tel: 515-472-2227 ext.105 Fax: 515-472-8131 E-Mail: cmaclean@vaytek.com Web: www.vaytek.com Their product has done well on the PowerMac. Cheers, geoff ------------------------------------------------------------------------ Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ Assistant Professor _/ _/ _/ _/ _/ _/ Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ University of Saskatchewan _/ _/ _/ _/ _/ _/ A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ Saskatoon, SK S7N 5E5 CANADA Voice:(306)966-4079 Fax:(306)966-4298 E-mail:guttmann@duke.usask.ca ------------------------------------------------------------------------ From nih-image-request@io.ece.drexel.edu Tue Oct 20 17:06 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA29747; Tue, 20 Oct 1998 17:06:19 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 17:06:19 -0400 (EDT) Message-Id: Mime-Version: 1.0 Date: Tue, 20 Oct 1998 16:36:34 -0500 To: nih-image@io.ece.drexel.edu From: Joaquim Garrabou Subject: Labelling patches Resent-Message-ID: <"z7x2W3.0.oY4.IHFBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/509 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 685 Hello everybody, I have to measure polygons (patches) in several images. I've been looking at the measure procedures in NIH image and I've realized that NIH automatically labels all patches or alternativelly you can point go patch by patch and obtain the measurament. But in either case, one obtain a sequence of numbers as patch labels. I'd like to introduce my own labels pointing at the different patches (e.g. e23 or a12) during the measuring process. Is that possible with NIH? Thanks for all Joaquim Garrabou Joaquim Garrabou Dpt. of Zoology University of Maryland at College Park College Park MD 20742 Voice: 301-405 8021 Fax: 301-314 9358 e-mail: garrabou@wam.umd.edu From nih-image-request@io.ece.drexel.edu Tue Oct 20 18:46 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05316; Tue, 20 Oct 1998 18:46:16 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 18:46:16 -0400 (EDT) Date: Tue, 20 Oct 1998 15:28:33 -0700 (PDT) Message-Id: <199810202228.PAA11829@franc.ucdavis.edu> X-Sender: ez075141@peseta.ucdavis.edu (Unverified) X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: "Jason A. Melvin" Subject: Analysis of Genomic Fingerprints Resent-Message-ID: <"a4nee.0.N87.9xGBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/510 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 410 Does anyone use IMAGE to analyze genomic DNA fingerprints? I would like to know how to generate relative mobility values as well as compare lanes within one gel to lanes within another gel. Any suggestions would be appreciated. Jason Jason A. Melvin USDA/ARS Dept. Plant Pathology University of California One Shields Ave. Davis, CA 95616 tel: 530-752-8679 fax: 530-752-5674 email: jamelvin@ucdavis.edu From nih-image-request@io.ece.drexel.edu Tue Oct 20 22:10 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA19575; Tue, 20 Oct 1998 22:10:00 -0400 (EDT) Resent-Date: Tue, 20 Oct 1998 22:10:00 -0400 (EDT) From: wpchan@socrates.berkeley.edu Date: Tue, 20 Oct 1998 18:52:49 -0700 (PDT) To: nih-image@io.ece.drexel.edu Subject: video capture at 30 fps In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"KRzwV1.0.7H3.1wJBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/511 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 444 Recently we have bought a Scion LG3 PCI card to put in a Windows NT. The highest capture rate that we can get with 'blind capture' in 'make movie' is 17 fps. Scion Tech support confirmed that this is probably the highest one can get on a NT. Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and if so, under what condition and using what kind of computer? Thanks. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) From nih-image-request@io.ece.drexel.edu Wed Oct 21 05:28 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13295; Wed, 21 Oct 1998 05:28:12 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 05:28:12 -0400 (EDT) Message-ID: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it> From: "Eugenio Amendola" To: Subject: epoxy resin morphology Date: Wed, 21 Oct 1998 11:15:42 +0200 MIME-Version: 1.0 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"gpEUF2.0.MR1.GMQBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/512 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="----=_NextPart_000_00F0_01BDFCE4.24992040" Content-Length: 3352 This is a multi-part message in MIME format. ------=_NextPart_000_00F0_01BDFCE4.24992040 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Imagers, I would like to ask for some help on the following issue: I'm performing morphological analysis on mixtures of two different epoxy = resins, a Shell product and a liquid crystalline epoxy resin synthesized = in our labs. The mixture, after curing, is optically transparent. The = composition range of mixtures spans from 0 to 100%. We are interested in characterizing the phase separation, because the = high thoughness of the samples could be correlated with a complex = structure. However, we are unable to detect any definite structural = feature. Can someone suggest some staining or etching tecnique suitable to = differentiate between an amourphous and a liquid crystalline epoxy resin = in the cured sample. The sample is rigid at room temperature. TIA in advance to every one, and congratulation for the job that you are running. Eugenio=20 -------------------------------------------------------------------------= ------ Dr. Eugenio Amendola Institute of Composite Materials Technology C.N.R. P.le Tecchio 80 80125 Naples, ITALY Tel: (+) 39 81 768 2511 Fax: (+) 39 81 768 2404 e-mail: amendola@unina.it ------=_NextPart_000_00F0_01BDFCE4.24992040 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello Imagers,
I would like = to ask for some=20 help on the following issue:
I'm performing morphological analysis on mixtures of = two=20 different epoxy resins, a Shell product and a liquid crystalline epoxy = resin=20 synthesized in our labs. The mixture, after curing, is optically = transparent.=20 The composition range of mixtures spans from 0 to 100%.
We are interested in characterizing the phase = separation,=20 because the high thoughness of the samples could be correlated with a = complex=20 structure. However, we are unable to detect any definite structural=20 feature.
Can someone suggest some staining or etching = tecnique suitable=20 to differentiate between an amourphous and a liquid crystalline epoxy = resin in=20 the cured sample. The sample is rigid at room temperature.
TIA in advance to every one,
and congratulation for the job that you are=20 running.
Eugenio 
----------------------------------------------------------------= ---------------
Dr.=20 Eugenio Amendola
Institute of Composite Materials=20 Technology
C.N.R.
P.le Tecchio 80
80125 Naples, ITALY
Tel: = (+) 39 81=20 768 2511
Fax: (+) 39 81 768 2404
e-mail: amendola@unina.it
------=_NextPart_000_00F0_01BDFCE4.24992040-- From nih-image-d-request@io.ece.drexel.edu Wed Oct 21 05:28 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA13431; Wed, 21 Oct 1998 05:28:26 -0400 (EDT) Date: Wed, 21 Oct 1998 05:28:26 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810210928.FAA13431@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #93 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/93 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11269 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 93 Today's Topics: interior measurements [ "j.gregory" ] Advise on a commercial product [ "Baron, Paul A." ] Re: Advise on a commercial product [ "Geoffrey D. Guttmann" To: nih-image@io.ece.drexel.edu Subject: interior measurements Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Whilst there are many automated procedures for measuring the size of an object and the space it takes up, does anyone have a macro or method for measuring the largest ellipse, rectangle or other regular object(not constrained to horizontal and vertical axis) that can fill the interior of an irregular ROI? Thanks in advance, Jenny Gregory ---------------------- Jenny Gregory Department of Orthopaedics University of Aberdeen Aberdeen Scotland j.gregory@abdn.ac.uk ------------------------------ Date: Tue, 20 Oct 1998 08:39:58 -0400 From: "Baron, Paul A." To: "'nih-image@io.ece.drexel.edu'" Subject: Advise on a commercial product Message-ID: <75AC0E50AB70D111830700A02461F8E2655B0D@MCDC-CIN-1> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit I looked at a similar product that appeared to work from a company called Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone 515 472 2227 Fax 515 472 8131. This was several years ago and I don't even know if they are still in business. Paul Baron NIOSH MS R7 4676 Columbia Parkway Cincinnati OH 45226 Phone: 513 841 4278 Fax: 513 841 4500 Email: pab2@cdc.gov Hello all, Sorry to bother you with a non-Image related question but, Has anyone ever come across a Mac imaging package called Open Lab 2.0 by Improvision. Someone at the University here is considering purchasing a set-up from them (38 000: Camera, Z-Focus control, Mac, Software, No Microscope or objectives). Improvision are claiming that their software can produce con focal images from a standard fluorescent or white light source by mathematical de-convolution of a z series of standard images to discard the out of focus information in much the same way as the optics of a con focal would. To me it sounds possible, but I can not imagine that it would be as good as the real thing. They are not giving the module that performs this function away as a demo, for obvious reasons if it really works. Any thoughts on the plausibility of this? Many Thanks in advance, Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ : Advise on a commercial product >> << Message: BioRad 1024 z-series >> ------------------------------ Date: Tue, 20 Oct 1998 07:41:53 -0600 (CST) From: "Geoffrey D. Guttmann" To: "'nih-image@io.ece.drexel.edu'" cc: Paul Baron Subject: Re: Advise on a commercial product Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks >I looked at a similar product that appeared to work from a company called >Vay-Tek, 305 West Lowe, Suite 109, PO Box 732, Fairfield Iowa 52556 Phone >515 472 2227 Fax 515 472 8131. This was several years ago and I don't even >know if they are still in business. > >Paul Baron The answer is Vaytek is very much alive. I just checked their website. Below is a contact and address: Chris MacLean, Ph.D. VayTek, Inc. 305 West. Lowe, Suite 109 P.O. Box 732 Fairfield, Iowa, 52556-0732 Tel: 515-472-2227 ext.105 Fax: 515-472-8131 E-Mail: cmaclean@vaytek.com Web: www.vaytek.com Their product has done well on the PowerMac. Cheers, geoff ------------------------------------------------------------------------ Geoffrey D. Guttmann, Ph.D _/_/_/_/ _/_/ _/_/_/_/ _/ _/ Assistant Professor _/ _/ _/ _/ _/ _/ Dept. of Anatomy and Cell Biology _/ _/ _/ _/ _/ College of Medicine _/_/_/_/ _/_/_/_/ _/_/_/_/ _/_/ University of Saskatchewan _/ _/ _/ _/ _/ _/ A-315 Health Sciences Building _/ _/ _/ _/ _/ _/ 107 Wiggins Road _/_/_/_/ _/ _/ _/_/_/_/ _/ _/ _/ Saskatoon, SK S7N 5E5 CANADA Voice:(306)966-4079 Fax:(306)966-4298 E-mail:guttmann@duke.usask.ca ------------------------------------------------------------------------ ------------------------------ Date: Tue, 20 Oct 1998 16:36:34 -0500 From: Joaquim Garrabou To: nih-image@io.ece.drexel.edu Subject: Labelling patches Message-Id: Content-Type: text/plain; charset="us-ascii" Hello everybody, I have to measure polygons (patches) in several images. I've been looking at the measure procedures in NIH image and I've realized that NIH automatically labels all patches or alternativelly you can point go patch by patch and obtain the measurament. But in either case, one obtain a sequence of numbers as patch labels. I'd like to introduce my own labels pointing at the different patches (e.g. e23 or a12) during the measuring process. Is that possible with NIH? Thanks for all Joaquim Garrabou Joaquim Garrabou Dpt. of Zoology University of Maryland at College Park College Park MD 20742 Voice: 301-405 8021 Fax: 301-314 9358 e-mail: garrabou@wam.umd.edu ------------------------------ Date: Tue, 20 Oct 1998 15:28:33 -0700 (PDT) From: "Jason A. Melvin" To: nih-image@io.ece.drexel.edu Subject: Analysis of Genomic Fingerprints Message-Id: <199810202228.PAA11829@franc.ucdavis.edu> Content-Type: text/plain; charset="us-ascii" Does anyone use IMAGE to analyze genomic DNA fingerprints? I would like to know how to generate relative mobility values as well as compare lanes within one gel to lanes within another gel. Any suggestions would be appreciated. Jason Jason A. Melvin USDA/ARS Dept. Plant Pathology University of California One Shields Ave. Davis, CA 95616 tel: 530-752-8679 fax: 530-752-5674 email: jamelvin@ucdavis.edu ------------------------------ Date: Tue, 20 Oct 1998 18:52:49 -0700 (PDT) From: wpchan@socrates.berkeley.edu To: nih-image@io.ece.drexel.edu Subject: video capture at 30 fps Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Recently we have bought a Scion LG3 PCI card to put in a Windows NT. The highest capture rate that we can get with 'blind capture' in 'make movie' is 17 fps. Scion Tech support confirmed that this is probably the highest one can get on a NT. Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and if so, under what condition and using what kind of computer? Thanks. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) ------------------------------ Date: Wed, 21 Oct 1998 11:15:42 +0200 From: "Eugenio Amendola" To: Subject: epoxy resin morphology Message-ID: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it> Content-Type: multipart/alternative; boundary="----=_NextPart_000_00F0_01BDFCE4.24992040" This is a multi-part message in MIME format. ------=_NextPart_000_00F0_01BDFCE4.24992040 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Imagers, I would like to ask for some help on the following issue: I'm performing morphological analysis on mixtures of two different epoxy = resins, a Shell product and a liquid crystalline epoxy resin synthesized = in our labs. The mixture, after curing, is optically transparent. The = composition range of mixtures spans from 0 to 100%. We are interested in characterizing the phase separation, because the = high thoughness of the samples could be correlated with a complex = structure. However, we are unable to detect any definite structural = feature. Can someone suggest some staining or etching tecnique suitable to = differentiate between an amourphous and a liquid crystalline epoxy resin = in the cured sample. The sample is rigid at room temperature. TIA in advance to every one, and congratulation for the job that you are running. Eugenio=20 -------------------------------------------------------------------------= ------ Dr. Eugenio Amendola Institute of Composite Materials Technology C.N.R. P.le Tecchio 80 80125 Naples, ITALY Tel: (+) 39 81 768 2511 Fax: (+) 39 81 768 2404 e-mail: amendola@unina.it ------=_NextPart_000_00F0_01BDFCE4.24992040 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello Imagers,
I would like = to ask for some=20 help on the following issue:
I'm performing morphological analysis on mixtures of = two=20 different epoxy resins, a Shell product and a liquid crystalline epoxy = resin=20 synthesized in our labs. The mixture, after curing, is optically = transparent.=20 The composition range of mixtures spans from 0 to 100%.
We are interested in characterizing the phase = separation,=20 because the high thoughness of the samples could be correlated with a = complex=20 structure. However, we are unable to detect any definite structural=20 feature.
Can someone suggest some staining or etching = tecnique suitable=20 to differentiate between an amourphous and a liquid crystalline epoxy = resin in=20 the cured sample. The sample is rigid at room temperature.
TIA in advance to every one,
and congratulation for the job that you are=20 running.
Eugenio 
----------------------------------------------------------------= ---------------
Dr.=20 Eugenio Amendola
Institute of Composite Materials=20 Technology
C.N.R.
P.le Tecchio 80
80125 Naples, ITALY
Tel: = (+) 39 81=20 768 2511
Fax: (+) 39 81 768 2404
e-mail: amendola@unina.it
------=_NextPart_000_00F0_01BDFCE4.24992040-- -------------------------------- End of nih-image-d Digest V98 Issue #93 *************************************** From nih-image-request@io.ece.drexel.edu Wed Oct 21 08:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA21826; Wed, 21 Oct 1998 08:09:06 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 08:09:06 -0400 (EDT) X-Sender: cgustafs@ece.drexel.edu Message-Id: In-Reply-To: <00f301bdfcd3$6185ce60$99efe18f@amendola.unina.it> Mime-Version: 1.0 Date: Wed, 21 Oct 1998 07:59:21 -0400 To: nih-image@io.ece.drexel.edu From: Carl Gustafson Subject: Re: epoxy resin morphology Resent-Message-ID: <"UATK3.0.Xu3.ajSBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/513 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1047 ... >However, we are unable to detect any definite structural feature. Can >someone suggest some staining or etching tecnique suitable to >differentiate between an amourphous and a liquid crystalline epoxy resin >in the cured sample. ... Will some solvent swell the amorphous phase and not the crystalline one? Are there any substituents on one phase and not on the other that can be substitued with something that can be made to absorb light differently? It's been years since I did Real Chemistry. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== From nih-image-request@io.ece.drexel.edu Wed Oct 21 15:42 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA13324; Wed, 21 Oct 1998 15:42:54 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 15:42:54 -0400 (EDT) From: SolamereTG@aol.com Message-ID: <9b16cd57.362e3253@aol.com> Date: Wed, 21 Oct 1998 15:13:23 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: video capture at 30 fps Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"p_9N51.0._W6.IAZBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/514 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 348 We use blind capture with 266 and 300 Mhz G-3 desktop models to capture at 30 fps to system Ram. The LG-3 board you have should be able to go into a G-3 and do the same. I would borrow a G-3 MAC and try it out. You may still use NT but you may need to capture an ROI rather than the full 640x480 image. George Peeters Solamere Technology Group From nih-image-request@io.ece.drexel.edu Wed Oct 21 16:28 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA08968; Wed, 21 Oct 1998 16:28:31 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 16:28:31 -0400 (EDT) Date: Wed, 21 Oct 1998 16:02:11 -0400 (EDT) From: Cengizhan Ozturk X-Sender: cozturk@henryv To: nih-image@io.ece.drexel.edu Subject: Colorcamera info needed In-Reply-To: <9b16cd57.362e3253@aol.com> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"svp7I2.0.Rx5.StZBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/515 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 651 Hi, I need a fast color CCD camera for a machine vision/inspection type of application. I am at least 1 year behind what is the latest in the market. Anybody has done a recent search ? Can anybody give some pointers, web pages. Please send industrial responses directly to me by e-mail or fax (with prices) My system will be a matrox capture board housed in a PC. Thanks. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- From nih-image-request@io.ece.drexel.edu Wed Oct 21 19:15 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA15175; Wed, 21 Oct 1998 19:15:29 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 19:15:29 -0400 (EDT) Message-ID: <362E04FB.EE@dri.edu> Date: Wed, 21 Oct 1998 16:00:05 +0000 From: Pat Arnott Reply-To: pat@dri.edu Organization: Desert Research Institute X-Mailer: Mozilla 3.0-C-AICK1-2 (Macintosh; U; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #93 References: <199810210928.FAA13290@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"0JvKz.0.OU.yMcBs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/516 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 818 Hi: We loaded our lg3 with maximum memory and were able to digitize frames to card ram at 30 fps on any of our macs (8100 av, g3). We could do this within the memory available in RAM. I have also used the g3 av to digitize at 30 fps using adobe premier as the software, and the built in video card on the mac. However, the images are smaller than with the scion board, and you do not have control of the digitizer offset and gain like with the scion card. -- Regards, Pat Arnott ********************************************************** * W. Patrick Arnott 702-677-3123 -3157 fax * Atmospheric Sciences Center, Desert Research Institute * PO Box 60220, RENO NV 89506 * http://www.dri.edu/Projects/replica/webWPA ********************************************************** From nih-image-request@io.ece.drexel.edu Wed Oct 21 20:54 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA09940; Wed, 21 Oct 1998 20:54:33 -0400 (EDT) Resent-Date: Wed, 21 Oct 1998 20:54:33 -0400 (EDT) Message-ID: From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: Data from FFT's Date: Thu, 22 Oct 1998 10:36:41 +1000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"XIYNN3.0.pe.tudBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/517 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 2025 Hi, We are using NIH-Image to measure the spacings of groups of striations observed on fracture surfaces. The procedure is as follows using the FFT Macros. Open or display an Image, which is spatially calibrated in microns or mm. Select the size of square area to be used, Operator decision. Position the square over the selected group of striations. Type F (FFT). (This is now so quick on a G3-300 that it is no longer the slowest operation) Look at the Transform and position the cursor over one of the two distinct peaks which appear on each side of the centre. Read the value in the info window which tells about cycles per mm (Or micron), and also give the angle this makes with the x axis. Write down the numbers and proceed to the next place. My question is: Can I get this data into a macro so I don't have to write it down? I see it is written in the info window, so it is there, how do I get it into user1 and user2? I spent some time reading the manual and could find nothing. I could have a look at the source code, but thought I would ask first. I guess this is a measurement which does not yet appear as an option in the measurements option dialog, and may have to be added. What I would propose is maybe a mouse click at the desired location to record these parameters. But I really have no strong feelings about how to do this job. After all I am relying on a user decision about the location of the maximum peak on the transform. For really precise work I suppose we should fit up some 3-D surfaces across the peak and estimate the peak maximum position, or fit up some 2-d curves across and up and down to try to locate the maximum. Of course when you look at the scatter you get when measuring striations all of this precision becomes academic. The spacing will vary by a factor of 2 or more over a range of very small distances, and the only way you get good data is by getting lots of numbers. And doing it by using the FFT allows the accumulation of many measurements, quickly. Best regards Noel. From nih-image-request@io.ece.drexel.edu Thu Oct 22 04:08 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA12202; Thu, 22 Oct 1998 04:08:38 -0400 (EDT) Resent-Date: Thu, 22 Oct 1998 04:08:38 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu Date: Thu, 22 Oct 1998 18:00:50 GMT+1000 Subject: Re: Data from FFT's Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"J78My3.0.I_1.zLkBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/518 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3255 >From: "Goldsmith, Noel" >To: "'Image Mailing List'" >Subject: Data from FFT's >Date: Thu, 22 Oct 1998 10:36:41 +1000 > >Hi, >We are using NIH-Image to measure the spacings of groups of striations >observed on fracture surfaces. >The procedure is as follows using the FFT Macros. >Open or display an Image, which is spatially calibrated in microns or mm. >Select the size of square area to be used, Operator decision. >Position the square over the selected group of striations. >Type F (FFT). (This is now so quick on a G3-300 that it is no longer the >slowest operation) >Look at the Transform and position the cursor over one of the two distinct >peaks which appear on each side of the centre. >Read the value in the info window which tells about cycles per mm (Or >micron), and also give the angle this makes with the x axis. >Write down the numbers and proceed to the next place. > > >My question is: >Can I get this data into a macro so I don't have to write it down? >I see it is written in the info window, so it is there, how do I get it into >user1 and user2? > >I spent some time reading the manual and could find nothing. I could have a >look at the source code, but thought I would ask first. >I guess this is a measurement which does not yet appear as an option in the >measurements option dialog, and may have to be added. >What I would propose is maybe a mouse click at the desired location to >record these parameters. But I really have no strong feelings about how to >do this job. >After all I am relying on a user decision about the location of the maximum >peak on the transform. For really precise work I suppose we should fit up >some 3-D surfaces across the peak and estimate the peak maximum position, or >fit up some 2-d curves across and up and down to try to locate the maximum. >Of course when you look at the scatter you get when measuring striations all >of this precision becomes academic. The spacing will vary by a factor of 2 >or more over a range of very small distances, and the only way you get good >data is by getting lots of numbers. And doing it by using the FFT allows the >accumulation of many measurements, quickly. >Best regards >Noel. > Noel, the FFT window is essentially a spatially scaled image with the origin central and using polar coordinates, so the following macro will mimic the Info window values: Place the cursor in the FFT window and press [t] to demonstrate. macro'[t]est'; var x,y,c,w,h,scale,AspectRatio,xs,ys,r,theta:integer; unit:string;begin invertY(false); getPicSize(w,h);w:=w/2; getScale(scale,unit,AspectRatio); getMouse(x,y);c:=getPixel(x,y); xs:=x-w; ys:=w-y; if ys=0 then if xs>0 then theta:=0 else theta :=180 else theta:=90-arcTan(xs/ys)*45/arcTan(1); if ys<0 then theta:=theta+180; r:=sqrt(sqr(xs)+sqr(ys)); if r=0 then r:=999999 else r:=h/r; showMessage(x,y,c ,'\',(x-w),-(y-w) ,'\',xs,' ',ys ,'\',scale,unit,AspectRatio ,'\\r: ',r/scale,unit,' /c (',xs:4:0 ,')\theta: ',theta,' (',ys:4:0 ,')\Value:',c:4:0 ); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Thu Oct 22 04:12 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA13690; Thu, 22 Oct 1998 04:12:24 -0400 (EDT) Resent-Date: Thu, 22 Oct 1998 04:12:24 -0400 (EDT) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: ort056@abdn.ac.uk, nih-image@io.ece.drexel.edu Date: Thu, 22 Oct 1998 18:05:26 GMT+1000 Subject: Re: interior measurements Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"2sbyl3.0.0P2.MQkBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/519 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2173 >From: "j.gregory" >Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST) > > >Whilst there are many automated procedures for measuring the size of an object >and the space it takes up, does anyone have a macro or method for measuring >the largest ellipse, rectangle or other regular object(not constrained to >horizontal and >vertical axis) that can fill the interior of an irregular ROI? > >Thanks in advance, > >Jenny Gregory > >---------------------- >Jenny Gregory >Department of Orthopaedics >University of Aberdeen >Aberdeen >Scotland Jenny, your problem specs seem a little too unconstrained to me :-) , however, in the absence of other responses, the following may be of some interest. _________________________ macro'/0 maximum internal circle of a roi'; var x,y,w,h,d,i,mi,r,xm,xx:integer; begin getRoi(x,y,w,h); if w=0 then exit('selection required'); copy; d:=trunc(sqrt(sqr(w)+sqr(h))+0.5); if (d mod 2)=0 then d:=d+3 else d:=d+2; setForeGround(255);setBackGround(0); setNewSize(d,d); makeNewWindow('circle');paste;fill; binary('edm'); enhanceContrast; resetCounter; measure; r:=rMax[rcount]; showMessage('maximum enclosed circle radius',r); setDensitySlice(r-1,r); setOptions('Area X-Y Center Min/Max Major Minor Angle'); analyzeParticles(''); undo; mi:=2; for i:=2 to rCount do if rArea[i]>rArea[mi] then mi:=i; selectAll;copy; makeOvalRoi(rX[mi]-r,rY[mi]-r,r+r,r+r);drawBoundary; if rArea[mi]>3 then begin SetScaling('Same Window Bilinear'{Nearest'}); makeNewWindow('extend?'); selectAll; y:=trunc(d/2)+1; moveRoi(d/2-rX[mi],d/2-rY[mi]);paste;selectAll; scaleAndRotate(1,1,rAngle[mi]); y:=trunc(d/2)+1; getRow(0,y,d); x:=y;while lineBuffer[x]>=r-1 do x:=x-1;xm:=x+1; x:=y;while lineBuffer[x]>=r-1 do x:=x+1;xx:=x-1; makeOvalRoi(xm-r,y-r,r+r,r+r);drawBoundary; makeOvalRoi(xx-r,y-r,r+r,r+r);drawBoundary; makeRoi(xm,y-r,xx-xm+1,r+r);drawBoundary; showMessage(r,y,xm,xx); tileWindows; end; end _________________________ Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Thu Oct 22 04:15 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA14727; Thu, 22 Oct 1998 04:15:15 -0400 (EDT) Date: Thu, 22 Oct 1998 04:15:15 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810220815.EAA14727@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #94 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/94 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10544 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 94 Today's Topics: Re: epoxy resin morphology [ Carl Gustafson ] Data from FFT's [ "Goldsmith, Noel" To: nih-image@io.ece.drexel.edu Subject: Re: epoxy resin morphology Message-Id: Content-Type: text/plain; charset="us-ascii" ... >However, we are unable to detect any definite structural feature. Can >someone suggest some staining or etching tecnique suitable to >differentiate between an amourphous and a liquid crystalline epoxy resin >in the cured sample. ... Will some solvent swell the amorphous phase and not the crystalline one? Are there any substituents on one phase and not on the other that can be substitued with something that can be made to absorb light differently? It's been years since I did Real Chemistry. Carl Gustafson (215) 895-1383 =============================================================================== the Computer Vision Center for Vertebrate Brain Mapping =============================================================================== Imaging and Computer Vision Center | Software Guy Drexel University | Macintosh spoken here Philadelphia, Pennsylvania | I'd like to give you my opinion =============================================================================== ------------------------------ Date: Wed, 21 Oct 1998 15:13:23 EDT From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: video capture at 30 fps Message-ID: <9b16cd57.362e3253@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit We use blind capture with 266 and 300 Mhz G-3 desktop models to capture at 30 fps to system Ram. The LG-3 board you have should be able to go into a G-3 and do the same. I would borrow a G-3 MAC and try it out. You may still use NT but you may need to capture an ROI rather than the full 640x480 image. George Peeters Solamere Technology Group ------------------------------ Date: Wed, 21 Oct 1998 16:02:11 -0400 (EDT) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Colorcamera info needed Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I need a fast color CCD camera for a machine vision/inspection type of application. I am at least 1 year behind what is the latest in the market. Anybody has done a recent search ? Can anybody give some pointers, web pages. Please send industrial responses directly to me by e-mail or fax (with prices) My system will be a matrox capture board housed in a PC. Thanks. -------------------------------------------- Cengizhan Ozturk cozturk@mri.jhu.edu http://www.mri.jhu.edu/~cozturk Medical Imaging Laboratory Johns Hopkins University Phone: (410)614 5292 / (410)502 6905 Fax: (410)-502 6915 -------------------------------------------- ------------------------------ Date: Wed, 21 Oct 1998 16:00:05 +0000 From: Pat Arnott To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #93 Message-ID: <362E04FB.EE@dri.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi: We loaded our lg3 with maximum memory and were able to digitize frames to card ram at 30 fps on any of our macs (8100 av, g3). We could do this within the memory available in RAM. I have also used the g3 av to digitize at 30 fps using adobe premier as the software, and the built in video card on the mac. However, the images are smaller than with the scion board, and you do not have control of the digitizer offset and gain like with the scion card. -- Regards, Pat Arnott ********************************************************** * W. Patrick Arnott 702-677-3123 -3157 fax * Atmospheric Sciences Center, Desert Research Institute * PO Box 60220, RENO NV 89506 * http://www.dri.edu/Projects/replica/webWPA ********************************************************** ------------------------------ Date: Thu, 22 Oct 1998 10:36:41 +1000 From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: Data from FFT's Message-ID: Content-Type: text/plain Hi, We are using NIH-Image to measure the spacings of groups of striations observed on fracture surfaces. The procedure is as follows using the FFT Macros. Open or display an Image, which is spatially calibrated in microns or mm. Select the size of square area to be used, Operator decision. Position the square over the selected group of striations. Type F (FFT). (This is now so quick on a G3-300 that it is no longer the slowest operation) Look at the Transform and position the cursor over one of the two distinct peaks which appear on each side of the centre. Read the value in the info window which tells about cycles per mm (Or micron), and also give the angle this makes with the x axis. Write down the numbers and proceed to the next place. My question is: Can I get this data into a macro so I don't have to write it down? I see it is written in the info window, so it is there, how do I get it into user1 and user2? I spent some time reading the manual and could find nothing. I could have a look at the source code, but thought I would ask first. I guess this is a measurement which does not yet appear as an option in the measurements option dialog, and may have to be added. What I would propose is maybe a mouse click at the desired location to record these parameters. But I really have no strong feelings about how to do this job. After all I am relying on a user decision about the location of the maximum peak on the transform. For really precise work I suppose we should fit up some 3-D surfaces across the peak and estimate the peak maximum position, or fit up some 2-d curves across and up and down to try to locate the maximum. Of course when you look at the scatter you get when measuring striations all of this precision becomes academic. The spacing will vary by a factor of 2 or more over a range of very small distances, and the only way you get good data is by getting lots of numbers. And doing it by using the FFT allows the accumulation of many measurements, quickly. Best regards Noel. ------------------------------ Date: Thu, 22 Oct 1998 18:00:50 GMT+1000 From: GJOSS@rna.bio.mq.edu.au To: Noel.Goldsmith@dsto.defence.gov.au, nih-image@io.ece.drexel.edu Subject: Re: Data from FFT's Message-ID: >From: "Goldsmith, Noel" >To: "'Image Mailing List'" >Subject: Data from FFT's >Date: Thu, 22 Oct 1998 10:36:41 +1000 > >Hi, >We are using NIH-Image to measure the spacings of groups of striations >observed on fracture surfaces. >The procedure is as follows using the FFT Macros. >Open or display an Image, which is spatially calibrated in microns or mm. >Select the size of square area to be used, Operator decision. >Position the square over the selected group of striations. >Type F (FFT). (This is now so quick on a G3-300 that it is no longer the >slowest operation) >Look at the Transform and position the cursor over one of the two distinct >peaks which appear on each side of the centre. >Read the value in the info window which tells about cycles per mm (Or >micron), and also give the angle this makes with the x axis. >Write down the numbers and proceed to the next place. > > >My question is: >Can I get this data into a macro so I don't have to write it down? >I see it is written in the info window, so it is there, how do I get it into >user1 and user2? > >I spent some time reading the manual and could find nothing. I could have a >look at the source code, but thought I would ask first. >I guess this is a measurement which does not yet appear as an option in the >measurements option dialog, and may have to be added. >What I would propose is maybe a mouse click at the desired location to >record these parameters. But I really have no strong feelings about how to >do this job. >After all I am relying on a user decision about the location of the maximum >peak on the transform. For really precise work I suppose we should fit up >some 3-D surfaces across the peak and estimate the peak maximum position, or >fit up some 2-d curves across and up and down to try to locate the maximum. >Of course when you look at the scatter you get when measuring striations all >of this precision becomes academic. The spacing will vary by a factor of 2 >or more over a range of very small distances, and the only way you get good >data is by getting lots of numbers. And doing it by using the FFT allows the >accumulation of many measurements, quickly. >Best regards >Noel. > Noel, the FFT window is essentially a spatially scaled image with the origin central and using polar coordinates, so the following macro will mimic the Info window values: Place the cursor in the FFT window and press [t] to demonstrate. macro'[t]est'; var x,y,c,w,h,scale,AspectRatio,xs,ys,r,theta:integer; unit:string;begin invertY(false); getPicSize(w,h);w:=w/2; getScale(scale,unit,AspectRatio); getMouse(x,y);c:=getPixel(x,y); xs:=x-w; ys:=w-y; if ys=0 then if xs>0 then theta:=0 else theta :=180 else theta:=90-arcTan(xs/ys)*45/arcTan(1); if ys<0 then theta:=theta+180; r:=sqrt(sqr(xs)+sqr(ys)); if r=0 then r:=999999 else r:=h/r; showMessage(x,y,c ,'\',(x-w),-(y-w) ,'\',xs,' ',ys ,'\',scale,unit,AspectRatio ,'\\r: ',r/scale,unit,' /c (',xs:4:0 ,')\theta: ',theta,' (',ys:4:0 ,')\Value:',c:4:0 ); end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #94 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 22 10:23 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA13357; Thu, 22 Oct 1998 10:22:59 -0400 (EDT) Resent-Date: Thu, 22 Oct 1998 10:22:59 -0400 (EDT) X-Authentication-Warning: rodan.syr.edu: manorato owned process doing -bs Date: Thu, 22 Oct 1998 09:59:22 -0400 (EDT) From: "Michael A. Norato" X-Sender: manorato@rodan.syr.edu To: nih-image@io.ece.drexel.edu Subject: bubble measurements. Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"pype72.0.2S1.3hpBs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/520 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 225 Does anyone know of an existing macro to measure bubble size distributions? I want to measure bubbles which are less than 200 microns in diameter. mike norato Dept. Chem. Eng. & Mat. Sci. Syracuse University 315-443-3286 From nih-image-d-request@io.ece.drexel.edu Fri Oct 23 06:16 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA05247; Fri, 23 Oct 1998 06:16:29 -0400 (EDT) Date: Fri, 23 Oct 1998 06:16:29 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810231016.GAA05247@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #95 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/95 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3330 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 95 Today's Topics: Re: interior measurements [ GJOSS@rna.bio.mq.edu.au ] bubble measurements. [ "Michael A. Norato" >From: "j.gregory" >Date: Tue, 20 Oct 1998 13:09:00 +0100 (BST) > > >Whilst there are many automated procedures for measuring the size of an object >and the space it takes up, does anyone have a macro or method for measuring >the largest ellipse, rectangle or other regular object(not constrained to >horizontal and >vertical axis) that can fill the interior of an irregular ROI? > >Thanks in advance, > >Jenny Gregory > >---------------------- >Jenny Gregory >Department of Orthopaedics >University of Aberdeen >Aberdeen >Scotland Jenny, your problem specs seem a little too unconstrained to me :-) , however, in the absence of other responses, the following may be of some interest. _________________________ macro'/0 maximum internal circle of a roi'; var x,y,w,h,d,i,mi,r,xm,xx:integer; begin getRoi(x,y,w,h); if w=0 then exit('selection required'); copy; d:=trunc(sqrt(sqr(w)+sqr(h))+0.5); if (d mod 2)=0 then d:=d+3 else d:=d+2; setForeGround(255);setBackGround(0); setNewSize(d,d); makeNewWindow('circle');paste;fill; binary('edm'); enhanceContrast; resetCounter; measure; r:=rMax[rcount]; showMessage('maximum enclosed circle radius',r); setDensitySlice(r-1,r); setOptions('Area X-Y Center Min/Max Major Minor Angle'); analyzeParticles(''); undo; mi:=2; for i:=2 to rCount do if rArea[i]>rArea[mi] then mi:=i; selectAll;copy; makeOvalRoi(rX[mi]-r,rY[mi]-r,r+r,r+r);drawBoundary; if rArea[mi]>3 then begin SetScaling('Same Window Bilinear'{Nearest'}); makeNewWindow('extend?'); selectAll; y:=trunc(d/2)+1; moveRoi(d/2-rX[mi],d/2-rY[mi]);paste;selectAll; scaleAndRotate(1,1,rAngle[mi]); y:=trunc(d/2)+1; getRow(0,y,d); x:=y;while lineBuffer[x]>=r-1 do x:=x-1;xm:=x+1; x:=y;while lineBuffer[x]>=r-1 do x:=x+1;xx:=x-1; makeOvalRoi(xm-r,y-r,r+r,r+r);drawBoundary; makeOvalRoi(xx-r,y-r,r+r,r+r);drawBoundary; makeRoi(xm,y-r,xx-xm+1,r+r);drawBoundary; showMessage(r,y,xm,xx); tileWindows; end; end _________________________ Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 22 Oct 1998 09:59:22 -0400 (EDT) From: "Michael A. Norato" To: nih-image@io.ece.drexel.edu Subject: bubble measurements. Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know of an existing macro to measure bubble size distributions? I want to measure bubbles which are less than 200 microns in diameter. mike norato Dept. Chem. Eng. & Mat. Sci. Syracuse University 315-443-3286 -------------------------------- End of nih-image-d Digest V98 Issue #95 *************************************** From nih-image-request@io.ece.drexel.edu Fri Oct 23 06:53 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09987; Fri, 23 Oct 1998 06:53:56 -0400 (EDT) Resent-Date: Fri, 23 Oct 1998 06:53:56 -0400 (EDT) X-Sender: sdb@pop1.liv.ac.uk Message-Id: In-Reply-To: <199810231002.GAA03423@io.ece.drexel.edu> Mime-Version: 1.0 Date: Fri, 23 Oct 1998 11:40:13 +0100 To: nih-image@io.ece.drexel.edu From: Steve Barrett Subject: Re: bubble measurements Cc: "Michael A. Norato" Resent-Message-ID: <"NRLos.0.U02.Xq5Cs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/521 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 727 >Does anyone know of an existing macro to measure bubble size >distributions? I want to measure bubbles which are less than 200 microns >in diameter. The NIH Image spin-off 'Image SXM' can analyse circle size distributions. A copy of the Image SXM installer is in the spin-offs folder on the NIH Image server. You can find more information about Image SXM from http://reg.ssci.liv.ac.uk ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ From nih-image-request@io.ece.drexel.edu Fri Oct 23 11:59 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA15754; Fri, 23 Oct 1998 11:59:38 -0400 (EDT) Resent-Date: Fri, 23 Oct 1998 11:59:38 -0400 (EDT) From: MASandberg@aol.com Message-ID: <82ba1421.3630a107@aol.com> Date: Fri, 23 Oct 1998 11:30:15 EDT To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Annular ROI. Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"La2ch1.0.cD3.09ACs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/522 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 544 When I try to save an annular ROI, which I created manually, as an outline in NIH Image 1.62, I get the error message: "XY Coordinates are not available". I have also tried to create it automatically with a macro with an option command between the two makeovalROI commands, but only get the second (smaller) circle to appear. I would appreciate any advice on a solution. Thanks, Michael A. Sandberg, Ph.D. Berman-Gund Laboratory for the Study of Retinal Degenerations Massachusetts Eye and Ear Infirmary 243 Charles Street Boston, MA 02114 From nih-image-d-request@io.ece.drexel.edu Sat Oct 24 06:09 EDT 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA11464; Sat, 24 Oct 1998 06:09:53 -0400 (EDT) Date: Sat, 24 Oct 1998 06:09:53 -0400 (EDT) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810241009.GAA11464@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #96 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/96 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2242 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 96 Today's Topics: Re: bubble measurements [ Steve Barrett To: nih-image@io.ece.drexel.edu Cc: "Michael A. Norato" Subject: Re: bubble measurements Message-Id: Content-Type: text/plain; charset="us-ascii" >Does anyone know of an existing macro to measure bubble size >distributions? I want to measure bubbles which are less than 200 microns >in diameter. The NIH Image spin-off 'Image SXM' can analyse circle size distributions. A copy of the Image SXM installer is in the spin-offs folder on the NIH Image server. You can find more information about Image SXM from http://reg.ssci.liv.ac.uk ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ ------------------------------ Date: Fri, 23 Oct 1998 11:30:15 EDT From: MASandberg@aol.com To: nih-image@io.ece.drexel.edu Subject: Annular ROI. Message-ID: <82ba1421.3630a107@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit When I try to save an annular ROI, which I created manually, as an outline in NIH Image 1.62, I get the error message: "XY Coordinates are not available". I have also tried to create it automatically with a macro with an option command between the two makeovalROI commands, but only get the second (smaller) circle to appear. I would appreciate any advice on a solution. Thanks, Michael A. Sandberg, Ph.D. Berman-Gund Laboratory for the Study of Retinal Degenerations Massachusetts Eye and Ear Infirmary 243 Charles Street Boston, MA 02114 -------------------------------- End of nih-image-d Digest V98 Issue #96 *************************************** From nih-image-request@io.ece.drexel.edu Mon Oct 26 17:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA02798; Mon, 26 Oct 1998 17:22:07 -0500 (EST) Resent-Date: Mon, 26 Oct 1998 17:22:07 -0500 (EST) Message-Id: <3.0.5.32.19981027105320.00806610@uni.massey.ac.nz> X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 27 Oct 1998 10:53:20 +1300 To: nih-image@io.ece.drexel.edu From: Naomi Boxall Subject: Surely not the first.... Mime-Version: 1.0 Resent-Message-ID: <"Pm79q2.0.PN4.azEDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/523 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1250 Dear all, Hi. I am a very new user of this program and I am doing my Masters In Veterinary Studies (Epidemiology). The thesis is built of Image Analysis and Molecular Epidemiology. By word of mouth, I have heard that NIH Image is the best program to use for analysis of EtBr gels (from PFGE). However I have come across a few little roadblocks in my path to get the computer to say in numbers, what I see with my eyes! I'm sure I can't have been the only one with these problems and would really appreciate if someone could possibly help out. a) How can I calibrate a lambda ladder? I have read the 'help' file and I have read the NIH tutorial. I have no idea what the optical density of the bands are. How do I find this out??? b) How can I read the distances from the origin to the peaks without pointing the mouse over the peak (obtained using the GelPlot2 Macro) and reading the x-axis value? Presumably, because the macro delivers the results by way of graph, then the numerical values for the plot must be somewhere...where? Thanks for your time. Naomi Naomi S. Boxall BSc Epicentre Inst. of Vet, Animal & Biomedical Sciences Massey University Palmerston North New Zealand 064-6-3504008 (W) Naomi.Boxall.1@uni.massey.ac.nz From nih-image-request@io.ece.drexel.edu Tue Oct 27 04:29 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA17184; Tue, 27 Oct 1998 04:29:52 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 04:29:52 -0500 (EST) X-Sender: elk@129.233.21.18 Message-Id: Mime-Version: 1.0 Date: Tue, 27 Oct 1998 10:04:35 +0100 To: nih-image@io.ece.drexel.edu From: Ben Elkin Subject: digital photo camera f. microscopy Resent-Message-ID: <"HKSV12.0.YA1.4qODs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/524 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1140 Hallo everybody, we consider equipping still another microscope with a computer-connected camera. The idea now is to take one of these new digital *photographic* cameras which begin to penetrate consumer and professional photography market. They are sensitive enough for our purposes, offer color capture at the same or higher resolution as compared to video cameras, and cost (which is important for us now) below 2000 $. That computer can, but must not be connected to the camera, is also an advantage. The image compression is usually (or always?) built in, which may be a considerable drawback, but we could live with it. The problem is that these cameras have mostly (or always?) built-in lens, so we don't know how to adapt it to the microscope. Does anybody have the experience or any ideas? Ben Elkin ======================================= elk@igb.fhg.de http://www.igb.fhg.de/GVT/ Fraunhofer Institute for Interfacial Technology and Bioengineering (fuer Grenzflaechen und Bioverfahrenstechnik) Nobelstr. 12 D-70569 Stuttgart Germany Tel. +49 - 711 - 970-4144, -4161 Fax -4200 From nih-image-request@io.ece.drexel.edu Tue Oct 27 05:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA04274; Tue, 27 Oct 1998 05:02:54 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 05:02:54 -0500 (EST) Date: Tue, 27 Oct 1998 09:48:26 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: Re: digital photo camera f. microscopy In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"RnGcR.0.fc6.SSPDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/525 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2020 Hi Ben, have a look at Kodak MDS 120 System (Microscopy Documentation System) on their website www.kodak.com. They couple a consumer-market digital camera (DC 120, a somewhat dated model) with a non-removabel lens to a microscope with the help of a special adaptor. SLR-body digital cameras are a lot more expensive but better. You can get adaptors for SLR-body cameras (digital or not) to C-mounts etc. from Diagnostics Instruments (www.diaginc.com). There are many useful links for digital cameras and microscopy on: http://www.mwrn.com/product/image/camera.htm Hope that helps, Jan. Jan Kreft Phone +44 (0)1222 876036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Tue, 27 Oct 1998, Ben Elkin wrote: > Hallo everybody, > > we consider equipping still another microscope with a computer-connected > camera. The idea now is to take one of these new digital *photographic* > cameras which begin to penetrate consumer and professional photography > market. They are sensitive enough for our purposes, offer color capture at > the same or higher resolution as compared to video cameras, and cost (which > is important for us now) below 2000 $. That computer can, but must not be > connected to the camera, is also an advantage. The image compression is > usually (or always?) built in, which may be a considerable drawback, but we > could live with it. > > The problem is that these cameras have mostly (or always?) built-in lens, > so we don't know how to adapt it to the microscope. Does anybody have the > experience or any ideas? > > > Ben Elkin > > ======================================= > elk@igb.fhg.de > > http://www.igb.fhg.de/GVT/ > > Fraunhofer Institute for Interfacial Technology and Bioengineering > (fuer Grenzflaechen und Bioverfahrenstechnik) > > Nobelstr. 12 D-70569 Stuttgart Germany > > Tel. +49 - 711 - 970-4144, -4161 > Fax -4200 > > > > From nih-image-request@io.ece.drexel.edu Tue Oct 27 05:40 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA23973; Tue, 27 Oct 1998 05:40:31 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 05:40:31 -0500 (EST) Message-Id: <3.0.32.19981027101754.008c0c00@mail-server> X-Sender: wtm@mail-server X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 27 Oct 1998 10:18:00 +0000 To: nih-image@io.ece.drexel.edu From: Bill Mason Subject: New Digital Cameras for Mac and NIH Image Mime-Version: 1.0 X-Hops: 1 Resent-Message-ID: <"t9-6h.0.xP3.kwPDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/526 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1411 Readers of the list might like to know that our cooled precision digital CCD cameras for microscopy are now fully supported with a Photoshop and NIH Image-compatible plugin, as well as a new standalone software package for the Mac. We offer an outstanding range of high performance cameras for microscopy employing interline transfer, frame transfer and full frame CCD chips with a variety of readout speeds. The new plugin which is available operates with Mac OS7.5 or above or OS8 or above, and utilises a PCI card on PowerMacs or the new G3 Mac platform. The software support offers full use of all the camera facilities for control of binning, subarrays, integration time etc. We also offer RGB filter control for the Mac environment within NIH Image, for true colour imaging. This of course is in addition to our existing Windows 95 PC support. For further information, please contact us directly rather than sending a reply to the list! We also have some details on our Web site, the address of which is given below. I hope this information is helpful. Dr. Bill Mason Life Science Resources Ltd. Abberley House, Granham's Road Great Shelford, Cambridge CB2 5LQ United Kingdom Tel 44-(0)1223-845836 Fax 44-(0)1223-840342 In the USA at: Two Corporate Center Drive Melville, NY 11747-3157 Tel 516-8445085 Fax 516-8445093 Freephone 1-800-7479530 Email: WTM@LSR.CO.UK Web Site: http://www.lsr.co.uk From nih-image-request@io.ece.drexel.edu Tue Oct 27 07:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA10898; Tue, 27 Oct 1998 07:11:10 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 07:11:10 -0500 (EST) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: Mime-Version: 1.0 Date: Tue, 27 Oct 1998 13:53:57 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Problems with Scion Image for NT Cc: Gary Chinga Resent-Message-ID: <"3Ttl_3.0.uI.NGRDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/527 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 949 A friend of me is having problems with Scion Image running on Windows NT and asked me to post a request to the list if anyone knows any solution to the problem: He has a Cinet PC with NT 4.0 and 128 megs RAM. He has installed Scion Image for PC vers. 1.0.01. The program crashes frequently, several times an hour. Upon opening, the error message "Error getting handle to NT driver" appears. You may forward your reply directly to Gary Chinga . +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Tue Oct 27 10:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19610; Tue, 27 Oct 1998 10:27:59 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 10:27:59 -0500 (EST) Message-ID: <19981027145337.29598.rocketmail@web4.rocketmail.com> Date: Tue, 27 Oct 1998 06:53:37 -0800 (PST) From: Mark Vivino Subject: Re: Surely not the first.... To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"70KwT.0.mh.lyTDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/528 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1153 > a) How can I calibrate a lambda ladder? I have read the 'help' file and I > have read the NIH tutorial. I have no idea what the optical density of the > bands are. How do I find this out??? You can calibrate your data to any unit you want. OD is directly proportional to concentration by Beer's law so many use this, but if you have other actual units, by all means use these. > b) How can I read the distances from the origin to the peaks without > pointing the mouse over the peak (obtained using the GelPlot2 Macro) and > reading the x-axis value? Presumably, because the macro delivers the > results by way of graph, then the numerical values for the plot must be > somewhere...where? The program is setup to read area under the curve as the integral of densities for a band. I'm sure you can calibrate ("set scale") to distances like mm and measure distance if you need that as well. This should be very easy. See set scale in manual. Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Oct 27 10:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19672; Tue, 27 Oct 1998 10:28:05 -0500 (EST) Resent-Date: Tue, 27 Oct 1998 10:28:05 -0500 (EST) Message-ID: <19981027145435.9336.rocketmail@attach1.rocketmail.com> Date: Tue, 27 Oct 1998 06:54:35 -0800 (PST) From: Mark Vivino Subject: Re: bubble measurements. To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"D_Vee1.0.j61.k_TDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/529 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 468 > Does anyone know of an existing macro to measure bubble size > distributions? I want to measure bubbles which are less than 200 microns > in diameter. Did you try the analyze particles routines? Or did that not work for a variety of reasons? Do your bubbles touch? Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-d-request@io.ece.drexel.edu Tue Oct 27 10:32 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22224; Tue, 27 Oct 1998 10:32:32 -0500 (EST) Date: Tue, 27 Oct 1998 10:32:32 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810271532.KAA22224@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #97 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/97 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 10398 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 97 Today's Topics: Surely not the first.... [ Naomi Boxall ] Re: digital photo camera f. microsco [ Jan Kreft ] New Digital Cameras for Mac and NIH [ Bill Mason ] Problems with Scion Image for NT [ Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Surely not the first.... Message-Id: <3.0.5.32.19981027105320.00806610@uni.massey.ac.nz> Content-Type: text/plain; charset="us-ascii" Dear all, Hi. I am a very new user of this program and I am doing my Masters In Veterinary Studies (Epidemiology). The thesis is built of Image Analysis and Molecular Epidemiology. By word of mouth, I have heard that NIH Image is the best program to use for analysis of EtBr gels (from PFGE). However I have come across a few little roadblocks in my path to get the computer to say in numbers, what I see with my eyes! I'm sure I can't have been the only one with these problems and would really appreciate if someone could possibly help out. a) How can I calibrate a lambda ladder? I have read the 'help' file and I have read the NIH tutorial. I have no idea what the optical density of the bands are. How do I find this out??? b) How can I read the distances from the origin to the peaks without pointing the mouse over the peak (obtained using the GelPlot2 Macro) and reading the x-axis value? Presumably, because the macro delivers the results by way of graph, then the numerical values for the plot must be somewhere...where? Thanks for your time. Naomi Naomi S. Boxall BSc Epicentre Inst. of Vet, Animal & Biomedical Sciences Massey University Palmerston North New Zealand 064-6-3504008 (W) Naomi.Boxall.1@uni.massey.ac.nz ------------------------------ Date: Tue, 27 Oct 1998 10:04:35 +0100 From: Ben Elkin To: nih-image@io.ece.drexel.edu Subject: digital photo camera f. microscopy Message-Id: Content-Type: text/plain; charset="us-ascii" Hallo everybody, we consider equipping still another microscope with a computer-connected camera. The idea now is to take one of these new digital *photographic* cameras which begin to penetrate consumer and professional photography market. They are sensitive enough for our purposes, offer color capture at the same or higher resolution as compared to video cameras, and cost (which is important for us now) below 2000 $. That computer can, but must not be connected to the camera, is also an advantage. The image compression is usually (or always?) built in, which may be a considerable drawback, but we could live with it. The problem is that these cameras have mostly (or always?) built-in lens, so we don't know how to adapt it to the microscope. Does anybody have the experience or any ideas? Ben Elkin ======================================= elk@igb.fhg.de http://www.igb.fhg.de/GVT/ Fraunhofer Institute for Interfacial Technology and Bioengineering (fuer Grenzflaechen und Bioverfahrenstechnik) Nobelstr. 12 D-70569 Stuttgart Germany Tel. +49 - 711 - 970-4144, -4161 Fax -4200 ------------------------------ Date: Tue, 27 Oct 1998 09:48:26 +0000 (GMT) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: Re: digital photo camera f. microscopy Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Ben, have a look at Kodak MDS 120 System (Microscopy Documentation System) on their website www.kodak.com. They couple a consumer-market digital camera (DC 120, a somewhat dated model) with a non-removabel lens to a microscope with the help of a special adaptor. SLR-body digital cameras are a lot more expensive but better. You can get adaptors for SLR-body cameras (digital or not) to C-mounts etc. from Diagnostics Instruments (www.diaginc.com). There are many useful links for digital cameras and microscopy on: http://www.mwrn.com/product/image/camera.htm Hope that helps, Jan. Jan Kreft Phone +44 (0)1222 876036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK On Tue, 27 Oct 1998, Ben Elkin wrote: > Hallo everybody, > > we consider equipping still another microscope with a computer-connected > camera. The idea now is to take one of these new digital *photographic* > cameras which begin to penetrate consumer and professional photography > market. They are sensitive enough for our purposes, offer color capture at > the same or higher resolution as compared to video cameras, and cost (which > is important for us now) below 2000 $. That computer can, but must not be > connected to the camera, is also an advantage. The image compression is > usually (or always?) built in, which may be a considerable drawback, but we > could live with it. > > The problem is that these cameras have mostly (or always?) built-in lens, > so we don't know how to adapt it to the microscope. Does anybody have the > experience or any ideas? > > > Ben Elkin > > ======================================= > elk@igb.fhg.de > > http://www.igb.fhg.de/GVT/ > > Fraunhofer Institute for Interfacial Technology and Bioengineering > (fuer Grenzflaechen und Bioverfahrenstechnik) > > Nobelstr. 12 D-70569 Stuttgart Germany > > Tel. +49 - 711 - 970-4144, -4161 > Fax -4200 > > > > ------------------------------ Date: Tue, 27 Oct 1998 10:18:00 +0000 From: Bill Mason To: nih-image@io.ece.drexel.edu Subject: New Digital Cameras for Mac and NIH Image Message-Id: <3.0.32.19981027101754.008c0c00@mail-server> Content-Type: text/plain; charset="us-ascii" Readers of the list might like to know that our cooled precision digital CCD cameras for microscopy are now fully supported with a Photoshop and NIH Image-compatible plugin, as well as a new standalone software package for the Mac. We offer an outstanding range of high performance cameras for microscopy employing interline transfer, frame transfer and full frame CCD chips with a variety of readout speeds. The new plugin which is available operates with Mac OS7.5 or above or OS8 or above, and utilises a PCI card on PowerMacs or the new G3 Mac platform. The software support offers full use of all the camera facilities for control of binning, subarrays, integration time etc. We also offer RGB filter control for the Mac environment within NIH Image, for true colour imaging. This of course is in addition to our existing Windows 95 PC support. For further information, please contact us directly rather than sending a reply to the list! We also have some details on our Web site, the address of which is given below. I hope this information is helpful. Dr. Bill Mason Life Science Resources Ltd. Abberley House, Granham's Road Great Shelford, Cambridge CB2 5LQ United Kingdom Tel 44-(0)1223-845836 Fax 44-(0)1223-840342 In the USA at: Two Corporate Center Drive Melville, NY 11747-3157 Tel 516-8445085 Fax 516-8445093 Freephone 1-800-7479530 Email: WTM@LSR.CO.UK Web Site: http://www.lsr.co.uk ------------------------------ Date: Tue, 27 Oct 1998 13:53:57 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Cc: Gary Chinga Subject: Problems with Scion Image for NT Message-Id: Content-Type: text/plain; charset="us-ascii" A friend of me is having problems with Scion Image running on Windows NT and asked me to post a request to the list if anyone knows any solution to the problem: He has a Cinet PC with NT 4.0 and 128 megs RAM. He has installed Scion Image for PC vers. 1.0.01. The program crashes frequently, several times an hour. Upon opening, the error message "Error getting handle to NT driver" appears. You may forward your reply directly to Gary Chinga . +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Tue, 27 Oct 1998 06:53:37 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Surely not the first.... Message-ID: <19981027145337.29598.rocketmail@web4.rocketmail.com> Content-Type: text/plain; charset=us-ascii > a) How can I calibrate a lambda ladder? I have read the 'help' file and I > have read the NIH tutorial. I have no idea what the optical density of the > bands are. How do I find this out??? You can calibrate your data to any unit you want. OD is directly proportional to concentration by Beer's law so many use this, but if you have other actual units, by all means use these. > b) How can I read the distances from the origin to the peaks without > pointing the mouse over the peak (obtained using the GelPlot2 Macro) and > reading the x-axis value? Presumably, because the macro delivers the > results by way of graph, then the numerical values for the plot must be > somewhere...where? The program is setup to read area under the curve as the integral of densities for a band. I'm sure you can calibrate ("set scale") to distances like mm and measure distance if you need that as well. This should be very easy. See set scale in manual. Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com -------------------------------- End of nih-image-d Digest V98 Issue #97 *************************************** From nih-image-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA04530; Wed, 28 Oct 1998 03:34:00 -0500 (EST) Resent-Date: Wed, 28 Oct 1998 03:34:00 -0500 (EST) Date: Wed, 28 Oct 1998 09:16:53 +0100 From: Ard Jonker Subject: Re: digital photo camera f. microscopy In-reply-to: <199810271503.KAA06277@io.ece.drexel.edu> X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id DAA26942 Resent-Message-ID: <"5uMpx2.0.Qb6.PEjDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/531 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 590 >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras Keep your eye on http://www.imagek.com which has announced (and demonstrated) a digital film under $1000 for your current photocamera body. It takes the place of the ordinary film and after 30 exposures you take it out, connect it to an interface (mac or pc) and drain the cassete. 1280x1024 is said to be the resolution. I have no connections with the company, I'm just very curious for the results when used in microscopy. Ard From nih-image-d-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA04944; Wed, 28 Oct 1998 03:34:42 -0500 (EST) Date: Wed, 28 Oct 1998 03:34:42 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810280834.DAA04944@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #98 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/98 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1875 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 98 Today's Topics: Re: bubble measurements. [ Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: bubble measurements. Message-ID: <19981027145435.9336.rocketmail@attach1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > Does anyone know of an existing macro to measure bubble size > distributions? I want to measure bubbles which are less than 200 microns > in diameter. Did you try the analyze particles routines? Or did that not work for a variety of reasons? Do your bubbles touch? Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Wed, 28 Oct 1998 09:17:47 +0100 From: Vincenzo Della Mea To: nih-image@io.ece.drexel.edu Subject: Re: digital photo camera f. microscopy Message-Id: Content-Type: text/plain; charset="us-ascii" >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras which begin to penetrate consumer and professional photography try to look also at Olympus cameras: they are selling a consumer-based microscope digital camera which is cheap but very nice, with C-mount. (http://www.olympus-europa.com/mikro/dp10.htm). Vincenzo -------------------------------- End of nih-image-d Digest V98 Issue #98 *************************************** From nih-image-request@io.ece.drexel.edu Wed Oct 28 03:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA05055; Wed, 28 Oct 1998 03:34:53 -0500 (EST) Resent-Date: Wed, 28 Oct 1998 03:34:53 -0500 (EST) X-Sender: dellamea@ten.dimi.uniud.it Message-Id: In-Reply-To: <199810271521.KAA15779@io.ece.drexel.edu> Mime-Version: 1.0 Date: Wed, 28 Oct 1998 09:17:47 +0100 To: nih-image@io.ece.drexel.edu From: Vincenzo Della Mea Subject: Re: digital photo camera f. microscopy Resent-Message-ID: <"PXorH3.0.mT6.bDjDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/530 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 421 >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras which begin to penetrate consumer and professional photography try to look also at Olympus cameras: they are selling a consumer-based microscope digital camera which is cheap but very nice, with C-mount. (http://www.olympus-europa.com/mikro/dp10.htm). Vincenzo From nih-image-request@io.ece.drexel.edu Wed Oct 28 08:16 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA12203; Wed, 28 Oct 1998 08:16:55 -0500 (EST) Resent-Date: Wed, 28 Oct 1998 08:16:55 -0500 (EST) Message-ID: <36371457.6CC5557D@sdsc.edu> Date: Wed, 28 Oct 1998 04:55:51 -0800 From: "Harvey J. Karten" Reply-To: hjkarten@UCSD.EDU Organization: UCSD X-Mailer: Mozilla 4.04 [en] (Win95; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Olympus digital camera References: <199810280833.DAA04104@io.ece.drexel.edu> Resent-Message-ID: <"gkD9D.0.Ia.JHnDs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/532 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="------------1DB4DE75091445ED637D0443" Content-Length: 2116 --------------1DB4DE75091445ED637D0443 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Is that a one chip or a three chip camera? Can it be used as a full resolution monochrome at 1280x1024? What is the effective ASA? Can it be used for Nomarski? Fluorescence? Dark Field? Many thanks, Harvey Karten Vincenzo Della Mea wrote: try to look also at Olympus cameras: they are selling a consumer-based microscope digital camera which is cheap but very nice, with C-mount. (http://www.olympus-europa.com/mikro/dp10.htm). -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org --------------1DB4DE75091445ED637D0443 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Is that a one chip or a three chip camera? Can it be used as a full resolution monochrome at 1280x1024? What is the effective ASA? Can it be used for Nomarski? Fluorescence? Dark Field?

Many thanks,
Harvey Karten

Vincenzo Della Mea wrote:
try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).
 

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org
  --------------1DB4DE75091445ED637D0443-- From nih-image-request@io.ece.drexel.edu Wed Oct 28 09:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21664; Wed, 28 Oct 1998 09:43:32 -0500 (EST) Resent-Date: Wed, 28 Oct 1998 09:43:32 -0500 (EST) X-Authentication-Warning: rodan.syr.edu: manorato owned process doing -bs Date: Wed, 28 Oct 1998 09:22:14 -0500 (EST) From: "Michael A. Norato" X-Sender: manorato@rodan.syr.edu To: nih-image@io.ece.drexel.edu cc: nih-image-d@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #98 In-Reply-To: <199810280836.DAA05729@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"jEQtR1.0.Wu2.VYoDs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/533 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 300 I have tried the Analyse particles routines, but it does not appear to yield an explicit bubbles size distribution. Sometimes the bubbles touch, but not often. mike norato Syracuse University. On Wed, 28 Oct 1998 nih-image-d-request@io.ece.drexel.edu wrote: [NON-Text Body part not included] From nih-image-d-request@io.ece.drexel.edu Thu Oct 29 06:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29383; Thu, 29 Oct 1998 06:20:35 -0500 (EST) Date: Thu, 29 Oct 1998 06:20:35 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810291120.GAA29383@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #99 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/99 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4448 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 99 Today's Topics: Re: digital photo camera f. microsco [ Ard Jonker ] Re: Olympus digital camera [ "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: Re: digital photo camera f. microscopy Message-id: Content-type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras Keep your eye on http://www.imagek.com which has announced (and demonstrated) a digital film under $1000 for your current photocamera body. It takes the place of the ordinary film and after 30 exposures you take it out, connect it to an interface (mac or pc) and drain the cassete. 1280x1024 is said to be the resolution. I have no connections with the company, I'm just very curious for the results when used in microscopy. Ard ------------------------------ Date: Wed, 28 Oct 1998 04:55:51 -0800 From: "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: Re: Olympus digital camera Message-ID: <36371457.6CC5557D@sdsc.edu> Content-Type: multipart/alternative; boundary="------------1DB4DE75091445ED637D0443" --------------1DB4DE75091445ED637D0443 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Is that a one chip or a three chip camera? Can it be used as a full resolution monochrome at 1280x1024? What is the effective ASA? Can it be used for Nomarski? Fluorescence? Dark Field? Many thanks, Harvey Karten Vincenzo Della Mea wrote: try to look also at Olympus cameras: they are selling a consumer-based microscope digital camera which is cheap but very nice, with C-mount. (http://www.olympus-europa.com/mikro/dp10.htm). -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California at San Diego La Jolla, CA 92093-0608 Phone (Voice): 619-534-4938 FAX: 619-534-6602 EMail: HJKarten@ucsd.edu Alternate Email: kartenh@sdsc.edu Retina Information System: http://www-cajal.ucsd.edu WCBR Program for 1999: PLEASE NOTE CHANGE OF WEB ADDRESS http://www.wcbrBrain.org --------------1DB4DE75091445ED637D0443 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Is that a one chip or a three chip camera? Can it be used as a full resolution monochrome at 1280x1024? What is the effective ASA? Can it be used for Nomarski? Fluorescence? Dark Field?

Many thanks,
Harvey Karten

Vincenzo Della Mea wrote:
try to look also at Olympus cameras: they are selling a consumer-based
microscope digital camera which is cheap but very nice, with C-mount.
(http://www.olympus-europa.com/mikro/dp10.htm).
 

--
Harvey J. Karten, M.D.
Dept. of Neurosciences
University of California at San Diego
La Jolla, CA 92093-0608
Phone (Voice): 619-534-4938
FAX:  619-534-6602
EMail: HJKarten@ucsd.edu
Alternate Email: kartenh@sdsc.edu
Retina Information System: http://www-cajal.ucsd.edu

WCBR Program for 1999:
PLEASE NOTE CHANGE OF WEB ADDRESS
http://www.wcbrBrain.org
  --------------1DB4DE75091445ED637D0443-- ------------------------------ Date: Wed, 28 Oct 1998 09:22:14 -0500 (EST) From: "Michael A. Norato" To: nih-image@io.ece.drexel.edu cc: nih-image-d@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #98 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I have tried the Analyse particles routines, but it does not appear to yield an explicit bubbles size distribution. Sometimes the bubbles touch, but not often. mike norato Syracuse University. On Wed, 28 Oct 1998 nih-image-d-request@io.ece.drexel.edu wrote: [NON-Text Body part not included] -------------------------------- End of nih-image-d Digest V98 Issue #99 *************************************** From nih-image-request@io.ece.drexel.edu Thu Oct 29 07:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA29590; Thu, 29 Oct 1998 07:20:42 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 07:20:42 -0500 (EST) Message-Id: <3.0.5.32.19981029065646.007d86a0@mohawk.net> X-Sender: microbill@mohawk.net X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Thu, 29 Oct 1998 06:56:46 -0500 To: nih-image@io.ece.drexel.edu From: Bill Miller Subject: Re: digital photo camera f. microscopy In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"obrVP1.0.xR4.HX5Es"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/534 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1293 See http://www.soundvision.com digital made for microscopy w/o lens. At 10:04 AM 10/27/98 +0100, you wrote: >Hallo everybody, > >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras which begin to penetrate consumer and professional photography >market. They are sensitive enough for our purposes, offer color capture at >the same or higher resolution as compared to video cameras, and cost (which >is important for us now) below 2000 $. That computer can, but must not be >connected to the camera, is also an advantage. The image compression is >usually (or always?) built in, which may be a considerable drawback, but we >could live with it. > >The problem is that these cameras have mostly (or always?) built-in lens, >so we don't know how to adapt it to the microscope. Does anybody have the >experience or any ideas? > > >Ben Elkin > >======================================= >elk@igb.fhg.de > >http://www.igb.fhg.de/GVT/ > >Fraunhofer Institute for Interfacial Technology and Bioengineering > (fuer Grenzflaechen und Bioverfahrenstechnik) > >Nobelstr. 12 D-70569 Stuttgart Germany > >Tel. +49 - 711 - 970-4144, -4161 >Fax -4200 > > > > > From nih-image-request@io.ece.drexel.edu Thu Oct 29 11:05 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA27710; Thu, 29 Oct 1998 11:05:50 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 11:05:50 -0500 (EST) X-Sender: dellamea@ten.dimi.uniud.it Message-Id: In-Reply-To: <199810291114.GAA26458@io.ece.drexel.edu> Mime-Version: 1.0 Date: Thu, 29 Oct 1998 16:35:47 +0100 To: nih-image@io.ece.drexel.edu From: Vincenzo Della Mea Subject: Re: Olympus digital camera Resent-Message-ID: <"kJXHh3.0.zC6.qj8Es"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/535 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 607 > Is that a one chip or a three chip camera? Can it be used as a full >resolution monochrome at 1280x1024? What is the effective ASA? Can it be >used for Nomarski? Fluorescence? Dark Field? > >Many thanks, >Harvey Karten > >Vincenzo Della Mea wrote: >try to look also at Olympus cameras: they are selling a consumer-based >microscope digital camera which is cheap but very nice, with C-mount. >(http://www.olympus-europa.com/mikro/dp10.htm). I don't know deeply the technical features, I just saw one when it arrived at Olympus Italy (which is not my company...). Try to look at the www site. VIncenzo From nih-image-request@io.ece.drexel.edu Thu Oct 29 11:29 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA29513; Thu, 29 Oct 1998 11:29:24 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 11:29:24 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Thu, 29 Oct 1998 10:58:29 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Re: Olympus digital camera Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"U73ED.0.he6.349Es"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/536 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 358 In a message dated 10/29/98 10:53:17 AM, somone wrote: >try to look also at Olympus cameras: they are selling a consumer-based >>microscope digital camera which is cheap but very nice, with C-mount. the preliminary data I saw on this said that it did JPEG compression. If that "feature" can't be turned off I would strongly suggest NOT using the camera. From nih-image-request@io.ece.drexel.edu Thu Oct 29 18:56 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA22202; Thu, 29 Oct 1998 18:56:45 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 18:56:45 -0500 (EST) Message-ID: <19981029232109.3672.rocketmail@web1.rocketmail.com> Date: Thu, 29 Oct 1998 15:21:09 -0800 (PST) From: Mark Vivino Subject: Re: bubbles continued To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"oBcPp2.0.ak2.NkFEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/537 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 711 > I have tried the Analyse particles routines, but it does not appear to > yield an explicit bubbles size distribution. If you have calibrated the image to some units like "mm", then check area for measurement options you will then get a list of sizes after running the routine. It isn't a histogram of sizes but that could be done of course, it will simply be a list in the results window. Touching particles are another matter and there are multiple ways to handle this from simple to the very complex. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Thu Oct 29 20:30 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA10908; Thu, 29 Oct 1998 20:30:58 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 20:30:58 -0500 (EST) Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST) From: Lesley Weston Reply-To: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Imagemath Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Tagt41.0.XH7.p7HEs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/538 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 424 Can anybody help me with a macro problem concerning Imagemath in a stack manipulation? Everything seems to work except that I can't pass the parameter back to tell it where to store the enhanced image. Using something like "Imagemath('sub',.......,'Image'(i)) to make it store in a new set of images called "image1", "Image2" etc. doesn't work, and nor daoes anything else I've tried. Any ideas? Thanks. Lesley Weston. From nih-image-request@io.ece.drexel.edu Thu Oct 29 23:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA11901; Thu, 29 Oct 1998 23:28:58 -0500 (EST) Resent-Date: Thu, 29 Oct 1998 23:28:58 -0500 (EST) Date: Thu, 29 Oct 1998 18:15:41 -1000 From: Kathleen Annikki Moore X-Sender: moorekat@uhunix4 Reply-To: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu Subject: Can a snappy be used for? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"ykcnk.0.OH1.isJEs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/539 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1691 I'm a graduate student looking for a simple solution for capturing reasonable scientific images from several differing microscopes which each have a different brand name of video mounted to each individual microscope. I've read that 640 x 480 resolution is a minimal standard for video capture. I've also read that the Capsure card is not appropriate for this type of work as resolution is 320x240 which is interpolated up to 640x480. The following is a FAQ answer from Snappy's web site. A: Actually, video ISN'T 640 x 480. This is a common misconception in the computer world. .................... NTSC video is an analog signal with no fixed resolution. The more times you 'sample' the signal the better your digital representation gets............................ ..we can calculate based on the bandwidth of video that the point of diminishing returns is reached around 1500 samples per line. To sample at this resolution Play designed our own custom chip....................... time base correction, spatial and temporal filters, interpolation algorithms and more................................... Because NTSC video is only 480 lines tall Snappy interpolates the image vertically to maintain square pixels. This algorithm is called Third Order Polynomial Interpolation. My questions: Is an image treated to this inexpensive method of acquisition reasonable for scientific measurements (I'm working on bone histmorphometry measurements)? Will a Snappy framegrabber work well with PC notebooks? Are there any serious flaws created by using an inexpensive framegrabber or difficulties in capturing images on notebooks? Thank you very much for any answers. Kathleen Moore From nih-image-d-request@io.ece.drexel.edu Thu Oct 29 23:36 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA15693; Thu, 29 Oct 1998 23:36:05 -0500 (EST) Date: Thu, 29 Oct 1998 23:36:05 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810300436.XAA15693@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #100 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/100 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7515 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 100 Today's Topics: Re: digital photo camera f. microsco [ Bill Miller ] Re: Olympus digital camera [ Vincenzo Della Mea To: nih-image@io.ece.drexel.edu Subject: Re: digital photo camera f. microscopy Message-Id: <3.0.5.32.19981029065646.007d86a0@mohawk.net> Content-Type: text/plain; charset="us-ascii" See http://www.soundvision.com digital made for microscopy w/o lens. At 10:04 AM 10/27/98 +0100, you wrote: >Hallo everybody, > >we consider equipping still another microscope with a computer-connected >camera. The idea now is to take one of these new digital *photographic* >cameras which begin to penetrate consumer and professional photography >market. They are sensitive enough for our purposes, offer color capture at >the same or higher resolution as compared to video cameras, and cost (which >is important for us now) below 2000 $. That computer can, but must not be >connected to the camera, is also an advantage. The image compression is >usually (or always?) built in, which may be a considerable drawback, but we >could live with it. > >The problem is that these cameras have mostly (or always?) built-in lens, >so we don't know how to adapt it to the microscope. Does anybody have the >experience or any ideas? > > >Ben Elkin > >======================================= >elk@igb.fhg.de > >http://www.igb.fhg.de/GVT/ > >Fraunhofer Institute for Interfacial Technology and Bioengineering > (fuer Grenzflaechen und Bioverfahrenstechnik) > >Nobelstr. 12 D-70569 Stuttgart Germany > >Tel. +49 - 711 - 970-4144, -4161 >Fax -4200 > > > > > ------------------------------ Date: Thu, 29 Oct 1998 16:35:47 +0100 From: Vincenzo Della Mea To: nih-image@io.ece.drexel.edu Subject: Re: Olympus digital camera Message-Id: Content-Type: text/plain; charset="us-ascii" > Is that a one chip or a three chip camera? Can it be used as a full >resolution monochrome at 1280x1024? What is the effective ASA? Can it be >used for Nomarski? Fluorescence? Dark Field? > >Many thanks, >Harvey Karten > >Vincenzo Della Mea wrote: >try to look also at Olympus cameras: they are selling a consumer-based >microscope digital camera which is cheap but very nice, with C-mount. >(http://www.olympus-europa.com/mikro/dp10.htm). I don't know deeply the technical features, I just saw one when it arrived at Olympus Italy (which is not my company...). Try to look at the www site. VIncenzo ------------------------------ Date: Thu, 29 Oct 1998 10:58:29 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Re: Olympus digital camera Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 10/29/98 10:53:17 AM, somone wrote: >try to look also at Olympus cameras: they are selling a consumer-based >>microscope digital camera which is cheap but very nice, with C-mount. the preliminary data I saw on this said that it did JPEG compression. If that "feature" can't be turned off I would strongly suggest NOT using the camera. ------------------------------ Date: Thu, 29 Oct 1998 15:21:09 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: bubbles continued Message-ID: <19981029232109.3672.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > I have tried the Analyse particles routines, but it does not appear to > yield an explicit bubbles size distribution. If you have calibrated the image to some units like "mm", then check area for measurement options you will then get a list of sizes after running the routine. It isn't a histogram of sizes but that could be done of course, it will simply be a list in the results window. Touching particles are another matter and there are multiple ways to handle this from simple to the very complex. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST) From: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Imagemath Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Can anybody help me with a macro problem concerning Imagemath in a stack manipulation? Everything seems to work except that I can't pass the parameter back to tell it where to store the enhanced image. Using something like "Imagemath('sub',.......,'Image'(i)) to make it store in a new set of images called "image1", "Image2" etc. doesn't work, and nor daoes anything else I've tried. Any ideas? Thanks. Lesley Weston. ------------------------------ Date: Thu, 29 Oct 1998 18:15:41 -1000 From: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu Subject: Can a snappy be used for? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I'm a graduate student looking for a simple solution for capturing reasonable scientific images from several differing microscopes which each have a different brand name of video mounted to each individual microscope. I've read that 640 x 480 resolution is a minimal standard for video capture. I've also read that the Capsure card is not appropriate for this type of work as resolution is 320x240 which is interpolated up to 640x480. The following is a FAQ answer from Snappy's web site. A: Actually, video ISN'T 640 x 480. This is a common misconception in the computer world. .................... NTSC video is an analog signal with no fixed resolution. The more times you 'sample' the signal the better your digital representation gets............................ ..we can calculate based on the bandwidth of video that the point of diminishing returns is reached around 1500 samples per line. To sample at this resolution Play designed our own custom chip....................... time base correction, spatial and temporal filters, interpolation algorithms and more................................... Because NTSC video is only 480 lines tall Snappy interpolates the image vertically to maintain square pixels. This algorithm is called Third Order Polynomial Interpolation. My questions: Is an image treated to this inexpensive method of acquisition reasonable for scientific measurements (I'm working on bone histmorphometry measurements)? Will a Snappy framegrabber work well with PC notebooks? Are there any serious flaws created by using an inexpensive framegrabber or difficulties in capturing images on notebooks? Thank you very much for any answers. Kathleen Moore -------------------------------- End of nih-image-d Digest V98 Issue #100 **************************************** From nih-image-request@io.ece.drexel.edu Fri Oct 30 00:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA29028; Fri, 30 Oct 1998 00:01:34 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 00:01:34 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: lesley@interchange.ubc.ca, nih-image@io.ece.drexel.edu Date: Fri, 30 Oct 1998 14:52:27 GMT+1100 Subject: Re: Imagemath Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <7062F86C2D@rna.bio.mq.edu.au> Resent-Message-ID: <"5SQuR3.0.Rr5.gNKEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/540 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1169 >Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST) >From: Lesley Weston > >Can anybody help me with a macro problem concerning Imagemath in a stack >manipulation? Everything seems to work except that I can't pass the parameter >back to tell it where to store the enhanced image. Using something like >"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of >images called "image1", "Image2" etc. doesn't work, and nor daoes anything else >I've tried. Any ideas? Thanks. > >Lesley Weston. > macro'/0text';var i:integer; begin i:=3; Imagemath('sub',1,2,1,0,concat('Image',i:0)); end will subtract picNumbers 1,2 to produce 'Image3'. without the ':0' you would get 'Image...3' {where . is blank} but if as you suggest, you are doing "stack manipulation" for output, then you could do imageMath to the n'th slice of an existing stack whose pidNumber is stackId:= pidNumber; selectPic(stackId);selectSlice(n);Imagemath('sub',pid1,pid2,1,0,stackId); Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Fri Oct 30 04:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA12471; Fri, 30 Oct 1998 04:28:40 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 04:28:40 -0500 (EST) X-Sender: sdb@pop1.liv.ac.uk Message-Id: In-Reply-To: <199810291101.GAA20187@io.ece.drexel.edu> Mime-Version: 1.0 Date: Fri, 30 Oct 1998 09:16:00 +0000 To: nih-image@io.ece.drexel.edu From: Steve Barrett Subject: Re: Bubble size distribution Cc: Michael Norato Resent-Message-ID: <"t3S7b.0.DY1.cFOEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/541 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 831 >I have tried the Analyse particles routines, but it does not appear to >yield an explicit bubbles size distribution. > >Sometimes the bubbles touch, but not often. The NIH Image spin-off 'Image SXM' can analyse bubble size distributions. It uses a Hough transform algorithm, and so incomplete or touching bubbles are detected. A copy of the Image SXM installer is in the spin-offs folder on the NIH Image server. You can find more information about Image SXM from http://reg.ssci.liv.ac.uk ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ From nih-image-request@io.ece.drexel.edu Fri Oct 30 07:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA18416; Fri, 30 Oct 1998 07:41:28 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 07:41:28 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <59632dee.3639af54@aol.com> Date: Fri, 30 Oct 1998 07:21:40 EST To: nih-image@io.ece.drexel.edu Cc: moorekat@hawaii.edu Mime-Version: 1.0 Subject: Re: Can a snappy be used for? Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"kQ49s.0.l92.D-QEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/542 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2807 In a message dated 10/29/98 11:23:09 PM, moorekat@hawaii.edu wrote: ... > >The following is a FAQ answer from Snappy's web site. > >A: Actually, video ISN'T 640 x 480. This is a common misconception in the >computer world. .................... NTSC video is an analog signal with >no fixed resolution. The more times you 'sample' the signal the better >your digital representation gets............................ ..we can >calculate based on the bandwidth of video that the point of diminishing >returns is reached around 1500 samples per line. To sample at this >resolution Play designed our own custom chip....................... > time base correction, spatial and temporal filters, interpolation >algorithms and more................................... Because >NTSC video is only 480 lines tall Snappy interpolates the image vertically >to maintain square pixels. This algorithm is called Third Order >Polynomial Interpolation. > > My questions: Is an image treated to this inexpensive method of >acquisition reasonable for scientific measurements (I'm working on bone >histmorphometry measurements)? >Will a Snappy framegrabber work well with PC notebooks? >Are there any serious flaws created by using an inexpensive framegrabber >or difficulties in capturing images on notebooks? ... The snappy answer is correct but perhaps a bit optimistic. It is important to remember that video is an analog signal and that any digitizer ("framegrabber") samples it. The common use of 640x480 has more to do with the dimensions of standard VGA displays than anything in the video signal itself. Based on the bandwidth of the video signal the maximum number of discrete points that can be sampled along a line is actually about 330, far less than the 1500 snappy claims. But for visual purposes, the oversampling (empty magnification) is acceptable to make pretty images. Likewise few video images have more than 400 scan lines of actual image, although ideally there are 480 between vertical retrace events. The simple fact is that a video image digitized with Snappy is quite suitable for anything that video is good enough for in the first place (digital cameras are available with much higher resolution). The Snappy does a very good job - I would recommend not using the 1500 wide pixel image since there really isn't any more information than in a smaller and more convenient 640x480 size (which it will also grab), and I would further recommend using the mode in which you average together 8 frames which reduces noise quite a bit. But the basic answer is - yes, use the Snappy. It works great and will let you do good image analysis with a basic PC. I use one with a laptop (generic, running WinNT with Photoshop and the Image Processing Tool Kit) and am quite pleased with the results. John Russ From nih-image-request@io.ece.drexel.edu Fri Oct 30 09:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27645; Fri, 30 Oct 1998 09:07:22 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 09:07:22 -0500 (EST) X-Server-Uuid: 9b0d4bf4-4be9-11d2-b9cf-0008c7f450b1 X-Lotus-FromDomain: ARCO From: "Dan Frich" To: nih-image@io.ece.drexel.edu Message-ID: <852566AD.00498551.00@nsns-h01.arcochem.com> Date: Fri, 30 Oct 1998 08:35:43 -0500 Subject: watershed segmentation Mime-Version: 1.0 Resent-Message-ID: <"dyThF.0.t54.1CSEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/543 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 637 I was wondering if anyone could give me any help with the watershed segmentation routine in v. 1.61. I am using Image to analyze sizes and distributions in cellular materials. To do this, I use watershed segmentation to yield discrete cells and then use the analyze particles routine to measure individual cell sizes (areas). This technique works extremely well except for the fact that I tend to get some degree of oversegmentation (splitting of cells that should be counted as only one) in the watershed routine. Does anyone have any ideas or experience on how to correct this problem? My appreciation in advance, Dan Frich From nih-image-request@io.ece.drexel.edu Fri Oct 30 09:54 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21136; Fri, 30 Oct 1998 09:54:21 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 09:54:21 -0500 (EST) Message-ID: <01BE03E7.F6BA8460@OAKMONT.SEAS.UPENN.EDU> From: Eric Johnston To: "nih-image@io.ece.drexel.edu" Subject: RE: analog to digital (was: Can a snappy be used for?) Date: Fri, 30 Oct 1998 09:30:40 -0500 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA08662 Resent-Message-ID: <"J9iSX1.0.s72.vrSEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/544 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2176 Dr Russ Could you explain further how video bandwidth limits the digitization of a line of video signal to only about 330 pixels? For that matter, what is "bandwidth"? Is there is a distinction between "analog bandwidth" and the "digital bandwidth" we hear so much about? Eric Johnston Department of Bioengineering University of Pennsylvania 120 Hayden Hall 3320 Smith Walk Philadelphia, PA 19104-6392 215-898-1958 (F) 215-573-2071 ericdj@seas.upenn.edu ---------- From: DrJohnRuss@aol.com [SMTP:DrJohnRuss@aol.com] Sent: Friday, October 30, 1998 7:22 AM To: nih-image@io.ece.drexel.edu Cc: moorekat@hawaii.edu Subject: Re: Can a snappy be used for? The snappy answer is correct but perhaps a bit optimistic. It is important to remember that video is an analog signal and that any digitizer ("framegrabber") samples it. The common use of 640x480 has more to do with the dimensions of standard VGA displays than anything in the video signal itself. Based on the bandwidth of the video signal the maximum number of discrete points that can be sampled along a line is actually about 330, far less than the 1500 snappy claims. But for visual purposes, the oversampling (empty magnification) is acceptable to make pretty images. Likewise few video images have more than 400 scan lines of actual image, although ideally there are 480 between vertical retrace events. The simple fact is that a video image digitized with Snappy is quite suitable for anything that video is good enough for in the first place (digital cameras are available with much higher resolution). The Snappy does a very good job - I would recommend not using the 1500 wide pixel image since there really isn't any more information than in a smaller and more convenient 640x480 size (which it will also grab), and I would further recommend using the mode in which you average together 8 frames which reduces noise quite a bit. But the basic answer is - yes, use the Snappy. It works great and will let you do good image analysis with a basic PC. I use one with a laptop (generic, running WinNT with Photoshop and the Image Processing Tool Kit) and am quite pleased with the results. John Russ From nih-image-request@io.ece.drexel.edu Fri Oct 30 12:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA25302; Fri, 30 Oct 1998 12:01:47 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 12:01:47 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Fri, 30 Oct 1998 11:40:36 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: RE: analog to digital (was: Can a snappy be used for?) Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"HqTuL3.0.yv3.9oUEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/545 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 613 In a message dated 10/30/98 9:39:29 AM, you wrote: >Could you explain further how video bandwidth limits the digitization of a line >of video signal to only about 330 pixels? For that matter, what is "bandwidth"? > Is there is a distinction between "analog bandwidth" and the "digital bandwidth" >we hear so much about? Too long a question for email. Read a good book. Start with Inoue "Video Microscopy." There is also a lot of information in books like Pratt "Digital Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods "Digital Image Proc" and my own "Image Processing Handbook" From nih-image-request@io.ece.drexel.edu Fri Oct 30 12:44 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA16479; Fri, 30 Oct 1998 12:44:11 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 12:44:11 -0500 (EST) X-Sender: jreidler@10.0.0.1 Message-Id: In-Reply-To: <199810300420.XAA07340@io.ece.drexel.edu> Mime-Version: 1.0 Date: Fri, 30 Oct 1998 12:18:12 -0500 To: nih-image@io.ece.drexel.edu From: Jeff Reidler Subject: Re: Snappy in Digest V98 #100 Resent-Message-ID: <"BKLJl.0.Ep.GJVEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/546 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1289 Date: Thu, 29 Oct 1998 18:15:41 -1000 From: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu >I've read that 640 x 480 resolution is a minimal standard for video >capture. I've also read that the Capsure card is not appropriate for this >type of work as resolution is 320x240 which is interpolated up to 640x480. > >The following is a FAQ answer from Snappy's web site. >>A: Actually, video ISN'T 640 x 480...... >> The more times you 'sample' the signal the better your digital >> representation gets....... > My questions: Is an image treated to this inexpensive method of >acquisition reasonable for scientific measurements (I'm working on bone >histmorphometry measurements)? It depends on the detail you require. I can send you comparisons of different grabbers and different cameras of the same image field if you want to see side-by-side comparions of the same image. I have a comparison for the Snappy with the CG-7 from Scion. Reply to info@scioncorp.com if you are interested. Jeff Jeffry A. Reidler, PhD jreidler@scioncorp.com Commercial and Applications http://www.scioncorp.com Scion Corporation tel 301-695-7870 82 Wormans Mill Ct, Suite H fax 301-695-0035 Frederick, MD 21701 USA From nih-image-request@io.ece.drexel.edu Fri Oct 30 15:40 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA17452; Fri, 30 Oct 1998 15:40:26 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 15:40:26 -0500 (EST) Message-Id: <199810302011.MAA09986@oes.edu> From: "Lynn Huynh" Organization: Oregon Episcopal School To: nih-image@io.ece.drexel.edu Date: Fri, 30 Oct 1998 12:12:02 -0800 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: tracking asteroids... Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01b) Resent-Message-ID: <"trKrE3.0.501.BvXEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/547 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 298 hi, i am wondering if anyone knows how to use nih-image to track asteroids in photos taken off the net... or rather to make the question broader, does anyone have a detailed procedure on how to use the stacking feature of the program? thank you, lynn lynnh@us1.oes.edu supershiny@hotmail.com From nih-image-request@io.ece.drexel.edu Fri Oct 30 15:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA19060; Fri, 30 Oct 1998 15:43:36 -0500 (EST) Resent-Date: Fri, 30 Oct 1998 15:43:36 -0500 (EST) Message-Id: <199810302015.MAA09991@oes.edu> From: "Lynn Huynh" Organization: Oregon Episcopal School To: nih-image@io.ece.drexel.edu Date: Fri, 30 Oct 1998 12:16:01 -0800 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: electrophoretic gel reading... Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01b) Resent-Message-ID: <"fkhPz.0.4V1.lyXEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/548 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 426 how do i use nih-image to analyze electrophoretic gels? i need better readings on some gels that i have. i have been using page techniques and will be needing to analyze not just whether the band is detectable but also which bands are darker, i will be using this information to create a haplotype and do two-point lod score analysis with linkage 5.1 software thank you, lynn lynnh@us1.oes.edu supershiny@hotmail.com From nih-image-d-request@io.ece.drexel.edu Fri Oct 30 15:46 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA20514; Fri, 30 Oct 1998 15:46:33 -0500 (EST) Date: Fri, 30 Oct 1998 15:46:33 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810302046.PAA20514@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #101 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/101 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 13046 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 101 Today's Topics: Re: Imagemath [ GJOSS@rna.bio.mq.edu.au ] Re: Bubble size distribution [ Steve Barrett ] RE: analog to digital (was: Can a sn [ Eric Johnston ] ------------------------------ Date: Fri, 30 Oct 1998 14:52:27 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: lesley@interchange.ubc.ca, nih-image@io.ece.drexel.edu Subject: Re: Imagemath Message-ID: <7062F86C2D@rna.bio.mq.edu.au> >Date: Thu, 29 Oct 1998 17:09:04 -0800 (PST) >From: Lesley Weston > >Can anybody help me with a macro problem concerning Imagemath in a stack >manipulation? Everything seems to work except that I can't pass the parameter >back to tell it where to store the enhanced image. Using something like >"Imagemath('sub',.......,'Image'(i)) to make it store in a new set of >images called "image1", "Image2" etc. doesn't work, and nor daoes anything else >I've tried. Any ideas? Thanks. > >Lesley Weston. > macro'/0text';var i:integer; begin i:=3; Imagemath('sub',1,2,1,0,concat('Image',i:0)); end will subtract picNumbers 1,2 to produce 'Image3'. without the ':0' you would get 'Image...3' {where . is blank} but if as you suggest, you are doing "stack manipulation" for output, then you could do imageMath to the n'th slice of an existing stack whose pidNumber is stackId:= pidNumber; selectPic(stackId);selectSlice(n);Imagemath('sub',pid1,pid2,1,0,stackId); Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 30 Oct 1998 09:16:00 +0000 From: Steve Barrett To: nih-image@io.ece.drexel.edu Cc: Michael Norato Subject: Re: Bubble size distribution Message-Id: Content-Type: text/plain; charset="us-ascii" >I have tried the Analyse particles routines, but it does not appear to >yield an explicit bubbles size distribution. > >Sometimes the bubbles touch, but not often. The NIH Image spin-off 'Image SXM' can analyse bubble size distributions. It uses a Hough transform algorithm, and so incomplete or touching bubbles are detected. A copy of the Image SXM installer is in the spin-offs folder on the NIH Image server. You can find more information about Image SXM from http://reg.ssci.liv.ac.uk ___________________________________________________________________ Dr Steve Barrett Surface Science Research Centre University of Liverpool Liverpool L69 3BX United Kingdom Tel: 44-(0)151-794-3874 / 3894 / 3870 Fax: 44-(0)151-708-0662 Email: S.D.Barrett@liv.ac.uk ___________________________________________________________________ ------------------------------ Date: Fri, 30 Oct 1998 07:21:40 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Cc: moorekat@hawaii.edu Subject: Re: Can a snappy be used for? Message-ID: <59632dee.3639af54@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 10/29/98 11:23:09 PM, moorekat@hawaii.edu wrote: ... > >The following is a FAQ answer from Snappy's web site. > >A: Actually, video ISN'T 640 x 480. This is a common misconception in the >computer world. .................... NTSC video is an analog signal with >no fixed resolution. The more times you 'sample' the signal the better >your digital representation gets............................ ..we can >calculate based on the bandwidth of video that the point of diminishing >returns is reached around 1500 samples per line. To sample at this >resolution Play designed our own custom chip....................... > time base correction, spatial and temporal filters, interpolation >algorithms and more................................... Because >NTSC video is only 480 lines tall Snappy interpolates the image vertically >to maintain square pixels. This algorithm is called Third Order >Polynomial Interpolation. > > My questions: Is an image treated to this inexpensive method of >acquisition reasonable for scientific measurements (I'm working on bone >histmorphometry measurements)? >Will a Snappy framegrabber work well with PC notebooks? >Are there any serious flaws created by using an inexpensive framegrabber >or difficulties in capturing images on notebooks? ... The snappy answer is correct but perhaps a bit optimistic. It is important to remember that video is an analog signal and that any digitizer ("framegrabber") samples it. The common use of 640x480 has more to do with the dimensions of standard VGA displays than anything in the video signal itself. Based on the bandwidth of the video signal the maximum number of discrete points that can be sampled along a line is actually about 330, far less than the 1500 snappy claims. But for visual purposes, the oversampling (empty magnification) is acceptable to make pretty images. Likewise few video images have more than 400 scan lines of actual image, although ideally there are 480 between vertical retrace events. The simple fact is that a video image digitized with Snappy is quite suitable for anything that video is good enough for in the first place (digital cameras are available with much higher resolution). The Snappy does a very good job - I would recommend not using the 1500 wide pixel image since there really isn't any more information than in a smaller and more convenient 640x480 size (which it will also grab), and I would further recommend using the mode in which you average together 8 frames which reduces noise quite a bit. But the basic answer is - yes, use the Snappy. It works great and will let you do good image analysis with a basic PC. I use one with a laptop (generic, running WinNT with Photoshop and the Image Processing Tool Kit) and am quite pleased with the results. John Russ ------------------------------ Date: Fri, 30 Oct 1998 08:35:43 -0500 From: "Dan Frich" To: nih-image@io.ece.drexel.edu Subject: watershed segmentation Message-ID: <852566AD.00498551.00@nsns-h01.arcochem.com> Content-type: text/plain; charset=us-ascii I was wondering if anyone could give me any help with the watershed segmentation routine in v. 1.61. I am using Image to analyze sizes and distributions in cellular materials. To do this, I use watershed segmentation to yield discrete cells and then use the analyze particles routine to measure individual cell sizes (areas). This technique works extremely well except for the fact that I tend to get some degree of oversegmentation (splitting of cells that should be counted as only one) in the watershed routine. Does anyone have any ideas or experience on how to correct this problem? My appreciation in advance, Dan Frich ------------------------------ Date: Fri, 30 Oct 1998 09:30:40 -0500 From: Eric Johnston To: "nih-image@io.ece.drexel.edu" Subject: RE: analog to digital (was: Can a snappy be used for?) Message-ID: <01BE03E7.F6BA8460@OAKMONT.SEAS.UPENN.EDU> Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit Dr Russ Could you explain further how video bandwidth limits the digitization of a line of video signal to only about 330 pixels? For that matter, what is "bandwidth"? Is there is a distinction between "analog bandwidth" and the "digital bandwidth" we hear so much about? Eric Johnston Department of Bioengineering University of Pennsylvania 120 Hayden Hall 3320 Smith Walk Philadelphia, PA 19104-6392 215-898-1958 (F) 215-573-2071 ericdj@seas.upenn.edu ---------- From: DrJohnRuss@aol.com [SMTP:DrJohnRuss@aol.com] Sent: Friday, October 30, 1998 7:22 AM To: nih-image@io.ece.drexel.edu Cc: moorekat@hawaii.edu Subject: Re: Can a snappy be used for? The snappy answer is correct but perhaps a bit optimistic. It is important to remember that video is an analog signal and that any digitizer ("framegrabber") samples it. The common use of 640x480 has more to do with the dimensions of standard VGA displays than anything in the video signal itself. Based on the bandwidth of the video signal the maximum number of discrete points that can be sampled along a line is actually about 330, far less than the 1500 snappy claims. But for visual purposes, the oversampling (empty magnification) is acceptable to make pretty images. Likewise few video images have more than 400 scan lines of actual image, although ideally there are 480 between vertical retrace events. The simple fact is that a video image digitized with Snappy is quite suitable for anything that video is good enough for in the first place (digital cameras are available with much higher resolution). The Snappy does a very good job - I would recommend not using the 1500 wide pixel image since there really isn't any more information than in a smaller and more convenient 640x480 size (which it will also grab), and I would further recommend using the mode in which you average together 8 frames which reduces noise quite a bit. But the basic answer is - yes, use the Snappy. It works great and will let you do good image analysis with a basic PC. I use one with a laptop (generic, running WinNT with Photoshop and the Image Processing Tool Kit) and am quite pleased with the results. John Russ ------------------------------ Date: Fri, 30 Oct 1998 11:40:36 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: RE: analog to digital (was: Can a snappy be used for?) Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 10/30/98 9:39:29 AM, you wrote: >Could you explain further how video bandwidth limits the digitization of a line >of video signal to only about 330 pixels? For that matter, what is "bandwidth"? > Is there is a distinction between "analog bandwidth" and the "digital bandwidth" >we hear so much about? Too long a question for email. Read a good book. Start with Inoue "Video Microscopy." There is also a lot of information in books like Pratt "Digital Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods "Digital Image Proc" and my own "Image Processing Handbook" ------------------------------ Date: Fri, 30 Oct 1998 12:18:12 -0500 From: Jeff Reidler To: nih-image@io.ece.drexel.edu Subject: Re: Snappy in Digest V98 #100 Message-Id: Content-Type: text/plain; charset="us-ascii" Date: Thu, 29 Oct 1998 18:15:41 -1000 From: Kathleen Annikki Moore To: nih-image@io.ece.drexel.edu >I've read that 640 x 480 resolution is a minimal standard for video >capture. I've also read that the Capsure card is not appropriate for this >type of work as resolution is 320x240 which is interpolated up to 640x480. > >The following is a FAQ answer from Snappy's web site. >>A: Actually, video ISN'T 640 x 480...... >> The more times you 'sample' the signal the better your digital >> representation gets....... > My questions: Is an image treated to this inexpensive method of >acquisition reasonable for scientific measurements (I'm working on bone >histmorphometry measurements)? It depends on the detail you require. I can send you comparisons of different grabbers and different cameras of the same image field if you want to see side-by-side comparions of the same image. I have a comparison for the Snappy with the CG-7 from Scion. Reply to info@scioncorp.com if you are interested. Jeff Jeffry A. Reidler, PhD jreidler@scioncorp.com Commercial and Applications http://www.scioncorp.com Scion Corporation tel 301-695-7870 82 Wormans Mill Ct, Suite H fax 301-695-0035 Frederick, MD 21701 USA ------------------------------ Date: Fri, 30 Oct 1998 12:12:02 -0800 From: "Lynn Huynh" To: nih-image@io.ece.drexel.edu Subject: tracking asteroids... Message-Id: <199810302011.MAA09986@oes.edu> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT hi, i am wondering if anyone knows how to use nih-image to track asteroids in photos taken off the net... or rather to make the question broader, does anyone have a detailed procedure on how to use the stacking feature of the program? thank you, lynn lynnh@us1.oes.edu supershiny@hotmail.com -------------------------------- End of nih-image-d Digest V98 Issue #101 **************************************** From nih-image-d-request@io.ece.drexel.edu Sat Oct 31 10:36 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14150; Sat, 31 Oct 1998 10:36:40 -0500 (EST) Date: Sat, 31 Oct 1998 10:36:40 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199810311536.KAA14150@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #102 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/102 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1508 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 102 Today's Topics: electrophoretic gel reading... [ "Lynn Huynh" ] unsubscribe [ Sarah Krueger ] ------------------------------ Date: Fri, 30 Oct 1998 12:16:01 -0800 From: "Lynn Huynh" To: nih-image@io.ece.drexel.edu Subject: electrophoretic gel reading... Message-Id: <199810302015.MAA09991@oes.edu> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT how do i use nih-image to analyze electrophoretic gels? i need better readings on some gels that i have. i have been using page techniques and will be needing to analyze not just whether the band is detectable but also which bands are darker, i will be using this information to create a haplotype and do two-point lod score analysis with linkage 5.1 software thank you, lynn lynnh@us1.oes.edu supershiny@hotmail.com ------------------------------ Date: Sat, 31 Oct 1998 11:40:51 +0000 From: Sarah Krueger To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: <363AF740.98A9936C@fuse.net> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit PLEASE TAKE ME OFF THE MAILING LIST UNSUBSCRIBE TO NIH-IMAGE. -------------------------------- End of nih-image-d Digest V98 Issue #102 **************************************** From nih-image-request@io.ece.drexel.edu Sat Oct 31 10:39 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA16014; Sat, 31 Oct 1998 10:39:51 -0500 (EST) Resent-Date: Sat, 31 Oct 1998 10:39:51 -0500 (EST) Message-ID: <363AF740.98A9936C@fuse.net> Date: Sat, 31 Oct 1998 11:40:51 +0000 From: Sarah Krueger Reply-To: krueger@fuse.net X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: unsubscribe Content-Transfer-Encoding: 7bit Resent-Message-ID: <"DdBsA1.0.BO2.UooEs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/549 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 64 PLEASE TAKE ME OFF THE MAILING LIST UNSUBSCRIBE TO NIH-IMAGE. From nih-image-request@io.ece.drexel.edu Sat Oct 31 13:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA27974; Sat, 31 Oct 1998 13:01:20 -0500 (EST) Resent-Date: Sat, 31 Oct 1998 13:01:20 -0500 (EST) Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Modulus operation In-Reply-To: <199810311537.KAA14644@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"VoQFn2.0.6h4.3oqEs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/550 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 767 Attempts to create a modulus operation have been giving unpredictable results. Maybe someone can point out my mistake. I've been taking the quotient from division of 2 real vars, then subtracting the truncation of the quotient: var seglength,Mseglength,quotient,modulo:real; Trunk:integer; begin quotient:=MsegLength/segLength; Trunk:=trunc(quotient); modulo:=quotient-trunk; end; If SegLength is passed in as .N*MSegLength [to segment the midline into N divisions], then sometimes Trunk is N, other times it is N-1. TIA, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu From nih-image-request@io.ece.drexel.edu Sat Oct 31 21:12 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA11451; Sat, 31 Oct 1998 21:12:03 -0500 (EST) Resent-Date: Sat, 31 Oct 1998 21:12:03 -0500 (EST) Message-ID: <363BC0C3.5F93@thurston.com> Date: Sat, 31 Oct 1998 18:00:36 -0800 From: "Patrick T. Pringle" Reply-To: lespat@thurston.com X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: scanners and pixel aspect ratio References: <199810311530.KAA10944@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"V8K202.0.Pz.T0yEs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/551 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 957 Please excuse my naive question. I have been using two different scanners to obtain images for tree ring analysis. One is a Umax Astra 1200 (600 X 1200 true opt. res.) and the other an Epson that boasts 800 X 1600 TOR. 1. If I were to want to measure mean density of individual rings (assuming that's better than modal or integ density for dendro work) would I have to use the lower optical density value for each scanner in order to obtain homogeniety in resolution depth along both X and Y axes? ...or could I apply a pixel aspect ratio of 1/2 and actually take advantage of the greater resolution that scanners have in the direction of scanner head movement (long axis)? 2. The epson scanner has 12-bit an 16 bit settings (I scan in gray scale); is one preferable to the other considering I must import to 8-bit NIH or Scion image? When I do import, how do I know if the image I am importing is signed or unsigned, etc? Thanks -- Pat Pringle -- From nih-image-d-request@io.ece.drexel.edu Sun Nov 1 06:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA25864; Sun, 1 Nov 1998 06:17:35 -0500 (EST) Date: Sun, 1 Nov 1998 06:17:35 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811011117.GAA25864@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #103 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/103 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2734 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 103 Today's Topics: Modulus operation [ "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Modulus operation Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Attempts to create a modulus operation have been giving unpredictable results. Maybe someone can point out my mistake. I've been taking the quotient from division of 2 real vars, then subtracting the truncation of the quotient: var seglength,Mseglength,quotient,modulo:real; Trunk:integer; begin quotient:=MsegLength/segLength; Trunk:=trunc(quotient); modulo:=quotient-trunk; end; If SegLength is passed in as .N*MSegLength [to segment the midline into N divisions], then sometimes Trunk is N, other times it is N-1. TIA, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu ------------------------------ Date: Sat, 31 Oct 1998 18:00:36 -0800 From: "Patrick T. Pringle" To: nih-image@io.ece.drexel.edu Subject: scanners and pixel aspect ratio Message-ID: <363BC0C3.5F93@thurston.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse my naive question. I have been using two different scanners to obtain images for tree ring analysis. One is a Umax Astra 1200 (600 X 1200 true opt. res.) and the other an Epson that boasts 800 X 1600 TOR. 1. If I were to want to measure mean density of individual rings (assuming that's better than modal or integ density for dendro work) would I have to use the lower optical density value for each scanner in order to obtain homogeniety in resolution depth along both X and Y axes? ...or could I apply a pixel aspect ratio of 1/2 and actually take advantage of the greater resolution that scanners have in the direction of scanner head movement (long axis)? 2. The epson scanner has 12-bit an 16 bit settings (I scan in gray scale); is one preferable to the other considering I must import to 8-bit NIH or Scion image? When I do import, how do I know if the image I am importing is signed or unsigned, etc? Thanks -- Pat Pringle -- -------------------------------- End of nih-image-d Digest V98 Issue #103 **************************************** From nih-image-request@io.ece.drexel.edu Sun Nov 1 23:00 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA02255; Sun, 1 Nov 1998 23:00:09 -0500 (EST) Resent-Date: Sun, 1 Nov 1998 23:00:09 -0500 (EST) From: wpchan@socrates.berkeley.edu Date: Sun, 1 Nov 1998 19:28:45 -0800 (PST) To: nih-image@io.ece.drexel.edu cc: Bill Miller , SolamereTG@aol.com, Pat Arnott Subject: Re: video capture at 30 fps In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"9_w8c1.0.1p3.4SIFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/552 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2145 Many thanks for all the people that replied to my question. I further tested the LG-3 on the Mac and a Pentium machine myself. It is no doublt that the Scion LG-3 PCI card is built for the Mac (just look at the length of the card!). On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive 29.97 frames per sec at 640x480. The timing is right on the money. On a Dell Dimension with a 450 MHz Pentium II and 96 MB of RAM, STB nVidia 8MB VRAM running either Win95 or WinNT, the same procedure can only accquire video sequences at about 17 fps at 640x480. The only way to get it to accquire close to 30 fps is to cut down the size of the ROI for capturing to about half as suggested by various lister. Disabling various services, dropping the color depth of the display or adding more RAM did not make any differences. However, the timing of the capture fluctuates as system resources changes. Scion Image beta 3b has this strange memory leak that the system resources (users and GDI as well) drops steadily with each operation e.g. opening a large stack or make movie. Eventually, the capture rate in the make movie procedure will drop below 29.4 fps after a few of the said operation. Restarting the program will solve the problem. The conclusion from this exercise is that since we do want to maintain the quality of our digitized video by using the LG-3 PCI board, we do have to use a Mac for capturing full 30 fps at 640x480 with NIH-Image. For reason beyond my knowlegde, running Scion Image on a Windoz machine just won't do it. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Tue, 20 Oct 1998 wpchan@socrates.berkeley.edu wrote: > Recently we have bought a Scion LG3 PCI card to put in a Windows NT. The > highest capture rate that we can get with 'blind capture' in 'make movie' > is 17 fps. Scion Tech support confirmed that this is probably the highest > one can get on a NT. > > Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and > if so, under what condition and using what kind of computer? Thanks. From nih-image-request@io.ece.drexel.edu Mon Nov 2 04:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA19184; Mon, 2 Nov 1998 04:19:33 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 04:19:33 -0500 (EST) X-Sender: bmenard@pop-server.unil.ch Message-Id: Mime-Version: 1.0 Content-Transfer-Encoding: 8bit Date: Mon, 2 Nov 1998 09:59:09 +0100 To: nih-image@io.ece.drexel.edu From: Bertrand Menard Subject: RE : digital photo camera f. microscopy Resent-Message-ID: <"3-amA1.0.b74.XINFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/553 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1778 Hi Imagers, I've tried the Kodak digital camera with C-mount on a microscop. I don't think that's the good cameras for microscopy : 1- It's not a video camera, so you must take a snapshot, wait, look if it's good, change settings, retry, retry and retry. With video camera, you change settings in live, you see immediatly if image is good or not. When it's good, you take it. It's fast and easy. 2- With high magnification, the resolution of the camera (1500*1000) is highest than the optical resolution. With a 60x oel objective of 1.3 numerical aperture, the optical resolution is approximately the same than video resolution (500x700). So high camera resolution is only usefull for small magnification. A good product is the digital video camera of Leica : video, very friendly and usefull software, same price than Kodak with software and PCI card, very sensitive for fluorescence and resolution of 1400*1200 by interpolation (700*500 in normal mode). They announce for soon a new one with real 1400x1200 resolution and a Macintosh version. That's only my personnal experience. Best regards. Bertrand Mnard ********************************************************************* Bertrand MENARD Institute of Plant Biology Institut de Biologie et de and Physiology Physiologie Vgtales University of Lausanne Universit de Lausanne CH-1015 LAUSANNE CH-1015 LAUSANNE Switzerland Suisse Tel : 00 41 21 692 42 19 Fax : 00 41 21 692 41 95 E-Mail : Bertrand.Menard@ie-bpv.unil.ch ********************************************************************* From nih-image-request@io.ece.drexel.edu Mon Nov 2 09:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24043; Mon, 2 Nov 1998 09:41:22 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 09:41:22 -0500 (EST) X-Sender: zacchetti.daniele@mail.hsr.it Message-Id: Mime-Version: 1.0 Date: Mon, 2 Nov 1998 15:24:41 +0100 To: NIH Image mailing list From: Daniele Zacchetti Subject: Scion image for Windows Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/554 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 306 Does anybody know whether the Scion image source code (Windows95 or NT) is freely available? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it From nih-image-request@io.ece.drexel.edu Mon Nov 2 10:00 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA26231; Mon, 2 Nov 1998 10:00:01 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 10:00:01 -0500 (EST) Mime-Version: 1.0 Message-Id: In-Reply-To: Date: Mon, 2 Nov 1998 09:57:56 -0500 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: RE : digital photo camera f. microscopy Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA24286 Resent-Message-ID: <"HaZTX2.0.bx5.WKSFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/555 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 2448 While somewhat expensive I have been using the Sensys Camera for digital microscopy. It runs about 20,000 + but is a relatively high resolution (about 2000 x 1700 pixel resolution) camera and is a cooled low light camera as well. There is now a liquid crystal adaptor that will convert the camera to color (probably not good for very low light, but should work for bright fluorescence and does work well for darkfield images). The image quality is superb! >Hi Imagers, > >I've tried the Kodak digital camera with C-mount on a microscop. I don't >think that's the good cameras for microscopy : >1- It's not a video camera, so you must take a snapshot, wait, look if it's >good, change settings, retry, retry and retry. With video camera, you >change settings in live, you see immediatly if image is good or not. When >it's good, you take it. It's fast and easy. >2- With high magnification, the resolution of the camera (1500*1000) is >highest than the optical resolution. With a 60x oel objective of 1.3 >numerical aperture, the optical resolution is approximately the same than >video resolution (500x700). So high camera resolution is only usefull for >small magnification. > >A good product is the digital video camera of Leica : video, very friendly >and usefull software, same price than Kodak with software and PCI card, >very sensitive for fluorescence and resolution of 1400*1200 by >interpolation (700*500 in normal mode). They announce for soon a new one >with real 1400x1200 resolution and a Macintosh version. > >That's only my personnal experience. > >Best regards. > > > >Bertrand Mnard > >********************************************************************* > > Bertrand MENARD > >Institute of Plant Biology Institut de Biologie et de > and Physiology Physiologie Vgtales > University of Lausanne Universit de Lausanne > CH-1015 LAUSANNE CH-1015 LAUSANNE > Switzerland Suisse > > Tel : 00 41 21 692 42 19 > Fax : 00 41 21 692 41 95 > > E-Mail : Bertrand.Menard@ie-bpv.unil.ch > >********************************************************************* Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu From nih-image-request@io.ece.drexel.edu Mon Nov 2 10:38 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04623; Mon, 2 Nov 1998 10:38:40 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 10:38:40 -0500 (EST) Reply-To: From: "Ned Horning" To: Subject: RE: Scion image for Windows Date: Mon, 2 Nov 1998 18:12:00 +0300 Message-ID: <000401be0673$23d0e150$495499d0@nedh> MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 In-Reply-To: Resent-Message-ID: <"E-UhC1.0.Nq6.mpSFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/556 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1193 Daniele, I asked the folks at Scion Corp. about this nearly a year ago and the response I got was "At this time we will not be releasing any source code for Scion Image for Windows. This policy may change in the future but it is very doubtful." After I received this message my superiors tried to follow up to see if we could negotiate something but Scion did not respond. You may want to look at the source code for ImageJ. There are several advantages to using ImageJ since it does not have some of the limitations of NIH Image and Scion Image. Wayne is doing a great job with ImageJ and interest in it seems to be growing. I wish you luck in your search for the Scion Image source code. Ned -----Original Message----- From: Daniele Zacchetti [mailto:zacchetti.daniele@hsr.it] Sent: Monday, November 02, 1998 5:25 PM To: NIH Image mailing list Subject: Scion image for Windows Does anybody know whether the Scion image source code (Windows95 or NT) is freely available? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it From nih-image-request@io.ece.drexel.edu Mon Nov 2 10:47 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA09498; Mon, 2 Nov 1998 10:47:34 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 10:47:34 -0500 (EST) X-Sender: jfitz@crgdmail1.cr.usgs.gov Message-Id: Mime-Version: 1.0 Date: Mon, 2 Nov 1998 08:25:08 -0600 To: nih-image@io.ece.drexel.edu From: "Joan J. Fitzpatrick" Subject: unsubscribe Resent-Message-ID: <"U0VdU1.0.R57.szSFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/557 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 27 UNSUBSCRIBE TO NIH-IMAGE From nih-image-request@io.ece.drexel.edu Mon Nov 2 12:35 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22176; Mon, 2 Nov 1998 12:35:22 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 12:35:22 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 2 Nov 1998 13:07:27 -0400 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: Re: unsubscribe Resent-Message-ID: <"XotsM.0.sk4.RRUFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/558 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 3677 CourierHi everyone. The following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". 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Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Mon Nov 2 12:39 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22673; Mon, 2 Nov 1998 12:39:32 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 12:39:32 -0500 (EST) Message-Id: <363DE87E.7E4A67C2@cirl.meei.harvard.edu> Date: Mon, 02 Nov 1998 12:14:40 -0500 From: Scott Cramer Reply-To: srcramer@cirl.meei.harvard.edu Organization: HMS/MEEI/WHOI X-Mailer: Mozilla 4.05 (Macintosh; I; 68K) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Unsubscribe Resent-Message-ID: <"U5Rm63.0.Px4.XXUFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/559 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/mixed; boundary="------------98611CBC770253999159B05A" Content-Length: 931 This is a multi-part message in MIME format. --------------98611CBC770253999159B05A Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Unsubscribe me please. Thank you. --------------98611CBC770253999159B05A Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Scott Cramer Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Scott Cramer n: Cramer;Scott org: Massachusetts Eye & Ear Infirmary adr;dom: ;;243 Charles Street;Boston;MA;02114; email;internet: srcramer@cirl.meei.harvard.edu title: Research Assistant II tel;work: 617-573-4273 tel;fax: 617-573-4275 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------98611CBC770253999159B05A-- From nih-image-request@io.ece.drexel.edu Mon Nov 2 13:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25406; Mon, 2 Nov 1998 13:07:34 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 13:07:34 -0500 (EST) From: Vaughn Adams Message-Id: <199811021739.MAA18604@cbis.ece.drexel.edu> Subject: Administrative Help To: nih-image@io.ece.drexel.edu Date: Mon, 2 Nov 1998 12:39:27 -0500 (EST) X-Mailer: ELM [version 2.4ME+ PL48 (25)] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"EfA4j1.0.MY5.LvUFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/560 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: application/pgp; format=text; x-action=sign Content-Length: 1106 -----BEGIN PGP SIGNED MESSAGE----- Nih-Image List members: List administrative commands will be sent out the 15th of every month. It will contain commands to subscribe, unsubscribe and search the archives. I hope that this will cut down on the number of unsubscribe requests to the list itself. You can get the same information by sending mail to nih-image-request@biomed.drexel.edu with Help in the subject. I would also like to take the opportunity to mention that the nih-mailing list has reached 779 list members. - -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu -----BEGIN PGP SIGNATURE----- Version: 2.6.2 iQCVAwUBNj3uSooTfOp6Z5FxAQGjvwQAzBXku1i8qE9/Hc/TMNtlfeNL9A75s2xE faonRnBbmpr4HR0MKNbM/8bEipfexmJ1lwi0oPHx33RK6T5Xm11ESEufkqri0KlM nzjm0+IQehy9gMJ7K/6roa3sFzibaK9WLHpY3EYhtchTOJWsesGFe53xmHH1bIcN 3RxTCNPtAIA= =O58A -----END PGP SIGNATURE----- From nih-image-request@io.ece.drexel.edu Mon Nov 2 17:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA25097; Mon, 2 Nov 1998 17:15:51 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 17:15:51 -0500 (EST) Message-ID: <363E29FF.32792D8@netmatters.co.uk> Date: Mon, 02 Nov 1998 21:54:19 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: tracking asteroids... References: <199810302011.MAA09986@oes.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"PmwHz.0.ek3.vgYFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/561 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 721 Use ImageMath to determine if the position of the asteroids have changed between images. Subtract image n from image n+1 the length of the resultant white/black bits of the images will allow you to calculate the velocity of the asteroids and direction, assuming you can scale the images accurately. John Russ's Image Processing hand book covers this topic very nicely pp273-276. Jeremy Lynn Huynh wrote: > hi, i am wondering if anyone knows how to use nih-image to track > asteroids in photos taken off the net... or rather to make the > question broader, does anyone have a detailed procedure on how > to use the stacking feature of the program? > > thank you, > lynn > lynnh@us1.oes.edu > supershiny@hotmail.com From nih-image-request@io.ece.drexel.edu Mon Nov 2 17:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA26446; Mon, 2 Nov 1998 17:18:20 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 17:18:20 -0500 (EST) Message-ID: <363E1882.62A74C1D@netmatters.co.uk> Date: Mon, 02 Nov 1998 20:39:39 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: watershed segmentation References: <852566AD.00498551.00@nsns-h01.arcochem.com> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"NMWXj1.0.0m3.zgYFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/562 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 1234 A good cheat here is to convert your threshold / density slice image into binary, use AnalyzeParticles (with the label and outline function disabled) then threshold and makebinary again. This will fill any holes in the cells which may be contributing to the errors associated with the watershed algorithm. If you are interested in the greyscale values of the cells or their internal components you can use the X,Y location of the center of each cell in conjunction with Autooutline to apply a ROI to the original image and continue your analysis. Jeremy Dan Frich wrote: > I was wondering if anyone could give me any help with the watershed > segmentation routine in v. 1.61. I am using Image to analyze sizes and > distributions in cellular materials. To do this, I use watershed > segmentation to yield discrete cells and then use the analyze particles > routine to measure individual cell sizes (areas). This technique works > extremely well except for the fact that I tend to get some degree of > oversegmentation (splitting of cells that should be counted as only one) in > the watershed routine. Does anyone have any ideas or experience on how to > correct this problem? > > My appreciation in advance, > Dan Frich From nih-image-d-request@io.ece.drexel.edu Mon Nov 2 17:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA04636; Mon, 2 Nov 1998 17:34:07 -0500 (EST) Date: Mon, 2 Nov 1998 17:34:07 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811022234.RAA04636@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #104 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/104 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 19331 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 104 Today's Topics: Re: video capture at 30 fps [ wpchan@socrates.berkeley.edu ] Use of Scion Image with Imagraph Cor [ "Twilley, John" ] unsubscribe [ "Joan J. Fitzpatrick" , SolamereTG@aol.com, Pat Arnott Subject: Re: video capture at 30 fps Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Many thanks for all the people that replied to my question. I further tested the LG-3 on the Mac and a Pentium machine myself. It is no doublt that the Scion LG-3 PCI card is built for the Mac (just look at the length of the card!). On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive 29.97 frames per sec at 640x480. The timing is right on the money. On a Dell Dimension with a 450 MHz Pentium II and 96 MB of RAM, STB nVidia 8MB VRAM running either Win95 or WinNT, the same procedure can only accquire video sequences at about 17 fps at 640x480. The only way to get it to accquire close to 30 fps is to cut down the size of the ROI for capturing to about half as suggested by various lister. Disabling various services, dropping the color depth of the display or adding more RAM did not make any differences. However, the timing of the capture fluctuates as system resources changes. Scion Image beta 3b has this strange memory leak that the system resources (users and GDI as well) drops steadily with each operation e.g. opening a large stack or make movie. Eventually, the capture rate in the make movie procedure will drop below 29.4 fps after a few of the said operation. Restarting the program will solve the problem. The conclusion from this exercise is that since we do want to maintain the quality of our digitized video by using the LG-3 PCI board, we do have to use a Mac for capturing full 30 fps at 640x480 with NIH-Image. For reason beyond my knowlegde, running Scion Image on a Windoz machine just won't do it. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Tue, 20 Oct 1998 wpchan@socrates.berkeley.edu wrote: > Recently we have bought a Scion LG3 PCI card to put in a Windows NT. The > highest capture rate that we can get with 'blind capture' in 'make movie' > is 17 fps. Scion Tech support confirmed that this is probably the highest > one can get on a NT. > > Has anybody successfully get the LG3 PCI to capture to RAM at 30 fps and > if so, under what condition and using what kind of computer? Thanks. ------------------------------ Date: Sun, 1 Nov 1998 21:31:33 -0800 From: "Twilley, John" To: "'nih-image-d@biomed.drexel.edu'" Subject: Use of Scion Image with Imagraph Corp. frame grabbers Message-ID: <7366F79ECE20D21197A400805FA7629F0F8F3B@mercury.lacma.org> Content-Type: text/plain Does anyone have experience with using the frame averaging capabilities of the pc version of nih-image during dynamic acquisition on an Imagraph frame grabber such as the H-Def III, H-Def+ or Acura models? Is it possible to do this with a macro for those of us who already own a grabber other than the ones made by Scion? jtwilley@sprynet.com ------------------------------ Date: Mon, 2 Nov 1998 09:59:09 +0100 From: Bertrand Menard To: nih-image@io.ece.drexel.edu Subject: RE : digital photo camera f. microscopy Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hi Imagers, I've tried the Kodak digital camera with C-mount on a microscop. I don't think that's the good cameras for microscopy : 1- It's not a video camera, so you must take a snapshot, wait, look if it's good, change settings, retry, retry and retry. With video camera, you change settings in live, you see immediatly if image is good or not. When it's good, you take it. It's fast and easy. 2- With high magnification, the resolution of the camera (1500*1000) is highest than the optical resolution. With a 60x oel objective of 1.3 numerical aperture, the optical resolution is approximately the same than video resolution (500x700). So high camera resolution is only usefull for small magnification. A good product is the digital video camera of Leica : video, very friendly and usefull software, same price than Kodak with software and PCI card, very sensitive for fluorescence and resolution of 1400*1200 by interpolation (700*500 in normal mode). They announce for soon a new one with real 1400x1200 resolution and a Macintosh version. That's only my personnal experience. Best regards. Bertrand Mnard ********************************************************************* Bertrand MENARD Institute of Plant Biology Institut de Biologie et de and Physiology Physiologie Vgtales University of Lausanne Universit de Lausanne CH-1015 LAUSANNE CH-1015 LAUSANNE Switzerland Suisse Tel : 00 41 21 692 42 19 Fax : 00 41 21 692 41 95 E-Mail : Bertrand.Menard@ie-bpv.unil.ch ********************************************************************* ------------------------------ Date: Mon, 2 Nov 1998 15:24:41 +0100 From: Daniele Zacchetti To: NIH Image mailing list Subject: Scion image for Windows Message-Id: Content-Type: text/plain; charset="us-ascii" Does anybody know whether the Scion image source code (Windows95 or NT) is freely available? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it ------------------------------ Date: Mon, 2 Nov 1998 09:57:56 -0500 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: RE : digital photo camera f. microscopy Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit While somewhat expensive I have been using the Sensys Camera for digital microscopy. It runs about 20,000 + but is a relatively high resolution (about 2000 x 1700 pixel resolution) camera and is a cooled low light camera as well. There is now a liquid crystal adaptor that will convert the camera to color (probably not good for very low light, but should work for bright fluorescence and does work well for darkfield images). The image quality is superb! >Hi Imagers, > >I've tried the Kodak digital camera with C-mount on a microscop. I don't >think that's the good cameras for microscopy : >1- It's not a video camera, so you must take a snapshot, wait, look if it's >good, change settings, retry, retry and retry. With video camera, you >change settings in live, you see immediatly if image is good or not. When >it's good, you take it. It's fast and easy. >2- With high magnification, the resolution of the camera (1500*1000) is >highest than the optical resolution. With a 60x oel objective of 1.3 >numerical aperture, the optical resolution is approximately the same than >video resolution (500x700). So high camera resolution is only usefull for >small magnification. > >A good product is the digital video camera of Leica : video, very friendly >and usefull software, same price than Kodak with software and PCI card, >very sensitive for fluorescence and resolution of 1400*1200 by >interpolation (700*500 in normal mode). They announce for soon a new one >with real 1400x1200 resolution and a Macintosh version. > >That's only my personnal experience. > >Best regards. > > > >Bertrand Mnard > >********************************************************************* > > Bertrand MENARD > >Institute of Plant Biology Institut de Biologie et de > and Physiology Physiologie Vgtales > University of Lausanne Universit de Lausanne > CH-1015 LAUSANNE CH-1015 LAUSANNE > Switzerland Suisse > > Tel : 00 41 21 692 42 19 > Fax : 00 41 21 692 41 95 > > E-Mail : Bertrand.Menard@ie-bpv.unil.ch > >********************************************************************* Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Fax 410 706-2512 email gehoffma@umaryland.edu ------------------------------ Date: Mon, 2 Nov 1998 18:12:00 +0300 From: "Ned Horning" To: Subject: RE: Scion image for Windows Message-ID: <000401be0673$23d0e150$495499d0@nedh> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Daniele, I asked the folks at Scion Corp. about this nearly a year ago and the response I got was "At this time we will not be releasing any source code for Scion Image for Windows. This policy may change in the future but it is very doubtful." After I received this message my superiors tried to follow up to see if we could negotiate something but Scion did not respond. You may want to look at the source code for ImageJ. There are several advantages to using ImageJ since it does not have some of the limitations of NIH Image and Scion Image. Wayne is doing a great job with ImageJ and interest in it seems to be growing. I wish you luck in your search for the Scion Image source code. Ned -----Original Message----- From: Daniele Zacchetti [mailto:zacchetti.daniele@hsr.it] Sent: Monday, November 02, 1998 5:25 PM To: NIH Image mailing list Subject: Scion image for Windows Does anybody know whether the Scion image source code (Windows95 or NT) is freely available? TIA Daniele Dr. Daniele Zacchetti, PhD Cellular Neurophysiology Unit Dibit, San Raffaele Inst. via Olgettina 58 20132 Milano, Italy Phone: +39-02-2643-4812 Fax:+39-02-2643-4813 e-mail: zacchetti.daniele@hsr.it ------------------------------ Date: Mon, 2 Nov 1998 08:25:08 -0600 From: "Joan J. Fitzpatrick" To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" UNSUBSCRIBE TO NIH-IMAGE ------------------------------ Date: Mon, 2 Nov 1998 13:07:27 -0400 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-Id: Content-Type: text/enriched; charset="us-ascii" CourierHi everyone. The following is a reminder to everyone regarding administrative issues on the list. Those who desire the digest form, should unsubscribe from the regular list and resubscribe to the digest list. e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". 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As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- ------------------------------ Date: Mon, 02 Nov 1998 12:14:40 -0500 From: Scott Cramer To: nih-image@io.ece.drexel.edu Subject: Unsubscribe Message-Id: <363DE87E.7E4A67C2@cirl.meei.harvard.edu> Content-Type: multipart/mixed; boundary="------------98611CBC770253999159B05A" This is a multi-part message in MIME format. --------------98611CBC770253999159B05A Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Unsubscribe me please. Thank you. --------------98611CBC770253999159B05A Content-Type: text/x-vcard; charset=us-ascii; name="vcard.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Scott Cramer Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Scott Cramer n: Cramer;Scott org: Massachusetts Eye & Ear Infirmary adr;dom: ;;243 Charles Street;Boston;MA;02114; email;internet: srcramer@cirl.meei.harvard.edu title: Research Assistant II tel;work: 617-573-4273 tel;fax: 617-573-4275 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------98611CBC770253999159B05A-- ------------------------------ Date: Mon, 2 Nov 1998 12:39:27 -0500 (EST) From: Vaughn Adams To: nih-image@io.ece.drexel.edu Subject: Administrative Help Message-Id: <199811021739.MAA18604@cbis.ece.drexel.edu> Content-Type: application/pgp; format=text; x-action=sign Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNED MESSAGE----- Nih-Image List members: List administrative commands will be sent out the 15th of every month. It will contain commands to subscribe, unsubscribe and search the archives. I hope that this will cut down on the number of unsubscribe requests to the list itself. You can get the same information by sending mail to nih-image-request@biomed.drexel.edu with Help in the subject. I would also like to take the opportunity to mention that the nih-mailing list has reached 779 list members. - -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu -----BEGIN PGP SIGNATURE----- Version: 2.6.2 iQCVAwUBNj3uSooTfOp6Z5FxAQGjvwQAzBXku1i8qE9/Hc/TMNtlfeNL9A75s2xE faonRnBbmpr4HR0MKNbM/8bEipfexmJ1lwi0oPHx33RK6T5Xm11ESEufkqri0KlM nzjm0+IQehy9gMJ7K/6roa3sFzibaK9WLHpY3EYhtchTOJWsesGFe53xmHH1bIcN 3RxTCNPtAIA= =O58A -----END PGP SIGNATURE----- ------------------------------ Date: Mon, 02 Nov 1998 21:54:19 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: tracking asteroids... Message-ID: <363E29FF.32792D8@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Use ImageMath to determine if the position of the asteroids have changed between images. Subtract image n from image n+1 the length of the resultant white/black bits of the images will allow you to calculate the velocity of the asteroids and direction, assuming you can scale the images accurately. John Russ's Image Processing hand book covers this topic very nicely pp273-276. Jeremy Lynn Huynh wrote: > hi, i am wondering if anyone knows how to use nih-image to track > asteroids in photos taken off the net... or rather to make the > question broader, does anyone have a detailed procedure on how > to use the stacking feature of the program? > > thank you, > lynn > lynnh@us1.oes.edu > supershiny@hotmail.com -------------------------------- End of nih-image-d Digest V98 Issue #104 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 2 18:29 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA03453; Mon, 2 Nov 1998 18:29:17 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 18:29:17 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu, glenmac@u.washington.edu Date: Tue, 3 Nov 1998 9:18:36 GMT+1100 Subject: Re: Modulus operation Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"IOttC3.0.XP6.dqZFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/563 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1726 >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST) >From: "G. Macdonald" >To: nih-image@io.ece.drexel.edu >Subject: Modulus operation > >Attempts to create a modulus operation have been giving unpredictable >results. Maybe someone can point out my mistake. I've been taking the >quotient from division of 2 real vars, then subtracting the truncation of >the quotient: > >var > seglength,Mseglength,quotient,modulo:real; > Trunk:integer; >begin > quotient:=MsegLength/segLength; > Trunk:=trunc(quotient); > modulo:=quotient-trunk; > >end; > >If SegLength is passed in as .N*MSegLength [to segment the midline into N >divisions], then sometimes Trunk is N, other times it is N-1. > >TIA, >Glen integer<>real conversions can often be trickier than you expect but I suspect there is an inversion in your statement of your problem. trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to lose precision. You could set a limit on precision by eg trunc((rN*rM*1.001))/rM). Note however that the modulus operator is available in NIH-Image macros as well as Pascal. >From Appendix on Macros: " Operators + - * / DIV MOD := = < > <> <= >= AND OR NOT Types INTEGER REAL BOOLEAN STRING Both integer and real variables are stored internally in extended precision real format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits precision. Real numbers are automatically converted (by rounding) to integer without warning as needed. " Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Mon Nov 2 21:13 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA27035; Mon, 2 Nov 1998 21:13:34 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 21:13:34 -0500 (EST) Message-ID: <001301be06cd$63dc5900$08778dd2@oemcomputer> From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" To: Subject: For western blotting Date: Tue, 3 Nov 1998 10:57:21 +0900 MIME-Version: 1.0 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"c_Pke3.0.vl4.2DcFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/564 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01BE0718.BAF23E80" Content-Length: 970 This is a multi-part message in MIME format. ------=_NextPart_000_000F_01BE0718.BAF23E80 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Hello. Dose anyone know the paper which contains NIH image to use for analysing for Westen blotting? Ken Iwata ------=_NextPart_000_000F_01BE0718.BAF23E80 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable

Hello.
 Dose anyone know the paper which contains NIH = image to=20 use for analysing for Westen = blotting?
 Ken Iwata
------=_NextPart_000_000F_01BE0718.BAF23E80-- From nih-image-request@io.ece.drexel.edu Mon Nov 2 23:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA27809; Mon, 2 Nov 1998 23:14:15 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 23:14:15 -0500 (EST) Date: Mon, 2 Nov 1998 20:02:41 -0800 (PST) From: "G. Macdonald" To: GJOSS@rna.bio.mq.edu.au cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Modulus operation In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"6FHAt3.0.fM5.g1eFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/565 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 419 Dear Greg and Ray, thanks for the responses. Yes, it was rounding errors that were confounding me. I had over-simplified the statement regarding setting the segmentation value in my posting. The MSegLength is the length of a segment in a segmented line. SegLength is length of some fraction of the total length of the segmented line. I am moving along the segmented line dividing it in increments of Seglength. From nih-image-request@io.ece.drexel.edu Mon Nov 2 23:21 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA02073; Mon, 2 Nov 1998 23:21:51 -0500 (EST) Resent-Date: Mon, 2 Nov 1998 23:21:51 -0500 (EST) Date: Mon, 2 Nov 1998 20:14:10 -0800 (PST) From: "G. Macdonald" To: GJOSS@rna.bio.mq.edu.au cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Modulus operation In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Y4oNC1.0.eo6.NCeFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/566 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2287 Dear Greg and Ray, Thanks for the responses. Yes, it seems to be rounding errors and transferring quantities between differnt variable types were confounding me. The description of the length values being divided was oversimplified from what I am actually doing,but the warning on an inversion error is noted just the same. Ray, your modulus routine resolved the chronic rounding down. Glen On Tue, 3 Nov 1998 GJOSS@rna.bio.mq.edu.au wrote: > >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST) > >From: "G. Macdonald" > >To: nih-image@io.ece.drexel.edu > >Subject: Modulus operation > > > >Attempts to create a modulus operation have been giving unpredictable > >results. Maybe someone can point out my mistake. I've been taking the > >quotient from division of 2 real vars, then subtracting the truncation of > >the quotient: > > > >var > > seglength,Mseglength,quotient,modulo:real; > > Trunk:integer; > >begin > > quotient:=MsegLength/segLength; > > Trunk:=trunc(quotient); > > modulo:=quotient-trunk; > > > >end; > > > >If SegLength is passed in as .N*MSegLength [to segment the midline into N > >divisions], then sometimes Trunk is N, other times it is N-1. > > > >TIA, > >Glen > integer<>real conversions can often be trickier than you expect > but I suspect there is an inversion in your statement of your problem. > > trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to > lose precision. > > You could set a limit on precision by eg trunc((rN*rM*1.001))/rM). > > Note however that the modulus operator is available in NIH-Image macros as well as > Pascal. > > From Appendix on Macros: > " > Operators > + - * / DIV MOD := > = < > <> <= >= AND OR NOT > > > Types > INTEGER REAL BOOLEAN STRING > > Both integer and real variables are stored internally in extended precision real > format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits > precision. Real numbers are automatically converted (by rounding) to integer > without warning as needed. > " > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > From nih-image-request@io.ece.drexel.edu Tue Nov 3 09:24 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21009; Tue, 3 Nov 1998 09:24:16 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 09:24:16 -0500 (EST) Date: Tue, 03 Nov 1998 12:29:18 +0200 From: Ricardo Pujol Borrell Subject: unsuscribe To: nih-image@io.ece.drexel.edu Reply-to: IKHT4@cc.uab.es Message-id: <363EDAFC.5542EDEE@cc.uab.es> Organization: Hospital Universitario Germans Trias i Pujol MIME-version: 1.0 X-Mailer: Mozilla 4.5b2 (Macintosh; I; PPC) Content-transfer-encoding: 7bit References: <199811021739.MAA18604@cbis.ece.drexel.edu> Resent-Message-ID: <"VjtQN.0.Rg4.9vmFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/567 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854; charset=us-ascii Content-Length: 205 unsuscribe -- R. Pujol Borrell MD, PhD Head Immunology Unit Hospital Univ. Germans Trias i Pujol/UAB Crtra. del Canyet s/n 08916 Badalona Spain Tel 3493 4978893 Fax 3493 4978843 E-Mail IKHT4@cc.uab.es From nih-image-d-request@io.ece.drexel.edu Tue Nov 3 09:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21418; Tue, 3 Nov 1998 09:28:37 -0500 (EST) Date: Tue, 3 Nov 1998 09:28:37 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811031428.JAA21418@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #105 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/105 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9541 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 105 Today's Topics: Re: watershed segmentation [ Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: watershed segmentation Message-ID: <363E1882.62A74C1D@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit A good cheat here is to convert your threshold / density slice image into binary, use AnalyzeParticles (with the label and outline function disabled) then threshold and makebinary again. This will fill any holes in the cells which may be contributing to the errors associated with the watershed algorithm. If you are interested in the greyscale values of the cells or their internal components you can use the X,Y location of the center of each cell in conjunction with Autooutline to apply a ROI to the original image and continue your analysis. Jeremy Dan Frich wrote: > I was wondering if anyone could give me any help with the watershed > segmentation routine in v. 1.61. I am using Image to analyze sizes and > distributions in cellular materials. To do this, I use watershed > segmentation to yield discrete cells and then use the analyze particles > routine to measure individual cell sizes (areas). This technique works > extremely well except for the fact that I tend to get some degree of > oversegmentation (splitting of cells that should be counted as only one) in > the watershed routine. Does anyone have any ideas or experience on how to > correct this problem? > > My appreciation in advance, > Dan Frich ------------------------------ Date: Tue, 3 Nov 1998 9:18:36 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu, glenmac@u.washington.edu Subject: Re: Modulus operation Message-ID: >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST) >From: "G. Macdonald" >To: nih-image@io.ece.drexel.edu >Subject: Modulus operation > >Attempts to create a modulus operation have been giving unpredictable >results. Maybe someone can point out my mistake. I've been taking the >quotient from division of 2 real vars, then subtracting the truncation of >the quotient: > >var > seglength,Mseglength,quotient,modulo:real; > Trunk:integer; >begin > quotient:=MsegLength/segLength; > Trunk:=trunc(quotient); > modulo:=quotient-trunk; > >end; > >If SegLength is passed in as .N*MSegLength [to segment the midline into N >divisions], then sometimes Trunk is N, other times it is N-1. > >TIA, >Glen integer<>real conversions can often be trickier than you expect but I suspect there is an inversion in your statement of your problem. trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to lose precision. You could set a limit on precision by eg trunc((rN*rM*1.001))/rM). Note however that the modulus operator is available in NIH-Image macros as well as Pascal. >From Appendix on Macros: " Operators + - * / DIV MOD := = < > <> <= >= AND OR NOT Types INTEGER REAL BOOLEAN STRING Both integer and real variables are stored internally in extended precision real format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits precision. Real numbers are automatically converted (by rounding) to integer without warning as needed. " Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Tue, 3 Nov 1998 10:57:21 +0900 From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" To: Subject: For western blotting Message-ID: <001301be06cd$63dc5900$08778dd2@oemcomputer> Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01BE0718.BAF23E80" This is a multi-part message in MIME format. ------=_NextPart_000_000F_01BE0718.BAF23E80 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit Hello. Dose anyone know the paper which contains NIH image to use for analysing for Westen blotting? Ken Iwata ------=_NextPart_000_000F_01BE0718.BAF23E80 Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable
Hello.
 Dose anyone know the paper which contains NIH = image to=20 use for analysing for Westen = blotting?
 Ken Iwata
------=_NextPart_000_000F_01BE0718.BAF23E80-- ------------------------------ Date: Mon, 2 Nov 1998 20:02:41 -0800 (PST) From: "G. Macdonald" To: GJOSS@rna.bio.mq.edu.au cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Modulus operation Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Greg and Ray, thanks for the responses. Yes, it was rounding errors that were confounding me. I had over-simplified the statement regarding setting the segmentation value in my posting. The MSegLength is the length of a segment in a segmented line. SegLength is length of some fraction of the total length of the segmented line. I am moving along the segmented line dividing it in increments of Seglength. ------------------------------ Date: Mon, 2 Nov 1998 20:14:10 -0800 (PST) From: "G. Macdonald" To: GJOSS@rna.bio.mq.edu.au cc: rh208@cus.cam.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Modulus operation Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Greg and Ray, Thanks for the responses. Yes, it seems to be rounding errors and transferring quantities between differnt variable types were confounding me. The description of the length values being divided was oversimplified from what I am actually doing,but the warning on an inversion error is noted just the same. Ray, your modulus routine resolved the chronic rounding down. Glen On Tue, 3 Nov 1998 GJOSS@rna.bio.mq.edu.au wrote: > >Date: Sat, 31 Oct 1998 09:44:29 -0800 (PST) > >From: "G. Macdonald" > >To: nih-image@io.ece.drexel.edu > >Subject: Modulus operation > > > >Attempts to create a modulus operation have been giving unpredictable > >results. Maybe someone can point out my mistake. I've been taking the > >quotient from division of 2 real vars, then subtracting the truncation of > >the quotient: > > > >var > > seglength,Mseglength,quotient,modulo:real; > > Trunk:integer; > >begin > > quotient:=MsegLength/segLength; > > Trunk:=trunc(quotient); > > modulo:=quotient-trunk; > > > >end; > > > >If SegLength is passed in as .N*MSegLength [to segment the midline into N > >divisions], then sometimes Trunk is N, other times it is N-1. > > > >TIA, > >Glen > integer<>real conversions can often be trickier than you expect > but I suspect there is an inversion in your statement of your problem. > > trunc((rN*rM)/rM) can yield rN-1 if rM uses enough precision bits for (rN*rM) to > lose precision. > > You could set a limit on precision by eg trunc((rN*rM*1.001))/rM). > > Note however that the modulus operator is available in NIH-Image macros as well as > Pascal. > > From Appendix on Macros: > " > Operators > + - * / DIV MOD := > = < > <> <= >= AND OR NOT > > > Types > INTEGER REAL BOOLEAN STRING > > Both integer and real variables are stored internally in extended precision real > format, which has a range of 1.9 x 10-495 to 1.1 x 10 4932 and 19-20 digits > precision. Real numbers are automatically converted (by rounding) to integer > without warning as needed. > " > Greg Joss, > School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 > Macquarie University, Email gjoss@rna.bio.mq.edu.au > North Ryde, (Sydney,) NSW 2109, Australia > ------------------------------ Date: Tue, 03 Nov 1998 12:29:18 +0200 From: Ricardo Pujol Borrell To: nih-image@io.ece.drexel.edu Subject: unsuscribe Message-id: <363EDAFC.5542EDEE@cc.uab.es> Content-type: text/plain; x-mac-creator=4D4F5353; x-mac-type=54455854; charset=us-ascii Content-transfer-encoding: 7bit unsuscribe -- R. Pujol Borrell MD, PhD Head Immunology Unit Hospital Univ. Germans Trias i Pujol/UAB Crtra. del Canyet s/n 08916 Badalona Spain Tel 3493 4978893 Fax 3493 4978843 E-Mail IKHT4@cc.uab.es -------------------------------- End of nih-image-d Digest V98 Issue #105 **************************************** From nih-image-request@io.ece.drexel.edu Tue Nov 3 10:57 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA01256; Tue, 3 Nov 1998 10:57:31 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 10:57:31 -0500 (EST) Message-ID: <363F21FA.7F4BD1A3@earthlink.net> Date: Tue, 03 Nov 1998 07:32:10 -0800 From: Shawn Makanvand Reply-To: shawnmak@earthlink.net X-Mailer: Mozilla 4.06 [en] (WinNT; U) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: UNSUBSCRIBE References: <199811031419.JAA20366@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"BbZng2.0.Sl6.V6oFs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/568 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 22 UNSUBSCRIBE please. From nih-image-request@io.ece.drexel.edu Tue Nov 3 14:48 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA24176; Tue, 3 Nov 1998 14:48:53 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 14:48:53 -0500 (EST) Message-ID: <19981103192416.10573.rocketmail@attach1.rocketmail.com> Date: Tue, 3 Nov 1998 11:24:16 -0800 (PST) From: Mark Vivino Subject: Re: For western blotting To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"VbWJC.0.CH5.RcrFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/570 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1575 > Dose anyone know the paper which contains NIH image to use for analysing > for Westen blotting? Well I think this part of the FAQ still has valid links. If not let me know... * Is there any help in understanding densitometry and/or gel analysis? There are a number of documents available explaning anything from portions of the theoretical prinicples of densitomtry, to step by step help in using the gel analysis macros. Those interested in densitometry should strive to understand the "calibrate" command and why it is used. For explanation regarding basic underlying principles of densitometry read the section of Image Engineering on densitometry at: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry For simple explanation on the calibrate command, the NIH Image manual section should be read: http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate For basic step by step explanation on the gel macros the NIH Image manual, techniques section, section should be read: http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze For a longer and thorough step by step explanation as to how to use the gel macros refer to the gel analysis manual at: http://sunny.dcrt.nih.gov/itc/gel/ Calibrated optical density step tablets are made by Kodak and can be purchased from Kodak dealers. See Kodak's step table Web page at http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Nov 3 14:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA24242; Tue, 3 Nov 1998 14:49:19 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 14:49:19 -0500 (EST) Message-ID: <19981103191254.14852.rocketmail@web1.rocketmail.com> Date: Tue, 3 Nov 1998 11:12:53 -0800 (PST) From: Mark Vivino Subject: how to (un)subscribe & list info To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"DnO1r.0.PA5.jZrFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/569 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2778 Seems like most who need this miss it... e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Nov 3 14:55 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA25195; Tue, 3 Nov 1998 14:55:55 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 14:55:55 -0500 (EST) Message-ID: <19981103192334.17397.rocketmail@web1.rocketmail.com> Date: Tue, 3 Nov 1998 11:23:34 -0800 (PST) From: Mark Vivino Subject: Re: RE: analog to digital (was: Can a snappy be used for?) To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"Yb8kl1.0.2V5.djrFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/571 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1443 > >Could you explain further how video bandwidth limits the digitization of a > line > >of video signal to only about 330 pixels? For that matter, what is > "bandwidth"? > > Is there is a distinction between "analog bandwidth" and the "digital > bandwidth" > >we hear so much about? > > Too long a question for email. Read a good book. Start with Inoue "Video > Microscopy." There is also a lot of information in books like Pratt "Digital > Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods > "Digital Image Proc" and my own "Image Processing Handbook" Good set of refs, especially Inoue for this question. Aside from bandwidth limitations one also has to deal with signal to noise ratios which can ruin the bit depth. A formula is seen in Inside NIH Image on calculating how many significant bits one can get from the SNR of a camera, etc. While lots of bits may be needed for math operations on images, fact is most people out there are using about 7 real bits or so per pixel, and most don't even have a real eight bit. Spatial resolution wise, as per question, it is good to deal with digital. Digital data is transfered or not, analog data only degrades and is the simple answer to part of your question. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Nov 3 15:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA27036; Tue, 3 Nov 1998 15:14:01 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 15:14:01 -0500 (EST) Message-ID: <19981103193358.19997.rocketmail@web1.rocketmail.com> Date: Tue, 3 Nov 1998 11:33:58 -0800 (PST) From: Mark Vivino Subject: Re: electrophoretic gel reading... To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"rynck1.0.4p5.OtrFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/572 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1871 > how do i use nih-image to analyze electrophoretic gels? i need > better readings on some gels that i have. i have been using page > techniques and will be needing to analyze not just whether the > band is detectable but also which bands are darker, i will be using > this information to create a haplotype and do two-point lod score > analysis with linkage 5.1 software Again from the faq... I * Is there any help in understanding densitometry and/or gel analysis? There are a number of documents available explaning anything from portions of the theoretical prinicples of densitomtry, to step by step help in using the gel analysis macros. Those interested in densitometry should strive to understand the "calibrate" command and why it is used. For explanation regarding basic underlying principles of densitometry read the section of Image Engineering on densitometry at: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry For simple explanation on the calibrate command, the NIH Image manual section should be read: http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate For basic step by step explanation on the gel macros the NIH Image manual, techniques section, section should be read: http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze For a longer and thorough step by step explanation as to how to use the gel macros refer to the gel analysis manual at: http://sunny.dcrt.nih.gov/itc/gel/ Calibrated optical density step tablets are made by Kodak and can be purchased from Kodak dealers. See Kodak's step table Web page at http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Nov 3 20:58 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18023; Tue, 3 Nov 1998 20:58:58 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 20:58:58 -0500 (EST) Message-ID: <19981104013818.14801.rocketmail@send1e.yahoomail.com> Date: Tue, 3 Nov 1998 17:38:18 -0800 (PST) From: Larisa Haupt Subject: quantifying signal in histology sections To: nih-image@io.ece.drexel.edu Cc: malinda@asgard.cbu.edu MIME-Version: 1.0 Resent-Message-ID: <"2LKXy1.0.9k2.X3xFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/573 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 898 Hi, i am in dire need of some help. I only have access to a digital camera etc for the next couple of days, and i need to make sure i have the correct images downloaded to compare and hopefully quantify the signal in serial tissue sections obtained via in situ-pcr. Can you help me and let me know if image is capable of doing this, and most importantly, how to do this. I have tried to make sense of the online manual, with some minor success, if you could give me any pointers and help me out with things like image size, image type and apecifically the steps involved in comparing eight serial sections I would greatly appreciate it. I look forward to your response. You can also email me at L.Haupt@nhs.gu.edu.au after this week thanks larisa == _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Tue Nov 3 23:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA15435; Tue, 3 Nov 1998 23:19:57 -0500 (EST) Resent-Date: Tue, 3 Nov 1998 23:19:57 -0500 (EST) X-Sender: gtjr@eduserv.unimelb.edu.au Message-Id: In-Reply-To: <19981104013818.14801.rocketmail@send1e.yahoomail.com> Mime-Version: 1.0 Date: Wed, 4 Nov 1998 15:01:32 +1100 To: nih-image@io.ece.drexel.edu From: Garry Jolley-Rogers Subject: Re: quantifying signal in histology sections Resent-Message-ID: <"JdfEK1.0.4v1.L7zFs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/574 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2510 Hi Larisa, I know the feeling - In answer to your question - Yes NIH can - with the only qualification being in the detail. Is your signal well differentiated from background? by colour or intensity? If not - can it be improved prior to digitization? As for NIH image- it will allow you to address most questions that you could ask. As for image type and size - try and err on the side of caution. For instance, scan at higher resolution than you require then reduce to a size around twice the size of your smallest feature of interest(or bits of your feature of interest). File format - tiff. I believe NIH ver 1.6.2 has no restrictions on image width. Then you'll need to align the sections. They're are several macros that will do this. However, they do vary in how they work. What exactly are you trying to align? with what fidelity? do you have any fiducial markers? or features that will serve as markers? I'm going through the same process at the moment - just on a grander scale as I've got 100's of serial sections to align. I'm just about to start on the whole painful process. If i can help - email me & we can chew the cud a bit more without jamming this nice mail list. yours Garry Jolley-Rogers At 12:38 PM +1100 on 4/11/98, Larisa Haupt wrote: > Hi, > > i am in dire need of some help. I only have access to a digital > camera etc for the next couple of days, and i need to make sure i have > the correct images downloaded to compare and hopefully quantify the > signal in serial tissue sections obtained via in situ-pcr. Can you > help me and let me know if image is capable of doing this, and most > importantly, how to do this. > > I have tried to make sense of the online manual, with some minor > success, if you could give me any pointers and help me out with things > like image size, image type and apecifically the steps involved in > comparing eight serial sections I would greatly appreciate it. > > I look forward to your response. > > You can also email me at L.Haupt@nhs.gu.edu.au after this week > > thanks > > larisa > > > > > > > == > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com ----------------------------------------------------------- Garry Jolley-Rogers Dept. of Zoology University of Melbourne Ph x44846 or x44349 or 98836848 or 93620285 email :G.jolley-rogers@zoology.unimelb.edu.au ----------------------------------------------------------- From nih-image-d-request@io.ece.drexel.edu Wed Nov 4 06:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA26001; Wed, 4 Nov 1998 06:25:09 -0500 (EST) Date: Wed, 4 Nov 1998 06:25:09 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811041125.GAA26001@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #106 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/106 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 14486 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 106 Today's Topics: UNSUBSCRIBE [ Shawn Makanvand ] Re: quantifying signal in histology [ Garry Jolley-Rogers To: nih-image@io.ece.drexel.edu Subject: UNSUBSCRIBE Message-ID: <363F21FA.7F4BD1A3@earthlink.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit UNSUBSCRIBE please. ------------------------------ Date: Tue, 3 Nov 1998 12:06:22 -0400 From: Pierre-Olivier Tremblay To: nih-image-d@io.ece.drexel.edu Subject: UNSUBSCRIBE Message-Id: Content-Type: text/plain; charset="us-ascii" Unsubscribe me from the list Thank you. ------------------------------ Date: Tue, 3 Nov 1998 11:12:53 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: how to (un)subscribe & list info Message-ID: <19981103191254.14852.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii Seems like most who need this miss it... e-mail addresses of importance -------- nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Help -------------------- To obtain a listing of help items, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-request@biomed.drexel.edu Subject: help Help on Digest -------------------- To obtain a listing of help items on digest version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "help". As in: To: nih-image-d-request@biomed.drexel.edu Subject: help Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 3 Nov 1998 11:24:16 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: For western blotting Message-ID: <19981103192416.10573.rocketmail@attach1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > Dose anyone know the paper which contains NIH image to use for analysing > for Westen blotting? Well I think this part of the FAQ still has valid links. If not let me know... * Is there any help in understanding densitometry and/or gel analysis? There are a number of documents available explaning anything from portions of the theoretical prinicples of densitomtry, to step by step help in using the gel analysis macros. Those interested in densitometry should strive to understand the "calibrate" command and why it is used. For explanation regarding basic underlying principles of densitometry read the section of Image Engineering on densitometry at: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry For simple explanation on the calibrate command, the NIH Image manual section should be read: http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate For basic step by step explanation on the gel macros the NIH Image manual, techniques section, section should be read: http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze For a longer and thorough step by step explanation as to how to use the gel macros refer to the gel analysis manual at: http://sunny.dcrt.nih.gov/itc/gel/ Calibrated optical density step tablets are made by Kodak and can be purchased from Kodak dealers. See Kodak's step table Web page at http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 3 Nov 1998 11:23:34 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: RE: analog to digital (was: Can a snappy be used for?) Message-ID: <19981103192334.17397.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > >Could you explain further how video bandwidth limits the digitization of a > line > >of video signal to only about 330 pixels? For that matter, what is > "bandwidth"? > > Is there is a distinction between "analog bandwidth" and the "digital > bandwidth" > >we hear so much about? > > Too long a question for email. Read a good book. Start with Inoue "Video > Microscopy." There is also a lot of information in books like Pratt "Digital > Image Processing", Jain "Fundamentals of Digital Image Proc", Gonzalez&Woods > "Digital Image Proc" and my own "Image Processing Handbook" Good set of refs, especially Inoue for this question. Aside from bandwidth limitations one also has to deal with signal to noise ratios which can ruin the bit depth. A formula is seen in Inside NIH Image on calculating how many significant bits one can get from the SNR of a camera, etc. While lots of bits may be needed for math operations on images, fact is most people out there are using about 7 real bits or so per pixel, and most don't even have a real eight bit. Spatial resolution wise, as per question, it is good to deal with digital. Digital data is transfered or not, analog data only degrades and is the simple answer to part of your question. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 3 Nov 1998 11:33:58 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: electrophoretic gel reading... Message-ID: <19981103193358.19997.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > how do i use nih-image to analyze electrophoretic gels? i need > better readings on some gels that i have. i have been using page > techniques and will be needing to analyze not just whether the > band is detectable but also which bands are darker, i will be using > this information to create a haplotype and do two-point lod score > analysis with linkage 5.1 software Again from the faq... I * Is there any help in understanding densitometry and/or gel analysis? There are a number of documents available explaning anything from portions of the theoretical prinicples of densitomtry, to step by step help in using the gel analysis macros. Those interested in densitometry should strive to understand the "calibrate" command and why it is used. For explanation regarding basic underlying principles of densitometry read the section of Image Engineering on densitometry at: http://rsb.info.nih.gov/nih-image/more-docs/Engineering/ImgEngr.html#densitometry For simple explanation on the calibrate command, the NIH Image manual section should be read: http://rsb.info.nih.gov/nih-image/manual/menus/analyze.html#calibrate For basic step by step explanation on the gel macros the NIH Image manual, techniques section, section should be read: http://rsb.info.nih.gov/nih-image/manual/tech.html#analyze For a longer and thorough step by step explanation as to how to use the gel macros refer to the gel analysis manual at: http://sunny.dcrt.nih.gov/itc/gel/ Calibrated optical density step tablets are made by Kodak and can be purchased from Kodak dealers. See Kodak's step table Web page at http://www.kodak.com/aboutKodak/bu/dai/SIS/stepTab.shtml == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 3 Nov 1998 17:38:18 -0800 (PST) From: Larisa Haupt To: nih-image@io.ece.drexel.edu Cc: malinda@asgard.cbu.edu Subject: quantifying signal in histology sections Message-ID: <19981104013818.14801.rocketmail@send1e.yahoomail.com> Content-Type: text/plain; charset=us-ascii Hi, i am in dire need of some help. I only have access to a digital camera etc for the next couple of days, and i need to make sure i have the correct images downloaded to compare and hopefully quantify the signal in serial tissue sections obtained via in situ-pcr. Can you help me and let me know if image is capable of doing this, and most importantly, how to do this. I have tried to make sense of the online manual, with some minor success, if you could give me any pointers and help me out with things like image size, image type and apecifically the steps involved in comparing eight serial sections I would greatly appreciate it. I look forward to your response. You can also email me at L.Haupt@nhs.gu.edu.au after this week thanks larisa == _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Wed, 4 Nov 1998 15:01:32 +1100 From: Garry Jolley-Rogers To: nih-image@io.ece.drexel.edu Subject: Re: quantifying signal in histology sections Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Larisa, I know the feeling - In answer to your question - Yes NIH can - with the only qualification being in the detail. Is your signal well differentiated from background? by colour or intensity? If not - can it be improved prior to digitization? As for NIH image- it will allow you to address most questions that you could ask. As for image type and size - try and err on the side of caution. For instance, scan at higher resolution than you require then reduce to a size around twice the size of your smallest feature of interest(or bits of your feature of interest). File format - tiff. I believe NIH ver 1.6.2 has no restrictions on image width. Then you'll need to align the sections. They're are several macros that will do this. However, they do vary in how they work. What exactly are you trying to align? with what fidelity? do you have any fiducial markers? or features that will serve as markers? I'm going through the same process at the moment - just on a grander scale as I've got 100's of serial sections to align. I'm just about to start on the whole painful process. If i can help - email me & we can chew the cud a bit more without jamming this nice mail list. yours Garry Jolley-Rogers At 12:38 PM +1100 on 4/11/98, Larisa Haupt wrote: > Hi, > > i am in dire need of some help. I only have access to a digital > camera etc for the next couple of days, and i need to make sure i have > the correct images downloaded to compare and hopefully quantify the > signal in serial tissue sections obtained via in situ-pcr. Can you > help me and let me know if image is capable of doing this, and most > importantly, how to do this. > > I have tried to make sense of the online manual, with some minor > success, if you could give me any pointers and help me out with things > like image size, image type and apecifically the steps involved in > comparing eight serial sections I would greatly appreciate it. > > I look forward to your response. > > You can also email me at L.Haupt@nhs.gu.edu.au after this week > > thanks > > larisa > > > > > > > == > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com ----------------------------------------------------------- Garry Jolley-Rogers Dept. of Zoology University of Melbourne Ph x44846 or x44349 or 98836848 or 93620285 email :G.jolley-rogers@zoology.unimelb.edu.au ----------------------------------------------------------- -------------------------------- End of nih-image-d Digest V98 Issue #106 **************************************** From nih-image-request@io.ece.drexel.edu Wed Nov 4 13:45 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA13136; Wed, 4 Nov 1998 13:45:09 -0500 (EST) Resent-Date: Wed, 4 Nov 1998 13:45:09 -0500 (EST) Date: 04 Nov 98 11:06:34 -0700 From: Steven Moore Subject: RE:Scion image for Windows To: "nih-image" X-Mailer: QuickMail Pro 1.5.3 (Windows32) X-Priority: 3 MIME-Version: 1.0 Reply-To: Steven Moore Message-ID: <1301944690-68027714@mailhost.cipe.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id NAA01441 Resent-Message-ID: <"zWscW2.0.9N.7Y9Gs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/575 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-Ascii" Content-Length: 1684 My understanding is the Scion does not plan on releasing the source code for Scion Image. Steven Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ www.cipe.com On 11/2/98, nih-image wrote: >Does anybody know whether the Scion image source >code (Windows95 or NT) is >freely available? >TIA >Daniele > >Dr. Daniele Zacchetti, PhD >Cellular Neurophysiology Unit >Dibit, San Raffaele Inst. >via Olgettina 58 >20132 Milano, Italy >Phone: +39-02-2643-4812 >Fax:+39-02-2643-4813 >e-mail: zacchetti.daniele@hsr.it > > > > >RFC822 header >----------------------------------- > Return-Path: > Received: from io.ece.drexel.edu (144.118.32.3) by >mailhost.cipe.com > with ESMTP (Eudora Internet Mail Server 1.2.1b5); >Mon, 2 Nov 1998 07:32:10 -0700 > Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id >JAA22445; > Mon, 2 Nov 1998 09:27:22 -0500 (EST) > Resent-Date: Mon, 2 Nov 1998 09:27:22 -0500 (EST) > X-Sender: zacchetti.daniele@mail.hsr.it > Message-Id: > > Mime-Version: 1.0 > Content-Type: text/plain; charset="us-ascii" > Date: Mon, 2 Nov 1998 15:24:41 +0100 > To: NIH Image mailing list image@io.ece.drexel.edu> > From: Daniele Zacchetti > Subject: Scion image for Windows > Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@io> > Resent-From: nih-image@io.ece.drexel.edu > Reply-To: nih-image@io.ece.drexel.edu > X-Mailing-List: >archive/latest/554 > X-Loop: nih-image@biomed.drexel.edu > Precedence: list > Resent-Sender: nih-image-request@io.ece.drexel.edu > Status: R > > From nih-image-request@io.ece.drexel.edu Wed Nov 4 16:57 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA15400; Wed, 4 Nov 1998 16:57:33 -0500 (EST) Resent-Date: Wed, 4 Nov 1998 16:57:33 -0500 (EST) X-Authentication-Warning: sunspot.ccs.yorku.ca: rethoret owned process doing -bs Date: Wed, 4 Nov 1998 16:15:53 -0500 (EST) From: Karen Rethoret X-Sender: rethoret@sunspot.ccs.yorku.ca To: nih-image@io.ece.drexel.edu Subject: region selection tools Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"zZXjw2.0._d.LGCGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/576 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 430 Hello; In Image for PC This is probably straight-forward; but can you tell me the best way to draw a rectangular region in which to do plot profiles that is oriented at different angles (not just at right angles?) Have tried straight-line selection tool also but this is only 8 pixels wide maximum when vertical or horizontal (reduces to 1 pixel when line is tilted). Thanks in advance, Karen Rethoret York University From nih-image-request@io.ece.drexel.edu Wed Nov 4 18:50 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA21588; Wed, 4 Nov 1998 18:50:06 -0500 (EST) Resent-Date: Wed, 4 Nov 1998 18:50:06 -0500 (EST) Message-Id: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz> X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 05 Nov 1998 11:45:37 +1300 To: nih-image@io.ece.drexel.edu From: Naomi Boxall Subject: Extra band... Mime-Version: 1.0 Resent-Message-ID: <"3VQZB2.0.4K3.X9EGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/577 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 650 Hi all. I'm not quite sure if this is the correct forum for my query, but I was wondering if anyone out there has done PFGE before. If you have, could you please suggest a reason (other than a plasmid) for an extra band occurring on my gel in one isolate (epidemiologically related to the outbreak) which is the same as the outbreak strain in all other bands. If not then do you know of anyone I can ask, or any groups I can put this question to? Thanks very much, Naomi Naomi S. Boxall BSc Epicentre Inst. of Vet, Animal & Biomedical Sciences Massey University Palmerston North New Zealand 064-6-3504008 (W) Naomi.Boxall.1@uni.massey.ac.nz From nih-image-request@io.ece.drexel.edu Wed Nov 4 19:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA10913; Wed, 4 Nov 1998 19:49:00 -0500 (EST) Resent-Date: Wed, 4 Nov 1998 19:49:00 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <405655c9.3640efee@aol.com> Date: Wed, 4 Nov 1998 19:23:10 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Ann: Updates to Image Processing Tool Kit Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"aukVP1.0.Bf.j0FGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/578 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1264 Several updates to the Image Processing Tool Kit are now posted on the web site at http://members.aol.com/ImagProcTK/ These are all identical for Mac and PC, and can be downloaded, decompressed and placed in the same folder as your other plug-ins. The current list of updates to version 2.5 is Convolution and deconvolution of blur, motion and other point-spread functions using Fourier transforms Color-by-Value which labels features according to the value of any measured parameter Several recently published methods for image processing (sharpening, noise reduction and edge enhancement) Automatically drawing and labeling a magnification bar on the image Versions of the Ranking and Variance filters with adjustable size round neighborhoods. Bug reports and fixes are also posted on the site. The next update to be posted (check the web site periodically) will provide true Phong shading for surface rendering. In other related news, the third edition of The Image Processing Handbook (CRC Press, isbn # 0-8493-2532-3) is now available. In addition to lots of new examples and references, and new sections on digital cameras, surface imaging, and other topics, the book includes an order card offering a $50 discount on the Image Processing Tool Kit CD. From nih-image-d-request@io.ece.drexel.edu Thu Nov 5 06:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09396; Thu, 5 Nov 1998 06:22:39 -0500 (EST) Date: Thu, 5 Nov 1998 06:22:39 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811051122.GAA09396@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #107 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/107 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5747 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 107 Today's Topics: RE:Scion image for Windows [ Steven Moore ] region selection tools [ Karen Rethoret ] Extra band... [ Naomi Boxall To: "nih-image" Subject: RE:Scion image for Windows Message-ID: <1301944690-68027714@mailhost.cipe.com> Content-Type: text/plain; charset="US-Ascii" Content-Transfer-Encoding: 8bit My understanding is the Scion does not plan on releasing the source code for Scion Image. Steven Moore, Ph.D. Director of Evaluation Services Center for Image Processing in Education Tucson, AZ www.cipe.com On 11/2/98, nih-image wrote: >Does anybody know whether the Scion image source >code (Windows95 or NT) is >freely available? >TIA >Daniele > >Dr. Daniele Zacchetti, PhD >Cellular Neurophysiology Unit >Dibit, San Raffaele Inst. >via Olgettina 58 >20132 Milano, Italy >Phone: +39-02-2643-4812 >Fax:+39-02-2643-4813 >e-mail: zacchetti.daniele@hsr.it > > > > >RFC822 header >----------------------------------- > Return-Path: > Received: from io.ece.drexel.edu (144.118.32.3) by >mailhost.cipe.com > with ESMTP (Eudora Internet Mail Server 1.2.1b5); >Mon, 2 Nov 1998 07:32:10 -0700 > Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id >JAA22445; > Mon, 2 Nov 1998 09:27:22 -0500 (EST) > Resent-Date: Mon, 2 Nov 1998 09:27:22 -0500 (EST) > X-Sender: zacchetti.daniele@mail.hsr.it > Message-Id: > > Mime-Version: 1.0 > Content-Type: text/plain; charset="us-ascii" > Date: Mon, 2 Nov 1998 15:24:41 +0100 > To: NIH Image mailing list image@io.ece.drexel.edu> > From: Daniele Zacchetti > Subject: Scion image for Windows > Resent-Message-ID: <"9D9yI2.0.VD5.SxRFs"@io> > Resent-From: nih-image@io.ece.drexel.edu > Reply-To: nih-image@io.ece.drexel.edu > X-Mailing-List: >archive/latest/554 > X-Loop: nih-image@biomed.drexel.edu > Precedence: list > Resent-Sender: nih-image-request@io.ece.drexel.edu > Status: R > > ------------------------------ Date: Wed, 4 Nov 1998 16:15:53 -0500 (EST) From: Karen Rethoret To: nih-image@io.ece.drexel.edu Subject: region selection tools Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello; In Image for PC This is probably straight-forward; but can you tell me the best way to draw a rectangular region in which to do plot profiles that is oriented at different angles (not just at right angles?) Have tried straight-line selection tool also but this is only 8 pixels wide maximum when vertical or horizontal (reduces to 1 pixel when line is tilted). Thanks in advance, Karen Rethoret York University ------------------------------ Date: Thu, 05 Nov 1998 11:45:37 +1300 From: Naomi Boxall To: nih-image@io.ece.drexel.edu Subject: Extra band... Message-Id: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz> Content-Type: text/plain; charset="us-ascii" Hi all. I'm not quite sure if this is the correct forum for my query, but I was wondering if anyone out there has done PFGE before. If you have, could you please suggest a reason (other than a plasmid) for an extra band occurring on my gel in one isolate (epidemiologically related to the outbreak) which is the same as the outbreak strain in all other bands. If not then do you know of anyone I can ask, or any groups I can put this question to? Thanks very much, Naomi Naomi S. Boxall BSc Epicentre Inst. of Vet, Animal & Biomedical Sciences Massey University Palmerston North New Zealand 064-6-3504008 (W) Naomi.Boxall.1@uni.massey.ac.nz ------------------------------ Date: Wed, 4 Nov 1998 19:23:10 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Ann: Updates to Image Processing Tool Kit Message-ID: <405655c9.3640efee@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Several updates to the Image Processing Tool Kit are now posted on the web site at http://members.aol.com/ImagProcTK/ These are all identical for Mac and PC, and can be downloaded, decompressed and placed in the same folder as your other plug-ins. The current list of updates to version 2.5 is Convolution and deconvolution of blur, motion and other point-spread functions using Fourier transforms Color-by-Value which labels features according to the value of any measured parameter Several recently published methods for image processing (sharpening, noise reduction and edge enhancement) Automatically drawing and labeling a magnification bar on the image Versions of the Ranking and Variance filters with adjustable size round neighborhoods. Bug reports and fixes are also posted on the site. The next update to be posted (check the web site periodically) will provide true Phong shading for surface rendering. In other related news, the third edition of The Image Processing Handbook (CRC Press, isbn # 0-8493-2532-3) is now available. In addition to lots of new examples and references, and new sections on digital cameras, surface imaging, and other topics, the book includes an order card offering a $50 discount on the Image Processing Tool Kit CD. -------------------------------- End of nih-image-d Digest V98 Issue #107 **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 5 10:09 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22763; Thu, 5 Nov 1998 10:09:06 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 10:09:06 -0500 (EST) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: region selection tools Message-ID: Date: Thu, 5 Nov 1998 14:47:34 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"ew7ZR1.0.1v3.JfRGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/579 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 664 Karen, If you're in Scion Image then double click on the plotprofile icon it the tools menu bar. Set the line width option (up to 99 pixels) and then draw the line on the image in any direction you choose. Jenny Gregory > In Image for PC > > > This is probably straight-forward; but can you tell me the best way to > draw a rectangular region in which to do plot profiles that is > oriented > at different angles (not just at right angles?) > > Have tried straight-line selection tool also but this is only 8 pixels > wide maximum when vertical or horizontal (reduces to 1 pixel when line is > tilted). ---------------------- j.gregory@abdn.ac.uk From nih-image-request@io.ece.drexel.edu Thu Nov 5 11:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11298; Thu, 5 Nov 1998 11:06:12 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 11:06:12 -0500 (EST) X-Authentication-Warning: d2.hrz.uni-giessen.de: gh43 owned process doing -bs Date: Thu, 5 Nov 1998 16:40:57 +0100 (CET) From: Dietmar Tietz X-Sender: gh43@d2.hrz.uni-giessen.de To: nih-image@io.ece.drexel.edu cc: Naomi.Boxall.1@uni.massey.ac.nz Subject: Re: Extra band... In-Reply-To: <3.0.5.32.19981105114537.007c3630@uni.massey.ac.nz> Message-Id: MIME-Version: 1.0 Resent-Message-ID: <"D-rN2.0.ap.vSSGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/580 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1000 On Thu, 5 Nov 1998, Naomi Boxall wrote: > Hi all. > > I'm not quite sure if this is the correct forum for my query, but I was > wondering if anyone out there has done PFGE before. If you have, could you > please suggest a reason (other than a plasmid) for an extra band occurring > on my gel in one isolate (epidemiologically related to the outbreak) which > is the same as the outbreak strain in all other bands. > > If not then do you know of anyone I can ask, or any groups I can put this > question to? Thanks very much, > > Naomi > > Naomi S. Boxall BSc > Epicentre > Inst. of Vet, Animal & Biomedical Sciences > Massey University > Palmerston North > New Zealand > > 064-6-3504008 (W) > Naomi.Boxall.1@uni.massey.ac.nz > > You may want to post your message to the bionet.molbio.methds-reagnts Internet newsgroup. For details, please see http://www.bio.net/hypermail/METHDS-REAGNTS/ Hope you will get the necessary info soon, Dietmar Tietz http://www.his.com/~djt/ djt@his.com From nih-image-request@io.ece.drexel.edu Thu Nov 5 11:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11806; Thu, 5 Nov 1998 11:07:24 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 11:07:24 -0500 (EST) Message-Id: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.edu> X-Sender: jianshi@pop.service.ohio-state.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Thu, 05 Nov 1998 10:42:20 -0500 To: nih-image@io.ece.drexel.edu From: "j. shi" Subject: Re: region selection tools In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"HtB8K1.0.R61.KWSGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/581 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 503 hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 5 11:47 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA24594; Thu, 5 Nov 1998 11:47:31 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 11:47:31 -0500 (EST) Message-Id: <199811051627.LAA10913@mcfeely.concentric.net> Subject: Help with Image capture system Date: Thu, 5 Nov 98 08:28:32 -0800 From: Your Name To: Mime-Version: 1.0 Resent-Message-ID: <"-2Mh3.0.gU4.f7TGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/582 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 1671 Hello all, I hope someone out there can help me with information on how to put together a mobile digital image capture system. I have a Macintosh Powerbook that I would like to use for capturing images from an analog camera. However, I need to know if there are good framegrabber cards (scientific quality) that can be used with a Macintosh Powerbook. It would be an added plus if NIH-Image controlled the image capture. Therefore, I am requesting any information (ie. camera, framegrabber, storage) on how to build a digital image capture system using a Macintosh Powerbook (or laptop computer). Please e-mail me directly if you feel the NIH-Image user group will not benefit from information pertaining to my request. Thank you, Wilfred Denetclaw Jr., Ph.D. --------------------------------------- Department of Anatomy, Box 0452 School of Medicine University of California, San Francisco San Francisco, CA 94143-0452 (415)476-1530 (laboratory) (415)476-4845 (FAX) wtdenet@concentric.net --------------------------------------- >>>>-------------------------------//---------------------------------<<<< Wilfred Denetclaw Jr., Ph.D. Tina Denetclaw, Pharm.D., BCPS Department of Anatomy and Assistant Clinical Professor Cardiovascular Research Institute & School of Pharmacy (Box 0622) University of California University of California San Francisco, CA. 94143-0452 San Francisco, CA 94143 (415)476-1530 (Office) tdenet@itsa.ucsf.edu (E-mail) (415)476-3586 (FAX) wtdenet@concentric.net (E-mail) >>>>-------------------------------//---------------------------------<<<< From nih-image-request@io.ece.drexel.edu Thu Nov 5 12:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA07156; Thu, 5 Nov 1998 12:27:01 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 12:27:01 -0500 (EST) Message-ID: <19981105165942.10950.qmail@hotmail.com> X-Originating-IP: [139.165.30.112] From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Re: Help with Image capture system MIME-Version: 1.0 Date: Thu, 05 Nov 1998 08:59:41 PST Resent-Message-ID: <"pNyHy2.0.627.jcTGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/583 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 669 Wilfred, Maybe that this is not a good answer at your question, but you can take a look at the site http://www.ulg.ac.be/mica/page27.html, where you can found a kind of solution that I've developed for acquiring images with a "mobile" system. Enrico BONINO, geologist ------------------------ University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com http://www.ulg.ac.be/mica ------------------------- ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Thu Nov 5 12:39 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA11140; Thu, 5 Nov 1998 12:39:51 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 12:39:51 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <524412e3.3641dc83@aol.com> Date: Thu, 5 Nov 1998 12:12:35 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Help with Image capture system Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"mNPhW2.0.hj.loTGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/584 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1150 In a message dated 11/5/98 11:37:48 AM, you wrote: >I hope someone out there can help me with information on how to put >together a mobile digital image capture system. I have a Macintosh >Powerbook that I would like to use for capturing images from an analog >camera. However, I need to know if there are good framegrabber cards >(scientific quality) that can be used with a Macintosh Powerbook. It >would be an added plus if NIH-Image controlled the image capture. >Therefore, I am requesting any information (ie. camera, framegrabber, >storage) on how to build a digital image capture system using a Macintosh >Powerbook (or laptop computer). Please e-mail me directly if you feel the >NIH-Image user group will not benefit from information pertaining to my >request. I do lots of image analysis using a Mac Powerbook, but not using a video camera. Get yourself a good digital camera (I use the Polaroid DMC) with a SCSI connection. The results will be much better than a video camera (better resolution, more consistent color, less noise, etc.) and the cost will be comparable to what a video camera plus frame grabber would cost. From nih-image-request@io.ece.drexel.edu Thu Nov 5 17:30 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA09029; Thu, 5 Nov 1998 17:30:33 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 17:30:33 -0500 (EST) Message-Id: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> X-Sender: jianshi@pop.service.ohio-state.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Thu, 05 Nov 1998 17:05:48 -0500 To: nih-image@io.ece.drexel.edu From: "j. shi" Subject: looking for software for higher bits (>8) In-Reply-To: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> References: Mime-Version: 1.0 Resent-Message-ID: <"ybiZt1.0.hW.u7YGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/585 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 505 hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 5 18:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA18857; Thu, 5 Nov 1998 18:01:21 -0500 (EST) Resent-Date: Thu, 5 Nov 1998 18:01:21 -0500 (EST) Message-Id: In-Reply-To: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> References: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> Mime-Version: 1.0 Date: Thu, 5 Nov 1998 18:45:24 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: looking for software for higher bits (>8) Resent-Message-ID: <"YVGoq3.0.ft2.UaYGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/586 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 335 >hi, all: is there a new version of NIH image processing software that can >handle more than 8 bits (b/w images)? or any other similar package (cheap >or free)? mac or pc does't matter. thanks. jerry. My new Image/J program at http://rsb.info.nih.gov/ij/ can handle more than 8-bits per pixel. It runs on both Macs and PCs. -wayne From nih-image-d-request@io.ece.drexel.edu Fri Nov 6 06:23 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA18983; Fri, 6 Nov 1998 06:23:17 -0500 (EST) Date: Fri, 6 Nov 1998 06:23:17 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811061123.GAA18983@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #108 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/108 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 9744 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 108 Today's Topics: Re: region selection tools [ "j.gregory" ] Re: Extra band... [ Dietmar Tietz ] Re: Help with Image capture system [ "Enrico BONINO" ] ------------------------------ Date: Thu, 5 Nov 1998 14:47:34 +0000 (GMT) From: "j.gregory" To: nih-image@io.ece.drexel.edu Subject: Re: region selection tools Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Karen, If you're in Scion Image then double click on the plotprofile icon it the tools menu bar. Set the line width option (up to 99 pixels) and then draw the line on the image in any direction you choose. Jenny Gregory > In Image for PC > > > This is probably straight-forward; but can you tell me the best way to > draw a rectangular region in which to do plot profiles that is > oriented > at different angles (not just at right angles?) > > Have tried straight-line selection tool also but this is only 8 pixels > wide maximum when vertical or horizontal (reduces to 1 pixel when line is > tilted). ---------------------- j.gregory@abdn.ac.uk ------------------------------ Date: Thu, 5 Nov 1998 16:40:57 +0100 (CET) From: Dietmar Tietz To: nih-image@io.ece.drexel.edu cc: Naomi.Boxall.1@uni.massey.ac.nz Subject: Re: Extra band... Message-Id: Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 5 Nov 1998, Naomi Boxall wrote: > Hi all. > > I'm not quite sure if this is the correct forum for my query, but I was > wondering if anyone out there has done PFGE before. If you have, could you > please suggest a reason (other than a plasmid) for an extra band occurring > on my gel in one isolate (epidemiologically related to the outbreak) which > is the same as the outbreak strain in all other bands. > > If not then do you know of anyone I can ask, or any groups I can put this > question to? Thanks very much, > > Naomi > > Naomi S. Boxall BSc > Epicentre > Inst. of Vet, Animal & Biomedical Sciences > Massey University > Palmerston North > New Zealand > > 064-6-3504008 (W) > Naomi.Boxall.1@uni.massey.ac.nz > > You may want to post your message to the bionet.molbio.methds-reagnts Internet newsgroup. For details, please see http://www.bio.net/hypermail/METHDS-REAGNTS/ Hope you will get the necessary info soon, Dietmar Tietz http://www.his.com/~djt/ djt@his.com ------------------------------ Date: Thu, 05 Nov 1998 10:42:20 -0500 From: "j. shi" To: nih-image@io.ece.drexel.edu Subject: Re: region selection tools Message-Id: <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.edu> Content-Type: text/enriched; charset="us-ascii" hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** ------------------------------ Date: Thu, 5 Nov 98 08:28:32 -0800 From: Your Name To: Subject: Help with Image capture system Message-Id: <199811051627.LAA10913@mcfeely.concentric.net> Content-Type: text/plain; charset="US-ASCII" Hello all, I hope someone out there can help me with information on how to put together a mobile digital image capture system. I have a Macintosh Powerbook that I would like to use for capturing images from an analog camera. However, I need to know if there are good framegrabber cards (scientific quality) that can be used with a Macintosh Powerbook. It would be an added plus if NIH-Image controlled the image capture. Therefore, I am requesting any information (ie. camera, framegrabber, storage) on how to build a digital image capture system using a Macintosh Powerbook (or laptop computer). Please e-mail me directly if you feel the NIH-Image user group will not benefit from information pertaining to my request. Thank you, Wilfred Denetclaw Jr., Ph.D. --------------------------------------- Department of Anatomy, Box 0452 School of Medicine University of California, San Francisco San Francisco, CA 94143-0452 (415)476-1530 (laboratory) (415)476-4845 (FAX) wtdenet@concentric.net --------------------------------------- >>>>-------------------------------//---------------------------------<<<< Wilfred Denetclaw Jr., Ph.D. Tina Denetclaw, Pharm.D., BCPS Department of Anatomy and Assistant Clinical Professor Cardiovascular Research Institute & School of Pharmacy (Box 0622) University of California University of California San Francisco, CA. 94143-0452 San Francisco, CA 94143 (415)476-1530 (Office) tdenet@itsa.ucsf.edu (E-mail) (415)476-3586 (FAX) wtdenet@concentric.net (E-mail) >>>>-------------------------------//---------------------------------<<<< ------------------------------ Date: Thu, 05 Nov 1998 08:59:41 PST From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Re: Help with Image capture system Message-ID: <19981105165942.10950.qmail@hotmail.com> Content-Type: text/plain Wilfred, Maybe that this is not a good answer at your question, but you can take a look at the site http://www.ulg.ac.be/mica/page27.html, where you can found a kind of solution that I've developed for acquiring images with a "mobile" system. Enrico BONINO, geologist ------------------------ University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com http://www.ulg.ac.be/mica ------------------------- ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Thu, 5 Nov 1998 12:12:35 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Help with Image capture system Message-ID: <524412e3.3641dc83@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 11/5/98 11:37:48 AM, you wrote: >I hope someone out there can help me with information on how to put >together a mobile digital image capture system. I have a Macintosh >Powerbook that I would like to use for capturing images from an analog >camera. However, I need to know if there are good framegrabber cards >(scientific quality) that can be used with a Macintosh Powerbook. It >would be an added plus if NIH-Image controlled the image capture. >Therefore, I am requesting any information (ie. camera, framegrabber, >storage) on how to build a digital image capture system using a Macintosh >Powerbook (or laptop computer). Please e-mail me directly if you feel the >NIH-Image user group will not benefit from information pertaining to my >request. I do lots of image analysis using a Mac Powerbook, but not using a video camera. Get yourself a good digital camera (I use the Polaroid DMC) with a SCSI connection. The results will be much better than a video camera (better resolution, more consistent color, less noise, etc.) and the cost will be comparable to what a video camera plus frame grabber would cost. ------------------------------ Date: Thu, 05 Nov 1998 17:05:48 -0500 From: "j. shi" To: nih-image@io.ece.drexel.edu Subject: looking for software for higher bits (>8) Message-Id: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> Content-Type: text/enriched; charset="us-ascii" hi, all: is there a new version of NIH image processing software that can handle more than 8 bits (b/w images)? or any other similar package (cheap or free)? mac or pc does't matter. thanks. jerry. **************************************** j. shi dept. of geological sciences the ohio state university columbus, ohio 43210 0000,0000,ffff(614)-292-0585/6193 (o) ffff,0000,ffff(614)-688-9686 (h) **************************************** ------------------------------ Date: Thu, 5 Nov 1998 18:45:24 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: looking for software for higher bits (>8) Message-Id: Content-Type: text/plain; charset="us-ascii" >hi, all: is there a new version of NIH image processing software that can >handle more than 8 bits (b/w images)? or any other similar package (cheap >or free)? mac or pc does't matter. thanks. jerry. My new Image/J program at http://rsb.info.nih.gov/ij/ can handle more than 8-bits per pixel. It runs on both Macs and PCs. -wayne -------------------------------- End of nih-image-d Digest V98 Issue #108 **************************************** From nih-image-request@io.ece.drexel.edu Fri Nov 6 11:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA05495; Fri, 6 Nov 1998 11:17:23 -0500 (EST) Resent-Date: Fri, 6 Nov 1998 11:17:23 -0500 (EST) Date: Fri, 06 Nov 1998 10:31:05 -0500 From: Bill Christens-Barry Subject: Q: where is current doc / discussion on AverageFrames() macro command? To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"edI3W1.0.Rf4.dOnGs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/587 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 843 Somewhere, I discovered that I could pass "UseExternalTrigger" into the AverageFrames() macro command as a string option for acquiring images using the Scion LG-3 framegrabber. I've noted that the "Special>Video Control..." menu item has a "Use External Trigger" item that is surely the analogous to the macro command option. I am unable, however, to find any documentation on this is either the NIH Image or the Scion Image dox. I have no idea where I learned the syntax - it doesn't come up in my gopher searches of the list archives, and I can't find it in any persoanl email. Can anyone point me to the definitive doc or other discussion of usage etc? Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- From nih-image-request@io.ece.drexel.edu Fri Nov 6 15:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA04182; Fri, 6 Nov 1998 15:41:42 -0500 (EST) Resent-Date: Fri, 6 Nov 1998 15:41:42 -0500 (EST) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Message-ID: Date: Fri, 6 Nov 1998 15:16:13 -0500 (Eastern Standard Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.5 Build (43) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"v-uvg1.0.zE6.mYrGs"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/588 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 13 set nomail From nih-image-d-request@io.ece.drexel.edu Sat Nov 7 06:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA28184; Sat, 7 Nov 1998 06:11:38 -0500 (EST) Date: Sat, 7 Nov 1998 06:11:38 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811071111.GAA28184@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #109 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/109 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1878 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 109 Today's Topics: Q: where is current doc / discussion [ Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: Q: where is current doc / discussion on AverageFrames() macro command? Message-id: Content-type: text/plain; charset="us-ascii" Somewhere, I discovered that I could pass "UseExternalTrigger" into the AverageFrames() macro command as a string option for acquiring images using the Scion LG-3 framegrabber. I've noted that the "Special>Video Control..." menu item has a "Use External Trigger" item that is surely the analogous to the macro command option. I am unable, however, to find any documentation on this is either the NIH Image or the Scion Image dox. I have no idea where I learned the syntax - it doesn't come up in my gopher searches of the list archives, and I can't find it in any persoanl email. Can anyone point me to the definitive doc or other discussion of usage etc? Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- ------------------------------ Date: Fri, 6 Nov 1998 15:16:13 -0500 (Eastern Standard Time) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII set nomail -------------------------------- End of nih-image-d Digest V98 Issue #109 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 9 04:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA04609; Mon, 9 Nov 1998 04:11:08 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 04:11:08 -0500 (EST) Message-ID: <19981109085045.20550.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Measuring fibres with Object Image MIME-Version: 1.0 Date: Mon, 09 Nov 1998 00:50:45 PST Resent-Message-ID: <"YkVFJ1.0.4e6.7qgHs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/589 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1813 Hello Imagers, We are examining fibres in Image. We got so far, that we can use the standard Image to correctly binarize a stack picture, so Image can count the fibres and measure them. The stack comes from a Leica confocal microscope. However, the fibres will most often not lie flat, so we tried Object Image, and found out by measuring by hand, that a 2D measurement in Image NT is not exact enough. However, there are too many fibres to count by hand in Object Image. Is there a way to teach Object Image via a macro, to count and measure fibres? The problem is, because sometimes fibres will lie over another, and some are bent with the ends pointing upward, and the center lying down, making it difficult for a macro to say: "OK, there is a reflection, set a startingpoint, go through the stack, until the reflection ends. Measure the fibre." (Well, it would be nice if the macro would do at least THIS). Now our question: Could a projected and binarized image from ImageNT be used on Object Image on our Mac, to use it as a mask, so the computer knows where a fibre starts and ends? Is it possible for Object Image to automatically detect fibres in 3d and measure them? And another question: Since I couldn't find a help file in Object Image like in NT Image, I tried to mark the fibres by hand (i use a segmented line Object for this) and wanted to mark the glass carrier with a different colored polygomal object. Then export it to a .rot file and view it in Rotater. However, how do I switch over to the 2nd sort of object, after I finished marking the fibres with the segmented lines? Any help to this is really greatly appreciated. yours sincerely Michael Arm. ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Mon Nov 9 07:12 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA11713; Mon, 9 Nov 1998 07:12:44 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 07:12:44 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: arminator@hotmail.com, nih-image@io.ece.drexel.edu Date: Mon, 9 Nov 1998 22:57:29 GMT+1100 Subject: Re: Measuring fibres with Object Image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <16789F07CF1@rna.bio.mq.edu.au> Resent-Message-ID: <"6ymj-3.0.hA1.vVjHs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/590 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 4187 >From: "Michael Arm" >To: nih-image@io.ece.drexel.edu >Subject: Measuring fibres with Object Image >Date: Mon, 09 Nov 1998 00:50:45 PST > >Hello Imagers, > >We are examining fibres in Image. We got so far, that we can use the >standard Image to correctly binarize a stack picture, so Image can count >the fibres and measure them. The stack comes from a Leica confocal >microscope. > >However, the fibres will most often not lie flat, so we tried Object >Image, and found out by measuring by hand, that a 2D measurement in >Image NT is not exact enough. >However, there are too many fibres to count by hand in Object Image. > >Is there a way to teach Object Image via a macro, to count and measure >fibres? >The problem is, because sometimes fibres will lie over another, and some >are bent with the ends pointing upward, and the center lying down, >making it difficult for a macro to say: "OK, there is a reflection, set >a startingpoint, go through the stack, until the reflection ends. >Measure the fibre." >(Well, it would be nice if the macro would do at least THIS). > >Now our question: Could a projected and binarized image from ImageNT be >used on Object Image on our Mac, to use it as a mask, so the computer >knows where a fibre starts and ends? Is it possible for Object Image to >automatically detect fibres in 3d and measure them? > I have writen macros to produce an optimal focus projection from a stack of images taken at different focal planes. The quality of focus is measured as the maximum local contrast of a column through the stack or alternatively as the maxima or mimima of the intensities. A byproduct of the macro is a map of the image showing the frame in which the image is best in focus. Using the optimal focus projection to make a binary mask of the fibres to mask the depth contour map, it should be fairly straightforward to segment individual fibres together with a record of component (skeletonised) frame segments and the frames they traverse. This should give as good 3D geometry as the stack contains. The optimal focus projection macro was writen/tested for normal and disecting microscope images and works well with subjects that have a primary surface which comes to focus such as fish otoliths, hard microfossils, insects etc. As I dont have access to a confocal and of course a lot would on the nature of your images, it would be best if you could email a small sample stack. I would be happy to have a look at processing it to see if the macros are suitable or if some revision might be appropriate. Macros run under NIH-Image (or Object-Image). (haven't tested them on Image NT) Object-Image rLeft[],rTop[] arrays from analyzeParticles will be particularly useful for autoOutline(rLeft[i],rTop[i]); detail reprocessing of individual fibres. > >And another question: Since I couldn't find a help file in Object Image >like in NT Image, I tried to mark the fibres by hand (i use a segmented >line Object for this) and wanted to mark the glass carrier with a >different colored polygomal object. Then export it to a .rot file and >view it in Rotater. However, how do I switch over to the 2nd sort of >object, after I finished marking the fibres with the segmented lines? ? Object-Image has excellent on-line help file (one of the excellent extensions to Wayne's standard NIH-Image). The latest version has pull-down help on macro reference (standard and Object extensions), text editor and sequence window (accessed via normal Mac ? help pull-down menu). There are also tutorials at the website. http://simon.bio.uva.nl/object-image.html As the sequence window help is in the form of an image, and directly answers your question I will email as an attachment by separate direct email. > > >Any help to this is really greatly appreciated. > >yours sincerely >Michael Arm. > > >______________________________________________________ >Get Your Private, Free Email at http://www.hotmail.com > > Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Mon Nov 9 09:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21960; Mon, 9 Nov 1998 09:02:26 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 09:02:26 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 9 Nov 1998 08:48:35 -0400 To: nih-image@io.ece.drexel.edu From: David Milstone Subject: NIH Image as Photoshop substitute Resent-Message-ID: <"kPN5S2.0.vV3.K4lHs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/591 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 1266 GenevaDo you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. Any other suggestions? Freeware would be especially welcome. TIA. Dave David S. Milstone, M.D., Ph.D. Vascular Research Division Department of Pathology Brigham & Women's Hospital Harvard Medical School LMRC 421 221 Longwood Ave Boston, MA 02115 milstone@rascal.med.harvard.edu (617) 975-0896 (FAX) (617) 278-0173 (Tel) From nih-image-request@io.ece.drexel.edu Mon Nov 9 10:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14518; Mon, 9 Nov 1998 10:06:58 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 10:06:58 -0500 (EST) From: "James C. Fleet" Sender: jcfleet@uncg.edu Reply-To: jim_fleet@uncg.edu To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute In-Reply-To: Message-ID: Date: Mon, 9 Nov 1998 09:36:45 -0500 (Eastern Standard Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"WO5ut.0.t01.4ulHs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/592 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 2565 Dave, I don't think that NIH image is you best solution. My bet is that it isn't user friendly enough for elementary school students. As for Photoshop, why do you need 26 licenses? Not every computer needs to have this. (In fact, Photoshop probably isn't enough anyway - you probably want Pagemaker too (although you could also just import into MS Word)). Anyway, the kids can do most of their page design and layout off the computer. They would then use the one computer with a copy of Photoshop/Pagemaker to do the final copy. In addition, a lower version of Photoshop now comes with most flatbed scanners. My guess is that this is all the kids would need. If you are really concerned about the expense, the old fashioned way of cut and paste still works just fine. Just one mans opinion of course. Jim Fleet On Mon, 9 Nov 1998 08:48:35 -0400 David Milstone wrote: > GenevaDo you think that NIH Image > would function as a Photoshop substitute for elementary school students > wanting to turn digital camera and scanner output into a school > newspaper, class assignments, etc.? Even with an educational discount > we would have to put out more than $3,000 (I'm told that we really do > need 26 simultaneous-use licenses) for the real thing and this would be > vast overkill for our needs. > > > We are looking for basic pixel-based manipulations including cropping, > brightness, color correction, etc. Simple drawing functions would also > be useful. Text would probably be handled by other software. > > > The simplest solution (because the software is familiar to me) would be > outdated versions of Photoshop but these seem scarce. I thought that > Image could substitute but might be too complicated and that it might > not be easy to simplify the interface. > > > Any other suggestions? Freeware would be especially welcome. > > > TIA. > > > Dave > > > David S. Milstone, M.D., Ph.D. > > Vascular Research Division > > Department of Pathology > > Brigham & Women's Hospital > > Harvard Medical School > > LMRC 421 > > 221 Longwood Ave > > Boston, MA 02115 > > milstone@rascal.med.harvard.edu > > (617) 975-0896 (FAX) > > (617) 278-0173 (Tel) > ---------------------- James C. Fleet, Ph.D. Director, Graduate Program in Nutrition Dept. of Nutrition and Foodservice Systems University of North Carolina at Greensboro P.O. Box 26170 Greensboro, NC 27402-6170 (O)1-336-334-5313 (F)1-336-334-4129 jim_fleet@uncg.edu From nih-image-request@io.ece.drexel.edu Mon Nov 9 10:58 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02081; Mon, 9 Nov 1998 10:58:21 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 10:58:21 -0500 (EST) Message-Id: <364709A9.E077B5B4@maroon.tc.umn.edu> Date: Mon, 09 Nov 1998 09:26:34 -0600 From: Michael Herron Reply-To: Michael J Herron Organization: U of MN, Medicine, Infectious Diseases X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"GfGO23.0.lG5.ucmHs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/593 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1794 Adobe Photo Deluxe is a much cheaper alternative and very friendly compared to PS. Another cheaper alternative is GraphicsCinvertor a great shareware. David Milstone wrote: > > Do you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. > > We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. > > The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. > > Any other suggestions? Freeware would be especially welcome. > > TIA. > > Dave > David S. Milstone, M.D., Ph.D. > Vascular Research Division > Department of Pathology > Brigham & Women's Hospital > Harvard Medical School > LMRC 421 > 221 Longwood Ave > Boston, MA 02115 > milstone@rascal.med.harvard.edu > (617) 975-0896 (FAX) > (617) 278-0173 (Tel) -- _____________________________________________________________ / Michael J. Herron University of MN, Dept. of Medicine / / herro001@maroon.tc.umn.edu / / http://134.84.141.41/RASH.html / / Or my NEW site at http://128.101.243.213/ / _____________________________________________________________ From nih-image-request@io.ece.drexel.edu Mon Nov 9 13:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA15110; Mon, 9 Nov 1998 13:14:03 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 13:14:03 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 9 Nov 1998 09:37:33 -0800 To: nih-image@io.ece.drexel.edu From: Joel Brody Subject: Re: NIH Image as Photoshop substitute Resent-Message-ID: <"C9xd83.0.P01.8YoHs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/594 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 1937 Dave, I think that NIH-Image along with Pagemaker or Word would do fine for your school. Image can show kids elementary image processing (particularly Brightness/contrast and sharpen) and most word processors will do elementary layout. Thay can also use Image to do simple animation using stacks. My kids thought that was fin. Joel >>>> GenevaDo you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. Any other suggestions? Freeware would be especially welcome. TIA. Dave David S. Milstone, M.D., Ph.D. Vascular Research Division Department of Pathology Brigham & Women's Hospital Harvard Medical School LMRC 421 221 Longwood Ave Boston, MA 02115 milstone@rascal.med.harvard.edu (617) 975-0896 (FAX) (617) 278-0173 (Tel) <<<<<<<< **************************************************************************** CunhaLab, UCSF | Mount Zion Cancer Center, Box 0540 | 2340 Sutter Street, Room S241 | Tel: (415) 476-6746 San Francisco, CA 94115 | Fax: (415) 502-2270 From nih-image-request@io.ece.drexel.edu Mon Nov 9 13:47 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25701; Mon, 9 Nov 1998 13:47:24 -0500 (EST) Resent-Date: Mon, 9 Nov 1998 13:47:24 -0500 (EST) Message-Id: From: "Calvert, David B" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: NIH Image as Photoshop substitute Date: Mon, 9 Nov 1998 13:19:28 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"qrYfd3.0.724.58pHs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/595 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 2063 David, It's not freeware - but since you have some $$ you might want to look at Paint Shop Pro. http://www.jasc.com/ I use it everyday for simple presentation layouts, some image processing, image type conversions etc. In runs standard scanner/camera interfaces. The latest version has layers like PhotoShop and also includes an GIF animator, which is great fun. Take a look. (the usual boilerplate: I have no commercial interest in PSP etc). David B. Calvert Physical Chemistry Research Laboratory Eastman Chemical Co. voice (423) 229-4943 Fax (423) 229-4558 > -----Original Message----- > From: David Milstone [SMTP:milstone@rascal.med.harvard.edu] > Sent: Monday, November 09, 1998 7:49 AM > To: nih-image@io.ece.drexel.edu > Subject: NIH Image as Photoshop substitute > > Do you think that NIH Image would function as a Photoshop substitute > for elementary school students wanting to turn digital camera and > scanner output into a school newspaper, class assignments, etc.? Even > with an educational discount we would have to put out more than $3,000 > (I'm told that we really do need 26 simultaneous-use licenses) for the > real thing and this would be vast overkill for our needs. > > We are looking for basic pixel-based manipulations including cropping, > brightness, color correction, etc. Simple drawing functions would also > be useful. Text would probably be handled by other software. > > The simplest solution (because the software is familiar to me) would > be outdated versions of Photoshop but these seem scarce. I thought > that Image could substitute but might be too complicated and that it > might not be easy to simplify the interface. > > Any other suggestions? Freeware would be especially welcome. > > TIA. > > Dave > David S. Milstone, M.D., Ph.D. > Vascular Research Division > Department of Pathology > Brigham & Women's Hospital > Harvard Medical School > LMRC 421 > 221 Longwood Ave > Boston, MA 02115 > milstone@rascal.med.harvard.edu > (617) 975-0896 (FAX) > (617) 278-0173 (Tel) From nih-image-d-request@io.ece.drexel.edu Tue Nov 10 06:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09401; Tue, 10 Nov 1998 06:26:03 -0500 (EST) Date: Tue, 10 Nov 1998 06:26:03 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811101126.GAA09401@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #110 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/110 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 18496 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 110 Today's Topics: Measuring fibres with Object Image [ "Michael Arm" ] RE: NIH Image as Photoshop substitut [ "Calvert, David B" To: nih-image@io.ece.drexel.edu Subject: Measuring fibres with Object Image Message-ID: <19981109085045.20550.qmail@hotmail.com> Content-Type: text/plain Hello Imagers, We are examining fibres in Image. We got so far, that we can use the standard Image to correctly binarize a stack picture, so Image can count the fibres and measure them. The stack comes from a Leica confocal microscope. However, the fibres will most often not lie flat, so we tried Object Image, and found out by measuring by hand, that a 2D measurement in Image NT is not exact enough. However, there are too many fibres to count by hand in Object Image. Is there a way to teach Object Image via a macro, to count and measure fibres? The problem is, because sometimes fibres will lie over another, and some are bent with the ends pointing upward, and the center lying down, making it difficult for a macro to say: "OK, there is a reflection, set a startingpoint, go through the stack, until the reflection ends. Measure the fibre." (Well, it would be nice if the macro would do at least THIS). Now our question: Could a projected and binarized image from ImageNT be used on Object Image on our Mac, to use it as a mask, so the computer knows where a fibre starts and ends? Is it possible for Object Image to automatically detect fibres in 3d and measure them? And another question: Since I couldn't find a help file in Object Image like in NT Image, I tried to mark the fibres by hand (i use a segmented line Object for this) and wanted to mark the glass carrier with a different colored polygomal object. Then export it to a .rot file and view it in Rotater. However, how do I switch over to the 2nd sort of object, after I finished marking the fibres with the segmented lines? Any help to this is really greatly appreciated. yours sincerely Michael Arm. ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Mon, 9 Nov 1998 22:57:29 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: arminator@hotmail.com, nih-image@io.ece.drexel.edu Subject: Re: Measuring fibres with Object Image Message-ID: <16789F07CF1@rna.bio.mq.edu.au> >From: "Michael Arm" >To: nih-image@io.ece.drexel.edu >Subject: Measuring fibres with Object Image >Date: Mon, 09 Nov 1998 00:50:45 PST > >Hello Imagers, > >We are examining fibres in Image. We got so far, that we can use the >standard Image to correctly binarize a stack picture, so Image can count >the fibres and measure them. The stack comes from a Leica confocal >microscope. > >However, the fibres will most often not lie flat, so we tried Object >Image, and found out by measuring by hand, that a 2D measurement in >Image NT is not exact enough. >However, there are too many fibres to count by hand in Object Image. > >Is there a way to teach Object Image via a macro, to count and measure >fibres? >The problem is, because sometimes fibres will lie over another, and some >are bent with the ends pointing upward, and the center lying down, >making it difficult for a macro to say: "OK, there is a reflection, set >a startingpoint, go through the stack, until the reflection ends. >Measure the fibre." >(Well, it would be nice if the macro would do at least THIS). > >Now our question: Could a projected and binarized image from ImageNT be >used on Object Image on our Mac, to use it as a mask, so the computer >knows where a fibre starts and ends? Is it possible for Object Image to >automatically detect fibres in 3d and measure them? > I have writen macros to produce an optimal focus projection from a stack of images taken at different focal planes. The quality of focus is measured as the maximum local contrast of a column through the stack or alternatively as the maxima or mimima of the intensities. A byproduct of the macro is a map of the image showing the frame in which the image is best in focus. Using the optimal focus projection to make a binary mask of the fibres to mask the depth contour map, it should be fairly straightforward to segment individual fibres together with a record of component (skeletonised) frame segments and the frames they traverse. This should give as good 3D geometry as the stack contains. The optimal focus projection macro was writen/tested for normal and disecting microscope images and works well with subjects that have a primary surface which comes to focus such as fish otoliths, hard microfossils, insects etc. As I dont have access to a confocal and of course a lot would on the nature of your images, it would be best if you could email a small sample stack. I would be happy to have a look at processing it to see if the macros are suitable or if some revision might be appropriate. Macros run under NIH-Image (or Object-Image). (haven't tested them on Image NT) Object-Image rLeft[],rTop[] arrays from analyzeParticles will be particularly useful for autoOutline(rLeft[i],rTop[i]); detail reprocessing of individual fibres. > >And another question: Since I couldn't find a help file in Object Image >like in NT Image, I tried to mark the fibres by hand (i use a segmented >line Object for this) and wanted to mark the glass carrier with a >different colored polygomal object. Then export it to a .rot file and >view it in Rotater. However, how do I switch over to the 2nd sort of >object, after I finished marking the fibres with the segmented lines? ? Object-Image has excellent on-line help file (one of the excellent extensions to Wayne's standard NIH-Image). The latest version has pull-down help on macro reference (standard and Object extensions), text editor and sequence window (accessed via normal Mac ? help pull-down menu). There are also tutorials at the website. http://simon.bio.uva.nl/object-image.html As the sequence window help is in the form of an image, and directly answers your question I will email as an attachment by separate direct email. > > >Any help to this is really greatly appreciated. > >yours sincerely >Michael Arm. > > >______________________________________________________ >Get Your Private, Free Email at http://www.hotmail.com > > Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Mon, 9 Nov 1998 08:48:35 -0400 From: David Milstone To: nih-image@io.ece.drexel.edu Subject: NIH Image as Photoshop substitute Message-Id: Content-Type: text/enriched; charset="us-ascii" GenevaDo you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. Any other suggestions? Freeware would be especially welcome. TIA. Dave David S. Milstone, M.D., Ph.D. Vascular Research Division Department of Pathology Brigham & Women's Hospital Harvard Medical School LMRC 421 221 Longwood Ave Boston, MA 02115 milstone@rascal.med.harvard.edu (617) 975-0896 (FAX) (617) 278-0173 (Tel) ------------------------------ Date: Mon, 9 Nov 1998 09:36:45 -0500 (Eastern Standard Time) From: "James C. Fleet" To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dave, I don't think that NIH image is you best solution. My bet is that it isn't user friendly enough for elementary school students. As for Photoshop, why do you need 26 licenses? Not every computer needs to have this. (In fact, Photoshop probably isn't enough anyway - you probably want Pagemaker too (although you could also just import into MS Word)). Anyway, the kids can do most of their page design and layout off the computer. They would then use the one computer with a copy of Photoshop/Pagemaker to do the final copy. In addition, a lower version of Photoshop now comes with most flatbed scanners. My guess is that this is all the kids would need. If you are really concerned about the expense, the old fashioned way of cut and paste still works just fine. Just one mans opinion of course. Jim Fleet On Mon, 9 Nov 1998 08:48:35 -0400 David Milstone wrote: > GenevaDo you think that NIH Image > would function as a Photoshop substitute for elementary school students > wanting to turn digital camera and scanner output into a school > newspaper, class assignments, etc.? Even with an educational discount > we would have to put out more than $3,000 (I'm told that we really do > need 26 simultaneous-use licenses) for the real thing and this would be > vast overkill for our needs. > > > We are looking for basic pixel-based manipulations including cropping, > brightness, color correction, etc. Simple drawing functions would also > be useful. Text would probably be handled by other software. > > > The simplest solution (because the software is familiar to me) would be > outdated versions of Photoshop but these seem scarce. I thought that > Image could substitute but might be too complicated and that it might > not be easy to simplify the interface. > > > Any other suggestions? Freeware would be especially welcome. > > > TIA. > > > Dave > > > David S. Milstone, M.D., Ph.D. > > Vascular Research Division > > Department of Pathology > > Brigham & Women's Hospital > > Harvard Medical School > > LMRC 421 > > 221 Longwood Ave > > Boston, MA 02115 > > milstone@rascal.med.harvard.edu > > (617) 975-0896 (FAX) > > (617) 278-0173 (Tel) > ---------------------- James C. Fleet, Ph.D. Director, Graduate Program in Nutrition Dept. of Nutrition and Foodservice Systems University of North Carolina at Greensboro P.O. Box 26170 Greensboro, NC 27402-6170 (O)1-336-334-5313 (F)1-336-334-4129 jim_fleet@uncg.edu ------------------------------ Date: Mon, 09 Nov 1998 09:26:34 -0600 From: Michael Herron To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute Message-Id: <364709A9.E077B5B4@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Adobe Photo Deluxe is a much cheaper alternative and very friendly compared to PS. Another cheaper alternative is GraphicsCinvertor a great shareware. David Milstone wrote: > > Do you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. > > We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. > > The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. > > Any other suggestions? Freeware would be especially welcome. > > TIA. > > Dave > David S. Milstone, M.D., Ph.D. > Vascular Research Division > Department of Pathology > Brigham & Women's Hospital > Harvard Medical School > LMRC 421 > 221 Longwood Ave > Boston, MA 02115 > milstone@rascal.med.harvard.edu > (617) 975-0896 (FAX) > (617) 278-0173 (Tel) -- _____________________________________________________________ / Michael J. Herron University of MN, Dept. of Medicine / / herro001@maroon.tc.umn.edu / / http://134.84.141.41/RASH.html / / Or my NEW site at http://128.101.243.213/ / _____________________________________________________________ ------------------------------ Date: Mon, 9 Nov 1998 09:37:33 -0800 From: Joel Brody To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute Message-Id: Content-Type: text/enriched; charset="us-ascii" Dave, I think that NIH-Image along with Pagemaker or Word would do fine for your school. Image can show kids elementary image processing (particularly Brightness/contrast and sharpen) and most word processors will do elementary layout. Thay can also use Image to do simple animation using stacks. My kids thought that was fin. Joel >>>> GenevaDo you think that NIH Image would function as a Photoshop substitute for elementary school students wanting to turn digital camera and scanner output into a school newspaper, class assignments, etc.? Even with an educational discount we would have to put out more than $3,000 (I'm told that we really do need 26 simultaneous-use licenses) for the real thing and this would be vast overkill for our needs. We are looking for basic pixel-based manipulations including cropping, brightness, color correction, etc. Simple drawing functions would also be useful. Text would probably be handled by other software. The simplest solution (because the software is familiar to me) would be outdated versions of Photoshop but these seem scarce. I thought that Image could substitute but might be too complicated and that it might not be easy to simplify the interface. Any other suggestions? Freeware would be especially welcome. TIA. Dave David S. Milstone, M.D., Ph.D. Vascular Research Division Department of Pathology Brigham & Women's Hospital Harvard Medical School LMRC 421 221 Longwood Ave Boston, MA 02115 milstone@rascal.med.harvard.edu (617) 975-0896 (FAX) (617) 278-0173 (Tel) <<<<<<<< **************************************************************************** CunhaLab, UCSF | Mount Zion Cancer Center, Box 0540 | 2340 Sutter Street, Room S241 | Tel: (415) 476-6746 San Francisco, CA 94115 | Fax: (415) 502-2270 ------------------------------ Date: Mon, 9 Nov 1998 13:19:28 -0500 From: "Calvert, David B" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: NIH Image as Photoshop substitute Message-Id: Content-Type: text/plain David, It's not freeware - but since you have some $$ you might want to look at Paint Shop Pro. http://www.jasc.com/ I use it everyday for simple presentation layouts, some image processing, image type conversions etc. In runs standard scanner/camera interfaces. The latest version has layers like PhotoShop and also includes an GIF animator, which is great fun. Take a look. (the usual boilerplate: I have no commercial interest in PSP etc). David B. Calvert Physical Chemistry Research Laboratory Eastman Chemical Co. voice (423) 229-4943 Fax (423) 229-4558 > -----Original Message----- > From: David Milstone [SMTP:milstone@rascal.med.harvard.edu] > Sent: Monday, November 09, 1998 7:49 AM > To: nih-image@io.ece.drexel.edu > Subject: NIH Image as Photoshop substitute > > Do you think that NIH Image would function as a Photoshop substitute > for elementary school students wanting to turn digital camera and > scanner output into a school newspaper, class assignments, etc.? Even > with an educational discount we would have to put out more than $3,000 > (I'm told that we really do need 26 simultaneous-use licenses) for the > real thing and this would be vast overkill for our needs. > > We are looking for basic pixel-based manipulations including cropping, > brightness, color correction, etc. Simple drawing functions would also > be useful. Text would probably be handled by other software. > > The simplest solution (because the software is familiar to me) would > be outdated versions of Photoshop but these seem scarce. I thought > that Image could substitute but might be too complicated and that it > might not be easy to simplify the interface. > > Any other suggestions? Freeware would be especially welcome. > > TIA. > > Dave > David S. Milstone, M.D., Ph.D. > Vascular Research Division > Department of Pathology > Brigham & Women's Hospital > Harvard Medical School > LMRC 421 > 221 Longwood Ave > Boston, MA 02115 > milstone@rascal.med.harvard.edu > (617) 975-0896 (FAX) > (617) 278-0173 (Tel) -------------------------------- End of nih-image-d Digest V98 Issue #110 **************************************** From nih-image-request@io.ece.drexel.edu Tue Nov 10 08:33 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA22728; Tue, 10 Nov 1998 08:33:12 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 08:33:12 -0500 (EST) Date: Tue, 10 Nov 1998 08:10:05 -0500 (EST) From: Dongbai Guo X-Sender: dbg@mothra To: nih-image@io.ece.drexel.edu Subject: gimp is a good substitute for Photoshop. In-Reply-To: <199811101128.GAA09630@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"MicFL.0.yv4.Ej3Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/596 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 546 It is devoloped under free-ware fundation support, and it is continuely updating. We use it on unix desktop, in my opinion, it is better than the unix version of adobe photoshop. It has GNU type license. I don't know if gimp have a Win95 /Mac version though. You can check their web page: www.gimp.org dongbai -------------------------------------------------------------- Tel: 401-331-6424 (home) 401-863-7693 (graphics lab) http://www.cs.brown.edu/people/dbg --------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Tue Nov 10 10:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA01519; Tue, 10 Nov 1998 10:06:56 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 10:06:56 -0500 (EST) Mime-Version: 1.0 X-Sender: stwang@mail.clemson.edu Message-Id: In-Reply-To: Date: Tue, 10 Nov 1998 09:29:46 -0500 To: David Milstone From: Sam Wang Subject: Re: NIH Image as Photoshop substitute Cc: nih-image@io.ece.drexel.edu Resent-Message-ID: <"9ki4s.0.gg6.3t4Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/597 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="============_-1301414293==_ma============" Content-Length: 3056 --============_-1301414293==_ma============ Content-Type: text/plain; charset="us-ascii" Dave, There are a couple of solutions to your dilemma. One is to use ColorIt, a very powerful paint software from MicroFrontier in Iowa. It in some aspects is BETTER than Photoshop - for instance, it was fast, and offered multiple UNDOs years ago! It is bundled with some scanners, and sold for about $60 each. At one time they gave away a million copies of an earlier version, for a shipping fee of $8.95 each. Another solution is to use DeskPaint, a commercial program no longer sold. Zedcor, who produced it, put it on their web site as freebie about a year ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using, but DeskPaint is very capable, even though it has not been updated for a few years now. The people at Zedcor told me they simply couldn't compete with the likes of ClarisWorks, which included everything for $45, but the paint module in ClarisWorks is next to worthless. Both of these are more FUN to use than Photoshop. The latter is becoming more a professional tool that requires too much familiarity before it could be useful or fun. If Zedcor approves your use of DeskPaint, I can give you a copy of it. Please contact them first. Hope this helps. Sam -------- Sam Wang e-mail: stwang@clemson.edu Art Dept - Clemson University voice: 864/656-3924 142 Lee Hall, Clemson, SC 29634 FAX: 864/656-7523 --============_-1301414293==_ma============ Content-Type: text/enriched; charset="us-ascii" PalatinoDave, There are a couple of solutions to your dilemma. One is to use ColorIt, a very powerful paint software from MicroFrontier in Iowa. It in some aspects is BETTER than Photoshop - for instance, it was fast, and offered multiple UNDOs years ago! It is bundled with some scanners, and sold for about $60 each. At one time they gave away a million copies of an earlier version, for a shipping fee of $8.95 each. Another solution is to use DeskPaint, a commercial program no longer sold. Zedcor, who produced it, put it on their web site as freebie about a year ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using, but DeskPaint is very capable, even though it has not been updated for a few years now. The people at Zedcor told me they simply couldn't compete with the likes of ClarisWorks, which included everything for $45, but the paint module in ClarisWorks is next to worthless. Both of these are more FUN to use than Photoshop. The latter is becoming more a professional tool that requires too much familiarity before it could be useful or fun. If Zedcor approves your use of DeskPaint, I can give you a copy of it. Please contact them first. Hope this helps. Sam -------- Sam Wang e-mail: stwang@clemson.edu Art Dept - Clemson University voice: 864/656-3924 142 Lee Hall, Clemson, SC 29634 FAX: 864/656-7523 --============_-1301414293==_ma============-- From nih-image-request@io.ece.drexel.edu Tue Nov 10 11:55 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04122; Tue, 10 Nov 1998 11:55:17 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 11:55:17 -0500 (EST) Message-ID: <3648738B.22F253E0@att.net> Date: Tue, 10 Nov 1998 09:10:35 -0800 From: Chris X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: image Subject: shortcut for selection size? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"s4wU21.0.0e3.nM6Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/598 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 320 Hello all- Is there a way to set a standard selection size in Image? I need to make many (1000's) measurements within a standard area, and I'm wondering if there's a better way than adjusting the selection area by hand by looking in the "info" window until the size is right. TIA- Christine Cline Salt Lake City, UT From nih-image-request@io.ece.drexel.edu Tue Nov 10 12:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA15095; Tue, 10 Nov 1998 12:19:45 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 12:19:45 -0500 (EST) Message-ID: <36487ACC.ABF0E298@att.net> Date: Tue, 10 Nov 1998 09:41:32 -0800 From: Chris X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: image Subject: can image count pixels? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"1ko7U.0.cz6.qp6Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/599 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 664 Hello again I'm a new Image user (and new to this newsgroup), so I hope that this question isn't to irritatingly obvious to more experienced users of this software. I'm trying to quantitate an area that is dark vs. the light area within a set area. I think I can use the "threshold" command (and maybe "make binary" to convert my grey-scale image to a binary image, but what I'd like to do next is have IMAGE calculate the number of black pixels within the area. Is there a way to do this? Please reply to me directly unless you think this information would be of general interest to the readers of the newsgroup. Thanks- Christine Cline Salt Lake City, UT From nih-image-request@io.ece.drexel.edu Tue Nov 10 13:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA19724; Tue, 10 Nov 1998 13:41:53 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 13:41:53 -0500 (EST) Date: Tue, 10 Nov 1998 10:06:05 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re:NIH Image as Photoshop substitute In-Reply-To: <199811101127.GAA09578@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"R_N_A2.0.Bx.Q28Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/600 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 588 Dave, Take a look at Color-It, from MicroFrontier. Current version is about US$50. Site licenses are available. It will run plug-ins and does the levels adjustments and image manipulations for which Photoshop is commonly used. I use Color-It at home and Photoshop at the lab. My children's elementary school also uses Color-It on their Macs. Regards, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu From nih-image-request@io.ece.drexel.edu Tue Nov 10 14:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA28957; Tue, 10 Nov 1998 14:01:39 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 14:01:39 -0500 (EST) Message-Id: From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: shortcut for selection size? Date: Tue, 10 Nov 1998 13:29:43 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"ZGhXg3.0.0b3.pO8Is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/601 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1122 Chris: The "Restore Selection" command (Analyze menu or command-4) will transfer the active selection area from the most recent image to the current image: Set your selection where you want it in your "seed" image Open the next image Choose "Restore Selection" The selection marching ants should appear in the same relative location as in the seed. >From here, you can continue on (as long as the selection is still intact) or go back to your seed and repeat the process. Alternatively, you can write a simple little macro that creates the rectangular selection that you want. If you are going to be doing this on "thousands" of images over a long period of time, this is the preferred method. As for counting pixels in the binary image, you can do it "quick and dirty" by getting the histogram of the binary image and moving the mouse over the black and white peaks and noting the two counts, then doing the math. The better long-term answer is another quick little macro that gets the values of Histogram[0] and Histogram[255], then doing the math for you. Bill Heeschen The Dow Chemical Company Microscopy Group From nih-image-request@io.ece.drexel.edu Tue Nov 10 18:33 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA26022; Tue, 10 Nov 1998 18:33:59 -0500 (EST) Resent-Date: Tue, 10 Nov 1998 18:33:59 -0500 (EST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Measuring fibres with Object Image Date: Tue, 10 Nov 1998 22:51:49 +0000 Resent-Message-ID: <"DUknj2.0.Cm2.GFCIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/602 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2581 Michael, In the new version of Object-Image, switching to differently colored objects is much easier, because there are two collect modes to choose from: "Multiple" collect mode (bus symbol), is intended for structured point collection with several objects per cell, and now also "Single" collect mode (car symbol), intended for random switching between the available object types, but only allowing one object per cell. In your example, prepare the experiment by choosing the 'Define Objects..' dialog, drag two differently colored 'segmented lines' into the sequence area (the use of 3d polygons is currently blocked, because the area of such an object can be ambiguous). Then, click 'Single' and '3D objects' . Once this preparation is done, set 3D lines into one or several volume stacks. You can switch to another color by simply clicking onto the desired object symbol in the floating "Sequence" window. It's also possible to assign shortcut keys to the object types without using macros, so switching can be performed by key stroke. Also have a look at the "3d tracing" example in the "Examples" on the same ftp site, which explains the "live slicing" collect mode that allows to capture 3 coordinates (x, y and z) with one mouse click. All you do by hand, you also can do by macro, if the macro can calculate the marker positions. An automatic 3D tracer is not yet implemented, although algorithms to trace tubular 3D structures have been developed in our lab (see Houtsmuller: The homing cursor; Cytometry? ca. 1990?). I don't know how many people would be interested in an implementation, and whether I have the time to do it. At this moment, you could try to make 2D measurements which you subsequently connect in 3D by checking for overlaps. Before using the 'Export XYZ data', look whether you can create appropriate result columns and simply use 'Export Object Results..'. This provides a better data structure with correct column names and gives readily calculated results such as the length of 3D segmented lines or 3D angles. By the way, we also have a Leica confocal microscope, an old one which works under OS/9. Because the instrument has a non-standard ftp server (Fetch doesn't work), I implemented an ftp client into Object-Image to directly import properly scaled volume images via ftp protocol from this OS/9 server. Note that the documentation of Object-Image as well as the web site are several months old and don't mention some of the new features. Until this is fixed, look at the help panels under the help menu, or balloon help. N. Vischer From nih-image-d-request@io.ece.drexel.edu Wed Nov 11 06:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10615; Wed, 11 Nov 1998 06:22:03 -0500 (EST) Date: Wed, 11 Nov 1998 06:22:03 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811111122.GAA10615@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #111 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/111 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11854 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 111 Today's Topics: gimp is a good substitute for Photos [ Dongbai Guo ] Re: NIH Image as Photoshop substitut [ Sam Wang ] shortcut for selection size? [ Chris ] can image count pixels? [ Chris ] Re:NIH Image as Photoshop substitute [ "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: gimp is a good substitute for Photoshop. Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII It is devoloped under free-ware fundation support, and it is continuely updating. We use it on unix desktop, in my opinion, it is better than the unix version of adobe photoshop. It has GNU type license. I don't know if gimp have a Win95 /Mac version though. You can check their web page: www.gimp.org dongbai -------------------------------------------------------------- Tel: 401-331-6424 (home) 401-863-7693 (graphics lab) http://www.cs.brown.edu/people/dbg --------------------------------------------------------------- ------------------------------ Date: Tue, 10 Nov 1998 09:29:46 -0500 From: Sam Wang To: David Milstone Cc: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute Message-Id: Content-Type: multipart/alternative; boundary="============_-1301414293==_ma============" --============_-1301414293==_ma============ Content-Type: text/plain; charset="us-ascii" Dave, There are a couple of solutions to your dilemma. One is to use ColorIt, a very powerful paint software from MicroFrontier in Iowa. It in some aspects is BETTER than Photoshop - for instance, it was fast, and offered multiple UNDOs years ago! It is bundled with some scanners, and sold for about $60 each. At one time they gave away a million copies of an earlier version, for a shipping fee of $8.95 each. Another solution is to use DeskPaint, a commercial program no longer sold. Zedcor, who produced it, put it on their web site as freebie about a year ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using, but DeskPaint is very capable, even though it has not been updated for a few years now. The people at Zedcor told me they simply couldn't compete with the likes of ClarisWorks, which included everything for $45, but the paint module in ClarisWorks is next to worthless. Both of these are more FUN to use than Photoshop. The latter is becoming more a professional tool that requires too much familiarity before it could be useful or fun. If Zedcor approves your use of DeskPaint, I can give you a copy of it. Please contact them first. Hope this helps. Sam -------- Sam Wang e-mail: stwang@clemson.edu Art Dept - Clemson University voice: 864/656-3924 142 Lee Hall, Clemson, SC 29634 FAX: 864/656-7523 --============_-1301414293==_ma============ Content-Type: text/enriched; charset="us-ascii" PalatinoDave, There are a couple of solutions to your dilemma. One is to use ColorIt, a very powerful paint software from MicroFrontier in Iowa. It in some aspects is BETTER than Photoshop - for instance, it was fast, and offered multiple UNDOs years ago! It is bundled with some scanners, and sold for about $60 each. At one time they gave away a million copies of an earlier version, for a shipping fee of $8.95 each. Another solution is to use DeskPaint, a commercial program no longer sold. Zedcor, who produced it, put it on their web site as freebie about a year ago, along with DeskDraw. DeskDraw is indeed outdated and not worth using, but DeskPaint is very capable, even though it has not been updated for a few years now. The people at Zedcor told me they simply couldn't compete with the likes of ClarisWorks, which included everything for $45, but the paint module in ClarisWorks is next to worthless. Both of these are more FUN to use than Photoshop. The latter is becoming more a professional tool that requires too much familiarity before it could be useful or fun. If Zedcor approves your use of DeskPaint, I can give you a copy of it. Please contact them first. Hope this helps. Sam -------- Sam Wang e-mail: stwang@clemson.edu Art Dept - Clemson University voice: 864/656-3924 142 Lee Hall, Clemson, SC 29634 FAX: 864/656-7523 --============_-1301414293==_ma============-- ------------------------------ Date: Tue, 10 Nov 1998 09:10:35 -0800 From: Chris To: image Subject: shortcut for selection size? Message-ID: <3648738B.22F253E0@att.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all- Is there a way to set a standard selection size in Image? I need to make many (1000's) measurements within a standard area, and I'm wondering if there's a better way than adjusting the selection area by hand by looking in the "info" window until the size is right. TIA- Christine Cline Salt Lake City, UT ------------------------------ Date: Tue, 10 Nov 1998 09:41:32 -0800 From: Chris To: image Subject: can image count pixels? Message-ID: <36487ACC.ABF0E298@att.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello again I'm a new Image user (and new to this newsgroup), so I hope that this question isn't to irritatingly obvious to more experienced users of this software. I'm trying to quantitate an area that is dark vs. the light area within a set area. I think I can use the "threshold" command (and maybe "make binary" to convert my grey-scale image to a binary image, but what I'd like to do next is have IMAGE calculate the number of black pixels within the area. Is there a way to do this? Please reply to me directly unless you think this information would be of general interest to the readers of the newsgroup. Thanks- Christine Cline Salt Lake City, UT ------------------------------ Date: Tue, 10 Nov 1998 10:06:05 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re:NIH Image as Photoshop substitute Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dave, Take a look at Color-It, from MicroFrontier. Current version is about US$50. Site licenses are available. It will run plug-ins and does the levels adjustments and image manipulations for which Photoshop is commonly used. I use Color-It at home and Photoshop at the lab. My children's elementary school also uses Color-It on their Macs. Regards, Glen Glen MacDonald Research Scientist Hearing Research Laboratories of the Virginia Merrill Bloedel Hearing Research Center Box 35-7923 University of Washington Seattle, WA 98195-7923 (206) 616-4156 glenmac@u.washington.edu ------------------------------ Date: Tue, 10 Nov 1998 13:29:43 -0500 From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: shortcut for selection size? Message-Id: Content-Type: text/plain Chris: The "Restore Selection" command (Analyze menu or command-4) will transfer the active selection area from the most recent image to the current image: Set your selection where you want it in your "seed" image Open the next image Choose "Restore Selection" The selection marching ants should appear in the same relative location as in the seed. >From here, you can continue on (as long as the selection is still intact) or go back to your seed and repeat the process. Alternatively, you can write a simple little macro that creates the rectangular selection that you want. If you are going to be doing this on "thousands" of images over a long period of time, this is the preferred method. As for counting pixels in the binary image, you can do it "quick and dirty" by getting the histogram of the binary image and moving the mouse over the black and white peaks and noting the two counts, then doing the math. The better long-term answer is another quick little macro that gets the values of Histogram[0] and Histogram[255], then doing the math for you. Bill Heeschen The Dow Chemical Company Microscopy Group ------------------------------ Date: Tue, 10 Nov 1998 22:51:49 +0000 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Measuring fibres with Object Image Message-Id: Content-Type: text/plain; charset="us-ascii" Michael, In the new version of Object-Image, switching to differently colored objects is much easier, because there are two collect modes to choose from: "Multiple" collect mode (bus symbol), is intended for structured point collection with several objects per cell, and now also "Single" collect mode (car symbol), intended for random switching between the available object types, but only allowing one object per cell. In your example, prepare the experiment by choosing the 'Define Objects..' dialog, drag two differently colored 'segmented lines' into the sequence area (the use of 3d polygons is currently blocked, because the area of such an object can be ambiguous). Then, click 'Single' and '3D objects' . Once this preparation is done, set 3D lines into one or several volume stacks. You can switch to another color by simply clicking onto the desired object symbol in the floating "Sequence" window. It's also possible to assign shortcut keys to the object types without using macros, so switching can be performed by key stroke. Also have a look at the "3d tracing" example in the "Examples" on the same ftp site, which explains the "live slicing" collect mode that allows to capture 3 coordinates (x, y and z) with one mouse click. All you do by hand, you also can do by macro, if the macro can calculate the marker positions. An automatic 3D tracer is not yet implemented, although algorithms to trace tubular 3D structures have been developed in our lab (see Houtsmuller: The homing cursor; Cytometry? ca. 1990?). I don't know how many people would be interested in an implementation, and whether I have the time to do it. At this moment, you could try to make 2D measurements which you subsequently connect in 3D by checking for overlaps. Before using the 'Export XYZ data', look whether you can create appropriate result columns and simply use 'Export Object Results..'. This provides a better data structure with correct column names and gives readily calculated results such as the length of 3D segmented lines or 3D angles. By the way, we also have a Leica confocal microscope, an old one which works under OS/9. Because the instrument has a non-standard ftp server (Fetch doesn't work), I implemented an ftp client into Object-Image to directly import properly scaled volume images via ftp protocol from this OS/9 server. Note that the documentation of Object-Image as well as the web site are several months old and don't mention some of the new features. Until this is fixed, look at the help panels under the help menu, or balloon help. N. Vischer -------------------------------- End of nih-image-d Digest V98 Issue #111 **************************************** From nih-image-request@io.ece.drexel.edu Wed Nov 11 07:50 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA13084; Wed, 11 Nov 1998 07:50:55 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 07:50:55 -0500 (EST) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: can image count pixels? Message-ID: Date: Wed, 11 Nov 1998 12:26:54 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"XZ1pB.0._w.39OIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/603 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 699 Chris, I'm using Scion Image - PC spin off of NIH. In the macros provided with the program, there is one called measure. It includes an option to count the number of black and white pixels as suggested by Bill Heeschen. I've put a copy of it below, just in case. macro 'Count Black and White Pixels [B]'; { Counts the number of black and white pixels in the current selection and stores the counts in the User1 and User2 columns. } begin RequiresVersion(1.44); SetUser1Label('Black'); SetUser2Label('White'); Measure; rUser1[rCount]:=histogram[255]; rUser2[rCount]:=histogram[0]; UpdateResults; end; Hope it helps, Jenny Gregory ---------------------- j.gregory@abdn.ac.uk From nih-image-request@io.ece.drexel.edu Wed Nov 11 08:29 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA27040; Wed, 11 Nov 1998 08:29:06 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 08:29:06 -0500 (EST) Message-ID: <19981111125753.27404.rocketmail@web1.rocketmail.com> Date: Wed, 11 Nov 1998 04:57:53 -0800 (PST) From: Mark Vivino Subject: Re: can image count pixels? To: nih-image@io.ece.drexel.edu Cc: kokopellis@att.net MIME-Version: 1.0 Resent-Message-ID: <"TqOMf2.0.C05.9qOIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/604 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1005 > I'm a new Image user (and new to this newsgroup), so I hope that this > question isn't to irritatingly obvious to more experienced users of this > software. > > I'm trying to quantitate an area that is dark vs. the light area within > a set area. I think I can use the "threshold" command (and maybe "make > binary" to convert my grey-scale image to a binary image, but what I'd > like to do next is have IMAGE calculate the number of black pixels > within the area. Is there a way to do this? When NIH Image is in threshold mode and the measure command is issued the measurement of area will be the black thresholded area. White area would be the whole area minus the above, so very easy to calculate. Of course you can use a roi in all of this as well to measure say black area within the roi. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Wed Nov 11 12:32 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA16253; Wed, 11 Nov 1998 12:32:03 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 12:32:03 -0500 (EST) Message-Id: <199811111657.KAA25550@mail5.doit.wisc.edu> X-Sender: dlparker@facstaff.wisc.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 Date: Wed, 11 Nov 1998 11:00:49 -0600 To: nih-image@io.ece.drexel.edu From: David Parker Subject: automation of nih-image Mime-Version: 1.0 Resent-Message-ID: <"vjZ3X1.0.Cd1.H8SIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/605 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; types="text/plain,text/html"; boundary="=====================_3946354==_.ALT" Content-Length: 3439 --=====================_3946354==_.ALT Content-Type: text/plain; charset="us-ascii" Hello! This question is being posed programmer with experience with many languages, none being Image's macro language. I have briefly looked at the documentation, at some posts on a listserver and at the gopher site for possible macros. I've been asked to automate a process in nih-image macros language. The process to automate is to look for a "spark" (NOVA like flash) on an image and then to calculate several characteristics of the images. The user is interested in the following attributes: >>1. Ratio >>2. Duration >>3. Time to Peak >>4. Full time at half max/min >>5. Diameter >>6. Full width at half maximum The scan occurs from left to right. Each image is approximately 512 pixels across and 1000 pixels long. Once the images have been acquired they are stored as TIFFs on a server and then accessed by another workstation running NIH Image. These will depend on being able to find the center of mass of the spark. Does the macro language facilitate automation for scanning or the parsing of image file? Sincerely, David Parker dlparker@doit.wisc.edu Division of Information Technology, Tools and Methods, Emerging Technologies Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220 ICQ-Page Address: http://wwp.mirabilis.com/18694325 (608) 262-2104 (voice) (608) 265-6681(fax) --=====================_3946354==_.ALT Content-Type: text/html; charset="us-ascii"
Hello!

This question is being posed programmer with experience with many languages, none being Image's macro language.

I have briefly looked at the documentation, at some posts on a listserver and at the gopher site for possible macros.


I've been asked to automate a process in nih-image macros language.

The process to automate is to look for a "spark" (NOVA like flash) on an image and then to calculate several characteristics of the images. The user is interested in the following attributes:
>>1. Ratio
>>2. Duration
>>3. Time to Peak
>>4. Full time at half max/min
>>5. Diameter
>>6. Full width at half maximum

The scan occurs from left to right. Each image is approximately 512 pixels across and 1000 pixels long. Once the images have been acquired they are stored as TIFFs on a server and then accessed by another workstation running NIH Image.

These will depend on being able to find the center of mass of the spark.
Does the macro language facilitate automation for scanning or the parsing of image file?



Sincerely,
David Parker               dlparker@doit.wisc.edu

Division of Information Technology, Tools and Methods, Emerging Technologies
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220
ICQ-Page Address: http://wwp.mirabilis.com/18694325
            (608) 262-2104 (voice)  (608) 265-6681(fax)

--=====================_3946354==_.ALT-- From nih-image-request@io.ece.drexel.edu Wed Nov 11 13:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA04751; Wed, 11 Nov 1998 13:34:53 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 13:34:53 -0500 (EST) Message-Id: From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: automation of nih-image Date: Wed, 11 Nov 1998 12:59:00 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"44bpQ3.0.Ku5.o1TIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/606 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1110 David: The NIH Image macro language will allow you to inspect an image pixel-by-pixel, however you will find the execution fairly slow. My development path is to use the macro language to develop (and debug) the processing algorithms because of the rapid cycle time (no recompile and Wayne's macro parser is pretty quick). Once I am comfortable with it, I will commit it to source code for the speed improvement. The source code is Pascal under CodeWarrior and is freely available from the web page (http://rsb.info.nih.gov/nih-image/). The conversion from macro to source is not too bad as the calls are similarly named. It does require some time investment to dig through the source and figure out what happens when and where - the usual game with following someone else's logic. The result, however is a major time improvement, especially for pixel-by-pixel operations. Also, the control you have over the whole program is a lot of fun! IMHO, Wayne has created a good starting point for custom image processing solutions. Bill Heeschen The Dow Chemical Company Microscopy group waheeschen@dow.com From nih-image-request@io.ece.drexel.edu Wed Nov 11 14:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA12564; Wed, 11 Nov 1998 14:02:14 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 14:02:14 -0500 (EST) Message-ID: <3649D687.4E9E@pop.uky.edu> Date: Wed, 11 Nov 1998 13:25:11 -0500 From: alex gimelbrant Organization: U of K X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute References: <199811101128.GAA09630@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"QegRJ3.0.xR.NQTIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/607 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 930 I would like to add another option to the already vast list of suggested Photoshop substitutes. You can get GraphicConverter from any shareware source (shareware.com , ...). The author keeps putting out new versions, so it's up to date and not a dead end. In my experience, it has everything needed for image manipulation, and is pretty easy to learn and use. The only problem I used to have was low final quality of text put on image. Since it is the same problem (with the same cause; see Image FAQ) as with NIH-Image, the way to deal with it might be of some interest to Image users: The image is converted to higher resolution (this operation is in the standard menu of Gr.Conv.), and the high-resolutuion text on the printout is of publication quality. It is very memory-consuming, and interpolation involved in the conversion might distort the data, so all analysis should be done prior to that step. Alex Gimelbrant From nih-image-request@io.ece.drexel.edu Wed Nov 11 14:30 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA21176; Wed, 11 Nov 1998 14:30:27 -0500 (EST) Resent-Date: Wed, 11 Nov 1998 14:30:27 -0500 (EST) Message-ID: <19981111185423.4975.qmail@hotmail.com> X-Originating-IP: [130.132.65.250] From: "John Elsworth" To: nih-image@io.ece.drexel.edu Subject: Autorads: Seeing the light? MIME-Version: 1.0 Date: Wed, 11 Nov 1998 10:54:23 PST Resent-Message-ID: <"SITGW2.0.Ib2.HsTIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/608 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1404 I am just setting up my new imaging equipment (Northern Lights light box, Cohu CCD camera 4913 with Nikon Micro-Nikkor 55 mm f2.8 lens) for quantifying autoradiograms of brain sections. My question concerns the relative advantages of the different ways of adjusting the brightness and contrast of the image on the screen. The light passing through the film can be adjusted at the light box. Alternatively, in Image the offset (brightness) and gain (contrast) can be adjusted under Video Control. What is the best way to balance the light box output with the Image settings? Furthermore, the camera has 8 different shutter speeds but I suspect that as this is a still image, this is not critical. The Highlight Saturated Pixel option appears to be useful, but it hasn't helped me answer the above quesion, as there are different "correct" setting for offset and gain for each different light box transillumination intensity. The Display Histogram function would appear to be useful also, however the manual suggests spreading out the histogram as much as possible. To my eye, anyway, the best-looking image occurs when there is a "tall but not thin" peak to the left in the histogram. Any insights into any of these issues would be much appreciated. John Elsworth Ph.D. ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Thu Nov 12 03:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA28707; Thu, 12 Nov 1998 03:26:38 -0500 (EST) Resent-Date: Thu, 12 Nov 1998 03:26:38 -0500 (EST) Date: Thu, 12 Nov 1998 09:03:59 +0100 (CET) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Morphological operations In-Reply-To: <199811111657.KAA25550@mail5.doit.wisc.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"nGAr-3.0.qL5.3SfIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/609 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 265 Hi! I am wondering if it is possible to perform morphological operations such as pruning, thinning, thickening or the hit-or-miss transform with Image. Has somebody out there macroes that can be used in this context. Thanks. Gary Chinga NTNU-Trondheim Norway. From nih-image-d-request@io.ece.drexel.edu Thu Nov 12 03:36 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA02215; Thu, 12 Nov 1998 03:36:45 -0500 (EST) Date: Thu, 12 Nov 1998 03:36:45 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811120836.DAA02215@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #112 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/112 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11777 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 112 Today's Topics: Re: can image count pixels? [ "j.gregory" ] Re: can image count pixels? [ Mark Vivino ] ------------------------------ Date: Wed, 11 Nov 1998 12:26:54 +0000 (GMT) From: "j.gregory" To: nih-image@io.ece.drexel.edu Subject: Re: can image count pixels? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Chris, I'm using Scion Image - PC spin off of NIH. In the macros provided with the program, there is one called measure. It includes an option to count the number of black and white pixels as suggested by Bill Heeschen. I've put a copy of it below, just in case. macro 'Count Black and White Pixels [B]'; { Counts the number of black and white pixels in the current selection and stores the counts in the User1 and User2 columns. } begin RequiresVersion(1.44); SetUser1Label('Black'); SetUser2Label('White'); Measure; rUser1[rCount]:=histogram[255]; rUser2[rCount]:=histogram[0]; UpdateResults; end; Hope it helps, Jenny Gregory ---------------------- j.gregory@abdn.ac.uk ------------------------------ Date: Wed, 11 Nov 1998 04:57:53 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Cc: kokopellis@att.net Subject: Re: can image count pixels? Message-ID: <19981111125753.27404.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii > I'm a new Image user (and new to this newsgroup), so I hope that this > question isn't to irritatingly obvious to more experienced users of this > software. > > I'm trying to quantitate an area that is dark vs. the light area within > a set area. I think I can use the "threshold" command (and maybe "make > binary" to convert my grey-scale image to a binary image, but what I'd > like to do next is have IMAGE calculate the number of black pixels > within the area. Is there a way to do this? When NIH Image is in threshold mode and the measure command is issued the measurement of area will be the black thresholded area. White area would be the whole area minus the above, so very easy to calculate. Of course you can use a roi in all of this as well to measure say black area within the roi. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Wed, 11 Nov 1998 11:00:49 -0600 From: David Parker To: nih-image@io.ece.drexel.edu Subject: automation of nih-image Message-Id: <199811111657.KAA25550@mail5.doit.wisc.edu> Content-Type: multipart/alternative; types="text/plain,text/html"; boundary="=====================_3946354==_.ALT" --=====================_3946354==_.ALT Content-Type: text/plain; charset="us-ascii" Hello! This question is being posed programmer with experience with many languages, none being Image's macro language. I have briefly looked at the documentation, at some posts on a listserver and at the gopher site for possible macros. I've been asked to automate a process in nih-image macros language. The process to automate is to look for a "spark" (NOVA like flash) on an image and then to calculate several characteristics of the images. The user is interested in the following attributes: >>1. Ratio >>2. Duration >>3. Time to Peak >>4. Full time at half max/min >>5. Diameter >>6. Full width at half maximum The scan occurs from left to right. Each image is approximately 512 pixels across and 1000 pixels long. Once the images have been acquired they are stored as TIFFs on a server and then accessed by another workstation running NIH Image. These will depend on being able to find the center of mass of the spark. Does the macro language facilitate automation for scanning or the parsing of image file? Sincerely, David Parker dlparker@doit.wisc.edu Division of Information Technology, Tools and Methods, Emerging Technologies Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220 ICQ-Page Address: http://wwp.mirabilis.com/18694325 (608) 262-2104 (voice) (608) 265-6681(fax) --=====================_3946354==_.ALT Content-Type: text/html; charset="us-ascii"
Hello!

This question is being posed programmer with experience with many languages, none being Image's macro language.

I have briefly looked at the documentation, at some posts on a listserver and at the gopher site for possible macros.


I've been asked to automate a process in nih-image macros language.

The process to automate is to look for a "spark" (NOVA like flash) on an image and then to calculate several characteristics of the images. The user is interested in the following attributes:
>>1. Ratio
>>2. Duration
>>3. Time to Peak
>>4. Full time at half max/min
>>5. Diameter
>>6. Full width at half maximum

The scan occurs from left to right. Each image is approximately 512 pixels across and 1000 pixels long. Once the images have been acquired they are stored as TIFFs on a server and then accessed by another workstation running NIH Image.

These will depend on being able to find the center of mass of the spark.
Does the macro language facilitate automation for scanning or the parsing of image file?



Sincerely,
David Parker               dlparker@doit.wisc.edu

Division of Information Technology, Tools and Methods, Emerging Technologies
Ultratec Building, 5752 Tokay Blvd., Suite 200, Madison, WI 53719-1220
ICQ-Page Address: http://wwp.mirabilis.com/18694325
            (608) 262-2104 (voice)  (608) 265-6681(fax)

--=====================_3946354==_.ALT-- ------------------------------ Date: Wed, 11 Nov 1998 12:59:00 -0500 From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: automation of nih-image Message-Id: Content-Type: text/plain David: The NIH Image macro language will allow you to inspect an image pixel-by-pixel, however you will find the execution fairly slow. My development path is to use the macro language to develop (and debug) the processing algorithms because of the rapid cycle time (no recompile and Wayne's macro parser is pretty quick). Once I am comfortable with it, I will commit it to source code for the speed improvement. The source code is Pascal under CodeWarrior and is freely available from the web page (http://rsb.info.nih.gov/nih-image/). The conversion from macro to source is not too bad as the calls are similarly named. It does require some time investment to dig through the source and figure out what happens when and where - the usual game with following someone else's logic. The result, however is a major time improvement, especially for pixel-by-pixel operations. Also, the control you have over the whole program is a lot of fun! IMHO, Wayne has created a good starting point for custom image processing solutions. Bill Heeschen The Dow Chemical Company Microscopy group waheeschen@dow.com ------------------------------ Date: Wed, 11 Nov 1998 13:25:11 -0500 From: alex gimelbrant To: nih-image@io.ece.drexel.edu Subject: Re: NIH Image as Photoshop substitute Message-ID: <3649D687.4E9E@pop.uky.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would like to add another option to the already vast list of suggested Photoshop substitutes. You can get GraphicConverter from any shareware source (shareware.com , ...). The author keeps putting out new versions, so it's up to date and not a dead end. In my experience, it has everything needed for image manipulation, and is pretty easy to learn and use. The only problem I used to have was low final quality of text put on image. Since it is the same problem (with the same cause; see Image FAQ) as with NIH-Image, the way to deal with it might be of some interest to Image users: The image is converted to higher resolution (this operation is in the standard menu of Gr.Conv.), and the high-resolutuion text on the printout is of publication quality. It is very memory-consuming, and interpolation involved in the conversion might distort the data, so all analysis should be done prior to that step. Alex Gimelbrant ------------------------------ Date: Wed, 11 Nov 1998 10:54:23 PST From: "John Elsworth" To: nih-image@io.ece.drexel.edu Subject: Autorads: Seeing the light? Message-ID: <19981111185423.4975.qmail@hotmail.com> Content-Type: text/plain I am just setting up my new imaging equipment (Northern Lights light box, Cohu CCD camera 4913 with Nikon Micro-Nikkor 55 mm f2.8 lens) for quantifying autoradiograms of brain sections. My question concerns the relative advantages of the different ways of adjusting the brightness and contrast of the image on the screen. The light passing through the film can be adjusted at the light box. Alternatively, in Image the offset (brightness) and gain (contrast) can be adjusted under Video Control. What is the best way to balance the light box output with the Image settings? Furthermore, the camera has 8 different shutter speeds but I suspect that as this is a still image, this is not critical. The Highlight Saturated Pixel option appears to be useful, but it hasn't helped me answer the above quesion, as there are different "correct" setting for offset and gain for each different light box transillumination intensity. The Display Histogram function would appear to be useful also, however the manual suggests spreading out the histogram as much as possible. To my eye, anyway, the best-looking image occurs when there is a "tall but not thin" peak to the left in the histogram. Any insights into any of these issues would be much appreciated. John Elsworth Ph.D. ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Thu, 12 Nov 1998 09:03:59 +0100 (CET) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Morphological operations Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I am wondering if it is possible to perform morphological operations such as pruning, thinning, thickening or the hit-or-miss transform with Image. Has somebody out there macroes that can be used in this context. Thanks. Gary Chinga NTNU-Trondheim Norway. -------------------------------- End of nih-image-d Digest V98 Issue #112 **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 12 04:50 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA25833; Thu, 12 Nov 1998 04:50:34 -0500 (EST) Resent-Date: Thu, 12 Nov 1998 04:50:34 -0500 (EST) Message-Id: <9811120942.AA00163@pp1.rheo.matse.fukui-u.ac.jp> Date: Thu, 12 Nov 1998 18:42:01 +0900 From: yokota@rheo.matse.fukui-u.ac.jp (=?ISO-2022-JP?B?GyRCMiNFRCEhT0I4dxsoSg==?= ) To: nih-image@io.ece.drexel.edu Subject: I can't recognize In-Reply-To: <9810290753.AA00147@pp1.rheo.matse.fukui-u.ac.jp> Mime-Version: 1.0 X-Mailer: AL-Mail 1.22 Resent-Message-ID: <"SYUrY.0.3Z4.KfgIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/610 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-2022-jp Content-Length: 1278 Hello,Imagers. EXPLANATION Before the question, I tell you about my studying. I want to learn the location of fibers,fibers move high speed,by the image analysis. These states are recorded by high speed VTR. These images are computed in my personal computer (Power Mac G3). For the location of moving fibers,it is nesessary to change the color to bluck or white(binarization). And I want to do labeling these images.I want to do labeling for each frame. QUESTION I want to recognize fibers, but each frame has many noise. And I can't recognize fibers. I hit idea that I decided the point on x-ycoodinate and,if part of white(white is fiber) is over 5cm from that point,I recognize the fiber. And I leave as it is. But it is not 5cm, I don't recognize the fiber. I want to change to black. Can I do those process by NIH-Image(V.1.62)? If you have the macro that I can do that process,please contact me by below E-mail. E-mail yokota@rheo.matse.fukui-u.ac.jp Thank you for your help. $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota) E-mail yokota@rheo.matse.fukui-u.ac.jp (fukui Univ./ thecnology / material chemical) From nih-image-request@io.ece.drexel.edu Thu Nov 12 04:52 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA26459; Thu, 12 Nov 1998 04:52:17 -0500 (EST) Resent-Date: Thu, 12 Nov 1998 04:52:17 -0500 (EST) Date: Thu, 12 Nov 1998 10:26:16 +0100 From: Ard Jonker Subject: NIH-Image archive Sherlock Plugin available? In-reply-to: <199811120811.DAA23694@io.ece.drexel.edu> X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"bzH1U1.0.3t4.vigIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/611 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 169 Well, the title says it all; maybe I should extend that to 'or is it easy to make one available?'.... It would sure help searching the archives in a mac manner. Ard From nih-image-request@io.ece.drexel.edu Thu Nov 12 15:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15627; Thu, 12 Nov 1998 15:27:21 -0500 (EST) Resent-Date: Thu, 12 Nov 1998 15:27:21 -0500 (EST) Message-ID: <012e01be0e77$18863be0$0100007e@papa> From: "JP.Plachot" To: Subject: Re: nih-image-d Digest V98 #110 Date: Thu, 12 Nov 1998 21:00:27 +0100 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"0PXSS2.0.633.mxpIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/613 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; boundary="----------------------------"; charset="iso-8859-1" Content-Length: 258 essai -----Message d'origine----- De : nih-image-d-request@io.ece.drexel.edu : nih-image-d@io.ece.drexel.edu Date : mardi 10 novembre 1998 12:18 Objet : nih-image-d Digest V98 #110 From nih-image-request@io.ece.drexel.edu Thu Nov 12 15:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15643; Thu, 12 Nov 1998 15:27:28 -0500 (EST) Resent-Date: Thu, 12 Nov 1998 15:27:28 -0500 (EST) Message-ID: <00e001be0e76$55aa3360$0100007e@papa> From: "JP.Plachot" To: Subject: Re: nih-image-d Digest V98 #112 Date: Thu, 12 Nov 1998 20:54:25 +0100 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Resent-Message-ID: <"SUCzs1.0.lu2.2spIs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/612 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; boundary="----------------------------"; charset="iso-8859-1" Content-Length: 258 merci -----Message d'origine----- De : nih-image-d-request@io.ece.drexel.edu : nih-image-d@io.ece.drexel.edu Date : jeudi 12 novembre 1998 09:27 Objet : nih-image-d Digest V98 #112 From nih-image-d-request@io.ece.drexel.edu Fri Nov 13 06:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17079; Fri, 13 Nov 1998 06:17:34 -0500 (EST) Date: Fri, 13 Nov 1998 06:17:34 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811131117.GAA17079@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #113 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/113 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4756 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 113 Today's Topics: I can't recognize [ yokota@rheo.matse.fukui-u.ac.jp (=? ] NIH-Image archive Sherlock Plugin av [ Ard Jonker ] inhibit redrawing when... [ Bill Saidel Content-Type: text/plain; charset=iso-2022-jp Hello,Imagers. EXPLANATION Before the question, I tell you about my studying. I want to learn the location of fibers,fibers move high speed,by the image analysis. These states are recorded by high speed VTR. These images are computed in my personal computer (Power Mac G3). For the location of moving fibers,it is nesessary to change the color to bluck or white(binarization). And I want to do labeling these images.I want to do labeling for each frame. QUESTION I want to recognize fibers, but each frame has many noise. And I can't recognize fibers. I hit idea that I decided the point on x-ycoodinate and,if part of white(white is fiber) is over 5cm from that point,I recognize the fiber. And I leave as it is. But it is not 5cm, I don't recognize the fiber. I want to change to black. Can I do those process by NIH-Image(V.1.62)? If you have the macro that I can do that process,please contact me by below E-mail. E-mail yokota@rheo.matse.fukui-u.ac.jp Thank you for your help. $BJ!0fBg3X!!!!9)3XIt!!!!:`NA2=3X2J!!!!9bJ,;R2C9)3X9V:B(J $B!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!2#ED!!!!OB8w(J (Kazumitsu Yokota) E-mail yokota@rheo.matse.fukui-u.ac.jp (fukui Univ./ thecnology / material chemical) ------------------------------ Date: Thu, 12 Nov 1998 10:26:16 +0100 From: Ard Jonker To: nih-image@io.ece.drexel.edu Subject: NIH-Image archive Sherlock Plugin available? Message-id: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Well, the title says it all; maybe I should extend that to 'or is it easy to make one available?'.... It would sure help searching the archives in a mac manner. Ard ------------------------------ Date: Thu, 12 Nov 1998 12:25:31 -0500 From: Bill Saidel To: nih-image-d@io.ece.drexel.edu Subject: inhibit redrawing when... Message-Id: <3.0.6.32.19981112122531.0085a210@crab.rutgers.edu> Content-Type: text/plain; charset="us-ascii" Without recompiling Image, is there a way to inhibit redrawing the image during the skeletonize function until the function has completed? ********************************************************************** Dr. Bill Saidel Assoc. Prof. Vocal phone (609) 225-6336 Department of Biology FAX (609) 225-6312 Science Building email: saidel@crab.rutgers.edu 315 Penn St. Rutgers, the State University of New Jersey Camden, NJ 08102 -1411 http://crab.rutgers.edu/~saidel/saidel.html ------------------------------ Date: Thu, 12 Nov 1998 20:54:25 +0100 From: "JP.Plachot" To: Subject: Re: nih-image-d Digest V98 #112 Message-ID: <00e001be0e76$55aa3360$0100007e@papa> Content-Transfer-Encoding: 8bit Content-Type: text/plain; boundary="----------------------------"; charset="iso-8859-1" merci -----Message d'origine----- De : nih-image-d-request@io.ece.drexel.edu : nih-image-d@io.ece.drexel.edu Date : jeudi 12 novembre 1998 09:27 Objet : nih-image-d Digest V98 #112 ------------------------------ Date: Thu, 12 Nov 1998 21:00:27 +0100 From: "JP.Plachot" To: Subject: Re: nih-image-d Digest V98 #110 Message-ID: <012e01be0e77$18863be0$0100007e@papa> Content-Transfer-Encoding: 8bit Content-Type: text/plain; boundary="----------------------------"; charset="iso-8859-1" essai -----Message d'origine----- De : nih-image-d-request@io.ece.drexel.edu : nih-image-d@io.ece.drexel.edu Date : mardi 10 novembre 1998 12:18 Objet : nih-image-d Digest V98 #110 -------------------------------- End of nih-image-d Digest V98 Issue #113 **************************************** From nih-image-request@io.ece.drexel.edu Fri Nov 13 07:53 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA27747; Fri, 13 Nov 1998 07:53:31 -0500 (EST) Resent-Date: Fri, 13 Nov 1998 07:53:31 -0500 (EST) Date: Fri, 13 Nov 1998 13:36:23 +0100 From: "U.Marti" Subject: Second-order stereology To: NIH List Reply-to: ulrich.marti@dkf2.unibe.ch Message-id: <364C27C3.23EF8763@dkf2.unibe.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) Content-transfer-encoding: 7bit X-Accept-Language: en,de Resent-Message-ID: <"5AOCw2.0.V96.HR2Js"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/614 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 182 Hello subscribers We would like do do some tissue caparisons using second-order stereology. Is there any macro for NIH image available that could be used for this work? Thank you From nih-image-request@io.ece.drexel.edu Fri Nov 13 16:31 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA18710; Fri, 13 Nov 1998 16:31:37 -0500 (EST) Resent-Date: Fri, 13 Nov 1998 16:31:37 -0500 (EST) Date: Fri, 13 Nov 1998 15:59:56 -0500 (EST) From: Lisa Rodrigues To: nih-image@io.ece.drexel.edu Subject: Video Capture Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"splbd3.0.0p3.Ot9Js"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/615 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 369 I am using NIH-Image to analyze behaviors, by directly capturing video images from my VCR. However, my problem is that I am only able to view the last frame of the digital capture on my desktop. How do I play back the entire video capture, frame-by-frame?? Is this possible? Thank You. ____________________________ Lisa J. Rodrigues lrodrigu@zoo.utoronto.ca From nih-image-request@io.ece.drexel.edu Fri Nov 13 19:32 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA05095; Fri, 13 Nov 1998 19:32:16 -0500 (EST) Resent-Date: Fri, 13 Nov 1998 19:32:16 -0500 (EST) Date: Fri, 13 Nov 1998 16:02:18 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: G3 digitizer and Image In-Reply-To: <199810082232.SAA03616@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"bwnpT2.0.OY.iYCJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/616 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1456 Hello, We bought a G3/266 with a built-in digitizer; we were hoping to replace an 8100/80AV (with built in digitizer). Of course, it turns out Image doesn't work with the G3 built in digitizer and noone seems to know how to fix this. So I am gathering my options and would like some info: 1) Does Image work with ANY other quicktime video digitizers on a G3? Specifically, I do not want to spend the money on the Scion or Data trans cards, because all I need is grey scale digitization of 640x480 at 1 Hz. Some would something like an ATI Rage card or Buz work with Image on a G3? Or any particular card that might cost under $400? 2) I guess my other option is to try to find a used 8500 and put in a G3 card, would this work? We have an 8500/120 which works fine, but I don't know if adding a g3 card would make Image go plooey. 3) I tried capturing video in Premiere and bringing it into Image but all I get is a single converted frame. This is on a G3/266 with stock 8.1 and QT 3.02. Any ideas on how to get Image to read a movie file from premiere? 4) Any other ideas would be appreciated as well. Thanks, Stephan ------------------------------ Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net ------------------------------ Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- From nih-image-d-request@io.ece.drexel.edu Sat Nov 14 06:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA08794; Sat, 14 Nov 1998 06:17:56 -0500 (EST) Date: Sat, 14 Nov 1998 06:17:56 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811141117.GAA08794@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #114 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/114 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3474 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 114 Today's Topics: Second-order stereology [ "U.Marti" To: NIH List Subject: Second-order stereology Message-id: <364C27C3.23EF8763@dkf2.unibe.ch> Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-transfer-encoding: 7bit Hello subscribers We would like do do some tissue caparisons using second-order stereology. Is there any macro for NIH image available that could be used for this work? Thank you ------------------------------ Date: Fri, 13 Nov 1998 15:59:56 -0500 (EST) From: Lisa Rodrigues To: nih-image@io.ece.drexel.edu Subject: Video Capture Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am using NIH-Image to analyze behaviors, by directly capturing video images from my VCR. However, my problem is that I am only able to view the last frame of the digital capture on my desktop. How do I play back the entire video capture, frame-by-frame?? Is this possible? Thank You. ____________________________ Lisa J. Rodrigues lrodrigu@zoo.utoronto.ca ------------------------------ Date: Fri, 13 Nov 1998 16:02:18 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: G3 digitizer and Image Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, We bought a G3/266 with a built-in digitizer; we were hoping to replace an 8100/80AV (with built in digitizer). Of course, it turns out Image doesn't work with the G3 built in digitizer and noone seems to know how to fix this. So I am gathering my options and would like some info: 1) Does Image work with ANY other quicktime video digitizers on a G3? Specifically, I do not want to spend the money on the Scion or Data trans cards, because all I need is grey scale digitization of 640x480 at 1 Hz. Some would something like an ATI Rage card or Buz work with Image on a G3? Or any particular card that might cost under $400? 2) I guess my other option is to try to find a used 8500 and put in a G3 card, would this work? We have an 8500/120 which works fine, but I don't know if adding a g3 card would make Image go plooey. 3) I tried capturing video in Premiere and bringing it into Image but all I get is a single converted frame. This is on a G3/266 with stock 8.1 and QT 3.02. Any ideas on how to get Image to read a movie file from premiere? 4) Any other ideas would be appreciated as well. Thanks, Stephan - ---------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net - ---------------------------- Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- -------------------------------- End of nih-image-d Digest V98 Issue #114 **************************************** From nih-image-request@io.ece.drexel.edu Sat Nov 14 11:30 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA10890; Sat, 14 Nov 1998 11:30:45 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 11:30:45 -0500 (EST) Message-ID: <19981114161228.6521.qmail@hotmail.com> X-Originating-IP: [209.63.112.64] From: "lynn huynh" To: nih-image@io.ece.drexel.edu Subject: nih-image stacking feature MIME-Version: 1.0 Date: Sat, 14 Nov 1998 08:12:28 PST Resent-Message-ID: <"BAaXy1.0.3A2.JmQJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/617 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 990 i need to know how to use the stacking feature of nih-image to track asteroids. i have tried image math, which will allow fo me to place the images on top of each other, all the objects present in one picture will show up in white and the objects present in the other picture will show up in black, but what i need is to flash the images on top of each other, what this requires is that i crop the images so that the fixed stars are centered on top of each other, when the images are stacked they will not move, non fixed object will appear to "move" across the screen if the two pictures are stacked back and forth. I need to know: 1. how do i use the stacking feature to stack at a certain rate, not controlled by hand, and 2. how do i crop an image and make the pictures equally proportional to each other using photoshop. please help! thank you lynn huynh ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Sat Nov 14 12:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA15881; Sat, 14 Nov 1998 12:15:41 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 12:15:41 -0500 (EST) Message-ID: <364D9FE1.5145EF75@czd.waw.pl> Date: Sat, 14 Nov 1998 16:21:05 +0100 From: Robert Prejs X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: signoff References: <199811141104.GAA07122@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"QSxQ_3.0.OQ3.fRRJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/618 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-2 Content-Length: 30 signoff nih-image-d Digest From nih-image-request@io.ece.drexel.edu Sat Nov 14 13:30 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA23838; Sat, 14 Nov 1998 13:30:33 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 13:30:33 -0500 (EST) Message-Id: In-Reply-To: <199811141110.GAA07959@io.ece.drexel.edu> Mime-Version: 1.0 Date: Sat, 14 Nov 1998 19:16:18 +0100 To: nih-image@io.ece.drexel.edu From: Michael Glotzer Subject: G3 digitizer and Image Resent-Message-ID: <"1Rh412.0._L5.JWSJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/619 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 838 > >3) I tried capturing video in Premiere and bringing it into Image but all >I get is a single converted frame. This is on a G3/266 with stock 8.1 and >QT 3.02. Any ideas on how to get Image to read a movie file from premiere? > >4) Any other ideas would be appreciated as well. Assuming Premier can save as qucktime, Image should be able to open it (the newer versions at least). THe trick is you have to go to MacOS Easy Open control panel and delete preferences and then NIH can open a quicktime movie as a stack. Good luck, Michael ___________________________________________________________________ Michael Glotzer Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA phone 43-(1)797-30-405 office phone 43-(1)797-30-525 lab fax 43-(1)798-7153 email mglotzer@nt.imp.univie.ac.at From nih-image-request@io.ece.drexel.edu Sat Nov 14 16:56 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA14709; Sat, 14 Nov 1998 16:56:17 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 16:56:17 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Sat, 14 Nov 1998 23:38:25 +0200 To: nih-image From: Matti Haveri Subject: How to open DICOM with a given density range Resent-Message-ID: <"DLqa2.0.X43.2YVJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/620 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 536 How can I open DICOM images with a given Window/Level? I can do this with File/Import/Custom/Set/Fixed Scale -command but this isn't practical because each DICOM file can have different Offset which must be manually calculated. If I open DICOM with File/Import/DICOM then there seems to be no possibility to open just a given density range? (I can adjust Brightness & Contrast but the result is not pretty because the whole density range is imported). -- Matti Haveri From nih-image-request@io.ece.drexel.edu Sat Nov 14 22:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA18554; Sat, 14 Nov 1998 22:43:02 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 22:43:02 -0500 (EST) Message-Id: <9811149111.AA911100457@chppm-ccmail.apgea.army.mil> X-Mailer: ccMail Link to SMTP R6.01.01 Date: Sat, 14 Nov 98 22:25:48 -0500 From: "Mike Terry" Cc: , Subject: Automating the analysis of a multilane gel MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"1fP_P1.0.P84.oeaJs"@io> To: nih-image@io.ece.drexel.edu Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/621 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1549 I have not yet used Nih-image. Can anyone help with the following? 1) the task I have is to automate is the analysis of a single multilane gel. There may only be three bands per lane, which may be the same three bands in each lane (if all bands are present in any particular lane). For now, the Mac is the desired platform where this automated system is to eventually run. But I do not have convenient access to a Mac while developing the automated system. So, does it make sense to run the Mac version of Nih-image on the Ardi Executor (win32 version) Mac emulation system, running on a pc running NT, while developing the automated system for the Mac? 2) I checked the abbreviated tutorial at scrc.cit.nih.gov/imaging. What I think(?) we would like to do for the Mac (at least initially) would be to automate the steps in II thru IV. Perhaps, the operator of the the automated system would select the image file. Then the automated system would calibrate (apparently necessary even for comparisons between lanes on the same gel), select all the lanes, "plot" all the lanes, automatically isolate signal from noise (apparently automatically draw base line and drop lines), use the wand to quantitate peak areas, and save results. Can this sequence of steps be automated? Thanks, Mike Terry, Ph.D. USACHPPM APG, MD 410 436-8288 (Tel) mike_terry@chppm-ccmail.apgea.army.mil From nih-image-request@io.ece.drexel.edu Sat Nov 14 23:05 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA20838; Sat, 14 Nov 1998 23:04:59 -0500 (EST) Resent-Date: Sat, 14 Nov 1998 23:04:59 -0500 (EST) Message-Id: <3.0.5.32.19981114225356.00827640@codon.nih.gov> X-Sender: wayne@codon.nih.gov X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sat, 14 Nov 1998 22:53:56 -0500 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: How to open DICOM with a given density range In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"gE7-22.0.Oh4.dyaJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/622 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 744 At 11:38 PM 11/14/98 +0200, you wrote: >How can I open DICOM images with a given Window/Level? > >I can do this with File/Import/Custom/Set/Fixed Scale -command but this >isn't practical because each DICOM file can have different Offset which >must be manually calculated. > >If I open DICOM with File/Import/DICOM then there seems to be no >possibility to open just a given density range? (I can adjust Brightness & >Contrast but the result is not pretty because the whole density range is >imported). Adjust brightness/contrast and then select Rescale (Revert), which re-imports the image using new window/level settings. You might also want to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as 16-bit images. -wayne From nih-image-d-request@io.ece.drexel.edu Sun Nov 15 06:24 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02591; Sun, 15 Nov 1998 06:24:19 -0500 (EST) Date: Sun, 15 Nov 1998 06:24:19 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811151124.GAA02591@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #115 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/115 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7300 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 115 Today's Topics: nih-image stacking feature [ "lynn huynh" ] G3 digitizer and Image [ Michael Glotzer ] ------------------------------ Date: Sat, 14 Nov 1998 08:12:28 PST From: "lynn huynh" To: nih-image@io.ece.drexel.edu Subject: nih-image stacking feature Message-ID: <19981114161228.6521.qmail@hotmail.com> Content-Type: text/plain i need to know how to use the stacking feature of nih-image to track asteroids. i have tried image math, which will allow fo me to place the images on top of each other, all the objects present in one picture will show up in white and the objects present in the other picture will show up in black, but what i need is to flash the images on top of each other, what this requires is that i crop the images so that the fixed stars are centered on top of each other, when the images are stacked they will not move, non fixed object will appear to "move" across the screen if the two pictures are stacked back and forth. I need to know: 1. how do i use the stacking feature to stack at a certain rate, not controlled by hand, and 2. how do i crop an image and make the pictures equally proportional to each other using photoshop. please help! thank you lynn huynh ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Sat, 14 Nov 1998 16:21:05 +0100 From: Robert Prejs To: nih-image@io.ece.drexel.edu Subject: signoff Message-ID: <364D9FE1.5145EF75@czd.waw.pl> Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit signoff nih-image-d Digest ------------------------------ Date: Sat, 14 Nov 1998 19:16:18 +0100 From: Michael Glotzer To: nih-image@io.ece.drexel.edu Subject: G3 digitizer and Image Message-Id: Content-Type: text/plain; charset="us-ascii" > >3) I tried capturing video in Premiere and bringing it into Image but all >I get is a single converted frame. This is on a G3/266 with stock 8.1 and >QT 3.02. Any ideas on how to get Image to read a movie file from premiere? > >4) Any other ideas would be appreciated as well. Assuming Premier can save as qucktime, Image should be able to open it (the newer versions at least). THe trick is you have to go to MacOS Easy Open control panel and delete preferences and then NIH can open a quicktime movie as a stack. Good luck, Michael ___________________________________________________________________ Michael Glotzer Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA phone 43-(1)797-30-405 office phone 43-(1)797-30-525 lab fax 43-(1)798-7153 email mglotzer@nt.imp.univie.ac.at ------------------------------ Date: Sat, 14 Nov 1998 23:38:25 +0200 From: Matti Haveri To: nih-image Subject: How to open DICOM with a given density range Message-Id: Content-Type: text/plain; charset="us-ascii" How can I open DICOM images with a given Window/Level? I can do this with File/Import/Custom/Set/Fixed Scale -command but this isn't practical because each DICOM file can have different Offset which must be manually calculated. If I open DICOM with File/Import/DICOM then there seems to be no possibility to open just a given density range? (I can adjust Brightness & Contrast but the result is not pretty because the whole density range is imported). -- Matti Haveri ------------------------------ Date: Sat, 14 Nov 98 22:25:48 -0500 From: "Mike Terry" To: nih-image@io.ece.drexel.edu Cc: , Subject: Automating the analysis of a multilane gel Message-Id: <9811149111.AA911100457@chppm-ccmail.apgea.army.mil> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I have not yet used Nih-image. Can anyone help with the following? 1) the task I have is to automate is the analysis of a single multilane gel. There may only be three bands per lane, which may be the same three bands in each lane (if all bands are present in any particular lane). For now, the Mac is the desired platform where this automated system is to eventually run. But I do not have convenient access to a Mac while developing the automated system. So, does it make sense to run the Mac version of Nih-image on the Ardi Executor (win32 version) Mac emulation system, running on a pc running NT, while developing the automated system for the Mac? 2) I checked the abbreviated tutorial at scrc.cit.nih.gov/imaging. What I think(?) we would like to do for the Mac (at least initially) would be to automate the steps in II thru IV. Perhaps, the operator of the the automated system would select the image file. Then the automated system would calibrate (apparently necessary even for comparisons between lanes on the same gel), select all the lanes, "plot" all the lanes, automatically isolate signal from noise (apparently automatically draw base line and drop lines), use the wand to quantitate peak areas, and save results. Can this sequence of steps be automated? Thanks, Mike Terry, Ph.D. USACHPPM APG, MD 410 436-8288 (Tel) mike_terry@chppm-ccmail.apgea.army.mil ------------------------------ Date: Sat, 14 Nov 1998 22:53:56 -0500 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: How to open DICOM with a given density range Message-Id: <3.0.5.32.19981114225356.00827640@codon.nih.gov> Content-Type: text/plain; charset="us-ascii" At 11:38 PM 11/14/98 +0200, you wrote: >How can I open DICOM images with a given Window/Level? > >I can do this with File/Import/Custom/Set/Fixed Scale -command but this >isn't practical because each DICOM file can have different Offset which >must be manually calculated. > >If I open DICOM with File/Import/DICOM then there seems to be no >possibility to open just a given density range? (I can adjust Brightness & >Contrast but the result is not pretty because the whole density range is >imported). Adjust brightness/contrast and then select Rescale (Revert), which re-imports the image using new window/level settings. You might also want to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as 16-bit images. -wayne -------------------------------- End of nih-image-d Digest V98 Issue #115 **************************************** From nih-image-request@io.ece.drexel.edu Sun Nov 15 12:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06999; Sun, 15 Nov 1998 12:14:52 -0500 (EST) Resent-Date: Sun, 15 Nov 1998 12:14:52 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Sun, 15 Nov 1998 19:01:24 +0200 To: nih-image From: Matti Haveri Subject: Re: How to open DICOM with a given density range Resent-Message-ID: <"T9U2B.0.xM1.ZZmJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/623 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1027 >>How can I open DICOM images with a given Window/Level? >> >>I can do this with File/Import/Custom/Set/Fixed Scale -command but this >>isn't practical because each DICOM file can have different Offset which >>must be manually calculated. >> >>If I open DICOM with File/Import/DICOM then there seems to be no >>possibility to open just a given density range? (I can adjust Brightness & >>Contrast but the result is not pretty because the whole density range is >>imported). > >Adjust brightness/contrast and then select Rescale (Revert), which >re-imports the image using new window/level settings. You might also want >to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as >16-bit images. Oh, I see, but how can I rescale _several_ images to the same density range? If I import 20 images as DICOM (Open all), choose windows to stack, adjust brightness/contrast for one slice and try to Rescale I get an "File I/O error". -- Matti Haveri From nih-image-request@io.ece.drexel.edu Sun Nov 15 21:24 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA28694; Sun, 15 Nov 1998 21:24:44 -0500 (EST) Resent-Date: Sun, 15 Nov 1998 21:24:44 -0500 (EST) Date: Sun, 15 Nov 1998 21:02:16 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199811160202.VAA26171@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"Mx5wQ1.0.3P6.gUuJs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/624 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1997 NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- From nih-image-request@io.ece.drexel.edu Mon Nov 16 06:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23385; Mon, 16 Nov 1998 06:15:19 -0500 (EST) Resent-Date: Mon, 16 Nov 1998 06:15:19 -0500 (EST) Message-ID: <3650141B.1BEF@dv.kp.dlr.de> Date: Mon, 16 Nov 1998 12:01:31 +0000 From: Stephan Sous Organization: DLR X-Mailer: Mozilla 3.01 [de] (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: ShowResults (read permission) Content-Transfer-Encoding: 7bit Resent-Message-ID: <"J4De03.0.5E5.RM0Ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/625 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 446 Hi Imagers, I hope somebody can help. I set the measurement options 'area, x-y-center', measure about 2500 particles. If the particles are bigger than 10 and smaller than 26 (pixel x pixel),I want to delete this particles from the image with the aid of the x-y-position (auto-outline and so ...). If the ShowResults-window (file) is bigger than 1400 counts (entries), I have no access (cannot read) to the higher entries. Yhanks in advance From nih-image-d-request@io.ece.drexel.edu Mon Nov 16 06:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24400; Mon, 16 Nov 1998 06:22:30 -0500 (EST) Date: Mon, 16 Nov 1998 06:22:30 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811161122.GAA24400@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #116 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/116 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6171 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 116 Today's Topics: Re: How to open DICOM with a given d [ Matti Haveri NIH image stack [ Peter Ahnelt ] ------------------------------ Date: Sun, 15 Nov 1998 19:01:24 +0200 From: Matti Haveri To: nih-image Subject: Re: How to open DICOM with a given density range Message-Id: Content-Type: text/plain; charset="us-ascii" >>How can I open DICOM images with a given Window/Level? >> >>I can do this with File/Import/Custom/Set/Fixed Scale -command but this >>isn't practical because each DICOM file can have different Offset which >>must be manually calculated. >> >>If I open DICOM with File/Import/DICOM then there seems to be no >>possibility to open just a given density range? (I can adjust Brightness & >>Contrast but the result is not pretty because the whole density range is >>imported). > >Adjust brightness/contrast and then select Rescale (Revert), which >re-imports the image using new window/level settings. You might also want >to try Image/J (http://rsb.info.nih.gov/ij/), which imports DICOM files as >16-bit images. Oh, I see, but how can I rescale _several_ images to the same density range? If I import 20 images as DICOM (Open all), choose windows to stack, adjust brightness/contrast for one slice and try to Rescale I get an "File I/O error". -- Matti Haveri ------------------------------ Date: Sun, 15 Nov 1998 21:02:16 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Message-Id: <199811160202.VAA26171@io.ece.drexel.edu> NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- ------------------------------ Date: Mon, 16 Nov 1998 09:12:38 +0100 From: Peter Ahnelt To: nih-image-d@io.ece.drexel.edu Subject: Photoshop planes <-> NIH image stacks? Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hello! An obvious advantage of Photoshop is the versatility of its plane tools, including color handling transparency modes etc.. NIH image on the other hand has lots of Macros ready for stack=plane processing. So: Is there anybody out there who could write some conversion to a) import PS-plane files as NIH-Stacks ? b) export stacks as PS-plane files ? c) export PS-planes as .TIF stack files importable by NIH ? It might be even worthwhile to include this in the NIH import options. Would be nice ... P.Ahnelt _ _ _ / \ / \ / \ e-mail: peter.ahnelt@univie.ac.at |R| |G| |B| Adress: Peter Ahnelt '| '| '| Dept. Gen. & Compar. Physiology [] [] [] University of Vienna, Medical School () () () Schwarzspanierstr. 17, A-1090 Vienna | | | Tel. 43 1 4277/ 62330,62301 FAX 43 1 4277/ 9623 __ __ _ http://www.univie.ac.at/Vergl-Physiologie/www/gphy_morph.html ------------------------------ Date: Mon, 16 Nov 1998 12:01:31 +0000 From: Stephan Sous To: nih-image@io.ece.drexel.edu Subject: ShowResults (read permission) Message-ID: <3650141B.1BEF@dv.kp.dlr.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Imagers, I hope somebody can help. I set the measurement options 'area, x-y-center', measure about 2500 particles. If the particles are bigger than 10 and smaller than 26 (pixel x pixel),I want to delete this particles from the image with the aid of the x-y-position (auto-outline and so ...). If the ShowResults-window (file) is bigger than 1400 counts (entries), I have no access (cannot read) to the higher entries. Yhanks in advance -------------------------------- End of nih-image-d Digest V98 Issue #116 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 16 10:24 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA18552; Mon, 16 Nov 1998 10:24:47 -0500 (EST) Resent-Date: Mon, 16 Nov 1998 10:24:47 -0500 (EST) Message-Id: In-Reply-To: <3.0.5.32.19981115164557.0082ae60@codon.nih.gov> References: Mime-Version: 1.0 Date: Mon, 16 Nov 1998 17:00:33 +0200 To: nih-image@io.ece.drexel.edu From: Matti Haveri Subject: Re: How to open DICOM with a given density range Resent-Message-ID: <"qLFvn2.0.Yt3.Sq3Ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/626 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1384 >>Oh, I see, but how can I rescale _several_ images to the same density range? >> >>If I import 20 images as DICOM (Open all), choose windows to stack, adjust >>brightness/contrast for one slice and try to Rescale I get an "File I/O >>error". > >The Rescale command does not work with stacks. Acoording to the manual, >when importing DICOMS using the "Open All" option, you can hold the shift >key down to fix 16-bit to 8-bit scaling. What I basically want to do is to open DICOM CT-slices to 1029-1099 densities (i.e. in Hounsfield units W/L 70/40). It seems that the best way to accomplish this is to DICOM import the slices with Shift down (fixed 16-bit to 8-bit scaling), then brightness/contrast one image to 1029-1099 with the mouse, choose Options/Propagate/LUT and Rescale each image separately? Is it possible to adjust brightness/contrast numerically (it is impossible to get exactly to right values via the mouse)? What still I miss is the possibility to DICOM-import a selected density range just like it is possible via Custom import/Fixed Scale. The problem with Custom import is that the Offset may be different for each CT slice. Custom import also doesn't automatically calibrate densities to Hounfield units like DICOM import does (although the HU-info gets lost when Rescaling). -- Matti Haveri From nih-image-request@io.ece.drexel.edu Mon Nov 16 14:03 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA06718; Mon, 16 Nov 1998 14:03:22 -0500 (EST) Resent-Date: Mon, 16 Nov 1998 14:03:22 -0500 (EST) Date: Mon, 16 Nov 1998 10:41:15 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Image and G3 In-Reply-To: <199811161120.GAA24063@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"adKSe3.0.xB1.H77Ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/627 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 496 Hi, can anyone tell me definitively if the ATI XClaim VR 4mb Rage II PCI video in/out card will work with Image? Thanks! All help is greatly appreciated! Stephan ------------------------------ Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net ------------------------------ Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- From nih-image-request@io.ece.drexel.edu Tue Nov 17 01:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA12000; Tue, 17 Nov 1998 01:18:04 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 01:18:04 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu Date: Tue, 17 Nov 1998 16:48:51 GMT+1100 Subject: Re: ShowResults (read permission) Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <22171922636@rna.bio.mq.edu.au> Resent-Message-ID: <"yhS7p1.0.o02.rsGKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/628 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1692 >Date: Mon, 16 Nov 1998 12:01:31 +0000 >From: Stephan Sous >....... >I set the measurement options 'area, x-y-center', measure about 2500 >particles. If the particles are bigger than 10 and smaller than 26 >(pixel x pixel),I want to delete this particles from the image with the >aid of the x-y-position (auto-outline and so ...). >If the ShowResults-window (file) is bigger than 1400 counts (entries), I >have no access (cannot read) to the higher entries. > >.... Stephan, NIH-Image uses Mac OS facilities to display text that are limited to 32K so that you cant display all characters of the results table but never-the-less the values are still in the results table (provided your MaxMeasurements is large enough; standard max results table size is/was 8000 measurements). Your macro code to access if (rArea[i]<10) or (rArea[i]>26) then begin autoOutline(rX[i],rY[i]); getRoi(x,y,w,h); if w<>0 then fill else exit(concat('particle',i,' not found??'); end; etc will still work You can increase the number of Results table entries you can see by reducing characters per line eg by reducing precision or viewing 'area, x-y-center' alternatly rather than together. A more effective way of viewing is to save results to disk and then open in an editor (such as bbedit) or spreadsheet (Xcell). If your image has illshaped particles where the centroid rX[i],rY[i] falls outside the particle, then Object-Image has rLeft[i],rTop[i] in the Results table for this purpose. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Nov 17 01:55 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16421; Tue, 17 Nov 1998 01:55:11 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 01:55:11 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu Date: Tue, 17 Nov 1998 17:25:09 GMT+1100 Subject: Re: ShowResults (read permission) (postscript) Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <2220C3A3CBC@rna.bio.mq.edu.au> Resent-Message-ID: <"tchVQ2.0.933.fOHKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/629 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1333 >Date: Mon, 16 Nov 1998 12:01:31 +0000 >From: Stephan Sous >..... >I set the measurement options 'area, x-y-center', measure about 2500 >particles. If the particles are bigger than 10 and smaller than 26 >(pixel x pixel),I want to delete this particles from the image with the >aid of the x-y-position (auto-outline and so ...). >If the ShowResults-window (file) is bigger than 1400 counts (entries), I >have no access (cannot read) to the higher entries. > >.... What I should have also pointed out previously :-) : You can also achieve your result by taking advantage of the coloring of the particles examined by analyzeParticles (to threshold-1 or lower-1) and of the 'outline' option. setParticleSize(10,26); analyzeParticles('outline reset'); setThreshold(254); analyzeParticles('outline include reset'); will result in the particles 10<=>26 being colored 254 and those originally thresholded or sliced but outside this size range being colored threshold-1. You can then use changeValues to convert the image to a binary mask for either counted or excluded particles to be applied to the original image. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Tue Nov 17 01:55 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16610; Tue, 17 Nov 1998 01:55:51 -0500 (EST) Date: Tue, 17 Nov 1998 01:55:51 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811170655.BAA16610@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #117 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/117 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6582 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 117 Today's Topics: Re: How to open DICOM with a given d [ Matti Haveri To: nih-image@io.ece.drexel.edu Subject: Re: How to open DICOM with a given density range Message-Id: Content-Type: text/plain; charset="us-ascii" >>Oh, I see, but how can I rescale _several_ images to the same density range? >> >>If I import 20 images as DICOM (Open all), choose windows to stack, adjust >>brightness/contrast for one slice and try to Rescale I get an "File I/O >>error". > >The Rescale command does not work with stacks. Acoording to the manual, >when importing DICOMS using the "Open All" option, you can hold the shift >key down to fix 16-bit to 8-bit scaling. What I basically want to do is to open DICOM CT-slices to 1029-1099 densities (i.e. in Hounsfield units W/L 70/40). It seems that the best way to accomplish this is to DICOM import the slices with Shift down (fixed 16-bit to 8-bit scaling), then brightness/contrast one image to 1029-1099 with the mouse, choose Options/Propagate/LUT and Rescale each image separately? Is it possible to adjust brightness/contrast numerically (it is impossible to get exactly to right values via the mouse)? What still I miss is the possibility to DICOM-import a selected density range just like it is possible via Custom import/Fixed Scale. The problem with Custom import is that the Offset may be different for each CT slice. Custom import also doesn't automatically calibrate densities to Hounfield units like DICOM import does (although the HU-info gets lost when Rescaling). -- Matti Haveri ------------------------------ Date: Mon, 16 Nov 1998 10:41:15 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Image and G3 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, can anyone tell me definitively if the ATI XClaim VR 4mb Rage II PCI video in/out card will work with Image? Thanks! All help is greatly appreciated! Stephan - ---------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net - ---------------------------- Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- ------------------------------ Date: Tue, 17 Nov 1998 16:48:51 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu Subject: Re: ShowResults (read permission) Message-ID: <22171922636@rna.bio.mq.edu.au> >Date: Mon, 16 Nov 1998 12:01:31 +0000 >From: Stephan Sous >....... >I set the measurement options 'area, x-y-center', measure about 2500 >particles. If the particles are bigger than 10 and smaller than 26 >(pixel x pixel),I want to delete this particles from the image with the >aid of the x-y-position (auto-outline and so ...). >If the ShowResults-window (file) is bigger than 1400 counts (entries), I >have no access (cannot read) to the higher entries. > >.... Stephan, NIH-Image uses Mac OS facilities to display text that are limited to 32K so that you cant display all characters of the results table but never-the-less the values are still in the results table (provided your MaxMeasurements is large enough; standard max results table size is/was 8000 measurements). Your macro code to access if (rArea[i]<10) or (rArea[i]>26) then begin autoOutline(rX[i],rY[i]); getRoi(x,y,w,h); if w<>0 then fill else exit(concat('particle',i,' not found??'); end; etc will still work You can increase the number of Results table entries you can see by reducing characters per line eg by reducing precision or viewing 'area, x-y-center' alternatly rather than together. A more effective way of viewing is to save results to disk and then open in an editor (such as bbedit) or spreadsheet (Xcell). If your image has illshaped particles where the centroid rX[i],rY[i] falls outside the particle, then Object-Image has rLeft[i],rTop[i] in the Results table for this purpose. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Tue, 17 Nov 1998 17:25:09 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: Stephan.Sous@dlr.de, nih-image@io.ece.drexel.edu Subject: Re: ShowResults (read permission) (postscript) Message-ID: <2220C3A3CBC@rna.bio.mq.edu.au> >Date: Mon, 16 Nov 1998 12:01:31 +0000 >From: Stephan Sous >..... >I set the measurement options 'area, x-y-center', measure about 2500 >particles. If the particles are bigger than 10 and smaller than 26 >(pixel x pixel),I want to delete this particles from the image with the >aid of the x-y-position (auto-outline and so ...). >If the ShowResults-window (file) is bigger than 1400 counts (entries), I >have no access (cannot read) to the higher entries. > >.... What I should have also pointed out previously :-) : You can also achieve your result by taking advantage of the coloring of the particles examined by analyzeParticles (to threshold-1 or lower-1) and of the 'outline' option. setParticleSize(10,26); analyzeParticles('outline reset'); setThreshold(254); analyzeParticles('outline include reset'); will result in the particles 10<=>26 being colored 254 and those originally thresholded or sliced but outside this size range being colored threshold-1. You can then use changeValues to convert the image to a binary mask for either counted or excluded particles to be applied to the original image. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #117 **************************************** From nih-image-request@io.ece.drexel.edu Tue Nov 17 11:37 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA17380; Tue, 17 Nov 1998 11:37:11 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 11:37:11 -0500 (EST) Mime-Version: 1.0 X-Sender: tmitchel@mail.med.upenn.edu (Unverified) Message-Id: Date: Tue, 17 Nov 1998 11:04:24 -0500 To: nih-image@io.ece.drexel.edu From: "Thomas W. Mitchell, V.M.D., Ph.D." Subject: I/O error Resent-Message-ID: <"yPzm51.0.3S3.IyPKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/630 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 829 This has been covered in this list server, and I did attempt to answer my question using the available archives. I have a macro for area analysis, and when I am saving a flat field, I continually get the following error message: A File I/O error has occurred. No such volume. Result code = -35. >From the zippy-obtained Systems error software, I know this is a volume searching error. To the best of my ability, I have tried to identify the volume searching error, but no luck. Any suggestions? Tom Thomas W. Mitchell, V.M.D., Ph.D. Center for Neurodegenerative Disease Research University of Pennsylvania School of Medicine Department of Pathology and Laboratory Medicine 3600 Spruce Street - 3rd Floor Maloney Philadelphia, PA 19104 Phone: 215-573-3258 (-2840) FAX: 215-349-5909 email: tmitchel@mail.med.upenn.edu From nih-image-request@io.ece.drexel.edu Tue Nov 17 15:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA14450; Tue, 17 Nov 1998 15:25:02 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 15:25:02 -0500 (EST) Date: Tue, 17 Nov 1998 11:36:01 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Iomega Buz works with Image in a G3 In-Reply-To: <199811170648.BAA15502@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"kuLMc3.0.Tx1.g0TKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/631 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1077 Hello all, Just thought I would update you on my search for a cheap digitizer to work with Image on a G3. As we know, the G3 built in digitizer does not work. Also, I didn't end up trying the ATI card, because it only supports 320x240. Well, I came across the Buz, and I thought what the heck. Well, the good news is that it works fine with Image on the G3. it supports 720 x 480 and cost me $259. Also it has some other goodies which may be useful in other work, as it has on the fly MPEG compression and a high-speed SCSI port on it as well for capturing directly to a jaz or zip. of course, the usual caveats about cheap frame grabbers apply (i.e.gain control, etc) but for what we are using it for those aren't a problem. Cheers, Stephan ------------------------------ Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net ------------------------------ Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- From nih-image-request@io.ece.drexel.edu Tue Nov 17 15:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA16309; Tue, 17 Nov 1998 15:43:23 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 15:43:23 -0500 (EST) X-Authentication-Warning: umbc7.umbc.edu: lei owned process doing -bs Date: Tue, 17 Nov 1998 14:58:39 -0500 (EST) From: "Dr. Tianhu Lei; MEDIC-UMAB" To: nih-image@io.ece.drexel.edu Subject: gray level setting Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Pl-2F.0.Ok2.rPTKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/632 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 365 Dear Sir/Madam: My laptop computer can only display image with 16 gray levels. When I open NIH Image, I always get the following message: To run image, the main monitor must be set to 256 colors or 256 gray levels. Can I change gray level setting of NIH Image (from 256 to 16) such that I can use it in my laptop computer (Powerbook 180)? Thanks. T. Lei From nih-image-request@io.ece.drexel.edu Tue Nov 17 16:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA22218; Tue, 17 Nov 1998 16:41:08 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 16:41:08 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: gray level setting Date: Tue, 17 Nov 1998 20:56:49 +0000 Resent-Message-ID: <"LwxpC.0._I4.nCUKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/633 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 518 >Dear Sir/Madam: > >My laptop computer can only display image with 16 gray levels. >When I open NIH Image, I always get the following message: > > To run image, the main monitor must be set to > 256 colors or 256 gray levels. > >Can I change gray level setting of NIH Image (from 256 to 16) >such that I can use it in my laptop computer (Powerbook 180)? > >Thanks. > >T. Lei Do you use an old version of Image? Newer versions even run on older Powerbooks like the PB140, which has only black and white. N. Vischer From nih-image-request@io.ece.drexel.edu Tue Nov 17 18:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA02387; Tue, 17 Nov 1998 18:18:58 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 18:18:58 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: tmitchel@mail.med.upenn.edu, nih-image@io.ece.drexel.edu Date: Wed, 18 Nov 1998 9:41:35 GMT+1100 Subject: Re: I/O error Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <23253CB7CE3@rna.bio.mq.edu.au> Resent-Message-ID: <"f2cuH2.0.co6.whVKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/634 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2118 >Date: Tue, 17 Nov 1998 11:04:24 -0500 >To: nih-image@io.ece.drexel.edu >From: "Thomas W. Mitchell, V.M.D., Ph.D." > >This has been covered in this list server, and I did attempt to answer my >question using the available archives. I have a macro for area analysis, >and when I am saving a flat field, I continually get the following error >message: > >A File I/O error has occurred. No such volume. Result code = -35. > >From the zippy-obtained Systems error software, I know this is a volume >searching error. To the best of my ability, I have tried to identify the >volume searching error, but no luck. Any suggestions? > >Tom > > >Thomas W. Mitchell, V.M.D., Ph.D. >Center for Neurodegenerative Disease Research >University of Pennsylvania School of Medicine >Department of Pathology and Laboratory Medicine >3600 Spruce Street - 3rd Floor Maloney >Philadelphia, PA 19104 > >Phone: 215-573-3258 (-2840) >FAX: 215-349-5909 >email: tmitchel@mail.med.upenn.edu > Tom, you didn't give much info on macro code but my guess would be that the 'name' you are attempting to save has included a colon ':' so that Image is treating it as a fully qualified name and searching for a volume. >From Object-Image help: SaveAs('name') Saves the current image using the specified file name. Use SetSave to specify the format. Uses the window title as the file name when saving a text file or if SaveAs is used with no argument. When saving images, the dialog box should only be displayed the first time SaveAs is called within a macro. For both image and text windows, 'name' can be a full folder path (e.g., 'HD400:Images:MyImage'). In this case, no dialog box is displayed. eg macro'/0test';begin SaveAs('name:suffix'); end fails with exactly that message because it is looking for a drive called 'name' on which to save 'suffix'. You cannot have imbedded colons in a filename. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Nov 17 18:44 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05724; Tue, 17 Nov 1998 18:44:18 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 18:44:18 -0500 (EST) X-Sender: jayers@pop.dac.neu.edu Message-Id: Mime-Version: 1.0 Date: Tue, 17 Nov 1998 17:57:54 -0500 To: nih-image@io.ece.drexel.edu From: Joseph Ayers Subject: MacOS Scientific Software Petition Resent-Message-ID: <"Vxljc3.0.x4.30WKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/635 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 341 Check out the: MacOS Scientific Software Petition at: http://members.aol.com/mattspete/ Joseph Ayers, Director Marine Science Center Northeastern University East Point, Nahant, MA 01908 (781) 581-7370 (office), (781) 581-6076 (fax) (781) 586-9128 (lab), (617) 755-7523 (cellular) Internet: lobster@neu.edu http://www.dac.neu.edu/msc/ From nih-image-request@io.ece.drexel.edu Tue Nov 17 21:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA23085; Tue, 17 Nov 1998 21:25:38 -0500 (EST) Resent-Date: Tue, 17 Nov 1998 21:25:38 -0500 (EST) Date: Wed, 18 Nov 1998 11:59:48 +1000 (EST) Message-Id: <199811180159.LAA01755@topaz.cqu.edu.au> X-Sender: mccannc@topaz.cqu.edu.au X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Cormac Subject: THANKSALOT! Resent-Message-ID: <"AGTfM.0.H_4.YeYKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/636 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 304 This is just a quick note to thank all those who replied to my queries and questions over the last semester as it really helped me out. I have finished my stint at Uni and can now become a professional bum with an engineering degree. Cormac McCann Mechanical Engineering student, CQU, QLD, Australia. From nih-image-d-request@io.ece.drexel.edu Wed Nov 18 06:33 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA20470; Wed, 18 Nov 1998 06:33:28 -0500 (EST) Date: Wed, 18 Nov 1998 06:33:28 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811181133.GAA20470@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #118 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/118 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8324 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 118 Today's Topics: I/O error [ "Thomas W. Mitchell, V.M.D., Ph.D." ] Iomega Buz works with Image in a G3 [ Stephan Anagnostaras ] THANKSALOT! [ Cormac ] ------------------------------ Date: Tue, 17 Nov 1998 11:04:24 -0500 From: "Thomas W. Mitchell, V.M.D., Ph.D." To: nih-image@io.ece.drexel.edu Subject: I/O error Message-Id: Content-Type: text/plain; charset="us-ascii" This has been covered in this list server, and I did attempt to answer my question using the available archives. I have a macro for area analysis, and when I am saving a flat field, I continually get the following error message: A File I/O error has occurred. No such volume. Result code = -35. >From the zippy-obtained Systems error software, I know this is a volume searching error. To the best of my ability, I have tried to identify the volume searching error, but no luck. Any suggestions? Tom Thomas W. Mitchell, V.M.D., Ph.D. Center for Neurodegenerative Disease Research University of Pennsylvania School of Medicine Department of Pathology and Laboratory Medicine 3600 Spruce Street - 3rd Floor Maloney Philadelphia, PA 19104 Phone: 215-573-3258 (-2840) FAX: 215-349-5909 email: tmitchel@mail.med.upenn.edu ------------------------------ Date: Tue, 17 Nov 1998 11:36:01 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Iomega Buz works with Image in a G3 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Just thought I would update you on my search for a cheap digitizer to work with Image on a G3. As we know, the G3 built in digitizer does not work. Also, I didn't end up trying the ATI card, because it only supports 320x240. Well, I came across the Buz, and I thought what the heck. Well, the good news is that it works fine with Image on the G3. it supports 720 x 480 and cost me $259. Also it has some other goodies which may be useful in other work, as it has on the fly MPEG compression and a high-speed SCSI port on it as well for capturing directly to a jaz or zip. of course, the usual caveats about cheap frame grabbers apply (i.e.gain control, etc) but for what we are using it for those aren't a problem. Cheers, Stephan - ---------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net - ---------------------------- Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- ------------------------------ Date: Tue, 17 Nov 1998 14:58:39 -0500 (EST) From: "Dr. Tianhu Lei; MEDIC-UMAB" To: nih-image@io.ece.drexel.edu Subject: gray level setting Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sir/Madam: My laptop computer can only display image with 16 gray levels. When I open NIH Image, I always get the following message: To run image, the main monitor must be set to 256 colors or 256 gray levels. Can I change gray level setting of NIH Image (from 256 to 16) such that I can use it in my laptop computer (Powerbook 180)? Thanks. T. Lei ------------------------------ Date: Tue, 17 Nov 1998 20:56:49 +0000 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: gray level setting Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear Sir/Madam: > >My laptop computer can only display image with 16 gray levels. >When I open NIH Image, I always get the following message: > > To run image, the main monitor must be set to > 256 colors or 256 gray levels. > >Can I change gray level setting of NIH Image (from 256 to 16) >such that I can use it in my laptop computer (Powerbook 180)? > >Thanks. > >T. Lei Do you use an old version of Image? Newer versions even run on older Powerbooks like the PB140, which has only black and white. N. Vischer ------------------------------ Date: Wed, 18 Nov 1998 9:41:35 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: tmitchel@mail.med.upenn.edu, nih-image@io.ece.drexel.edu Subject: Re: I/O error Message-ID: <23253CB7CE3@rna.bio.mq.edu.au> >Date: Tue, 17 Nov 1998 11:04:24 -0500 >To: nih-image@io.ece.drexel.edu >From: "Thomas W. Mitchell, V.M.D., Ph.D." > >This has been covered in this list server, and I did attempt to answer my >question using the available archives. I have a macro for area analysis, >and when I am saving a flat field, I continually get the following error >message: > >A File I/O error has occurred. No such volume. Result code = -35. > >From the zippy-obtained Systems error software, I know this is a volume >searching error. To the best of my ability, I have tried to identify the >volume searching error, but no luck. Any suggestions? > >Tom > > >Thomas W. Mitchell, V.M.D., Ph.D. >Center for Neurodegenerative Disease Research >University of Pennsylvania School of Medicine >Department of Pathology and Laboratory Medicine >3600 Spruce Street - 3rd Floor Maloney >Philadelphia, PA 19104 > >Phone: 215-573-3258 (-2840) >FAX: 215-349-5909 >email: tmitchel@mail.med.upenn.edu > Tom, you didn't give much info on macro code but my guess would be that the 'name' you are attempting to save has included a colon ':' so that Image is treating it as a fully qualified name and searching for a volume. >From Object-Image help: SaveAs('name') Saves the current image using the specified file name. Use SetSave to specify the format. Uses the window title as the file name when saving a text file or if SaveAs is used with no argument. When saving images, the dialog box should only be displayed the first time SaveAs is called within a macro. For both image and text windows, 'name' can be a full folder path (e.g., 'HD400:Images:MyImage'). In this case, no dialog box is displayed. eg macro'/0test';begin SaveAs('name:suffix'); end fails with exactly that message because it is looking for a drive called 'name' on which to save 'suffix'. You cannot have imbedded colons in a filename. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Tue, 17 Nov 1998 17:57:54 -0500 From: Joseph Ayers To: nih-image@io.ece.drexel.edu Subject: MacOS Scientific Software Petition Message-Id: Content-Type: text/plain; charset="us-ascii" Check out the: MacOS Scientific Software Petition at: http://members.aol.com/mattspete/ Joseph Ayers, Director Marine Science Center Northeastern University East Point, Nahant, MA 01908 (781) 581-7370 (office), (781) 581-6076 (fax) (781) 586-9128 (lab), (617) 755-7523 (cellular) Internet: lobster@neu.edu http://www.dac.neu.edu/msc/ ------------------------------ Date: Wed, 18 Nov 1998 11:59:48 +1000 (EST) From: Cormac To: nih-image@io.ece.drexel.edu Subject: THANKSALOT! Message-Id: <199811180159.LAA01755@topaz.cqu.edu.au> Content-Type: text/plain; charset="us-ascii" This is just a quick note to thank all those who replied to my queries and questions over the last semester as it really helped me out. I have finished my stint at Uni and can now become a professional bum with an engineering degree. Cormac McCann Mechanical Engineering student, CQU, QLD, Australia. -------------------------------- End of nih-image-d Digest V98 Issue #118 **************************************** From nih-image-request@io.ece.drexel.edu Wed Nov 18 07:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA28889; Wed, 18 Nov 1998 07:49:08 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 07:49:08 -0500 (EST) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: Mime-Version: 1.0 Date: Wed, 18 Nov 1998 14:30:08 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Microscope recommendations wanted Resent-Message-ID: <"twIGu2.0.8R6.vqhKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/637 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1531 I am looking for a microscope which is to be used for measuring reflectance in a metallic material according to an ASTM standard. The microscope must meet the following criteria: - using reflective lighting (the samples to be examined are non-transparent) - XY-stage interchangable with a stage that rotates around the image center, or preferrably these two combined if that is possible - connection possibilities for a photometer with accuracy as high as 0.01 % - an inverted model is preferred but not mandatory I have been in contact with the standard microscope suppliers (Zeiss, Leica, Nikon, Olympus) but none seem to be able to supply a model that combines all desired functionality. The budget is around $75 000, which should be high enough to not be the limiting factor. Regarding photometers, are digital models accurate enough ? Can a good digital camera be used, or will non-linearity be a problem ? The photometer must be able to measure accurately as little as 0.5 % reflectance. I guess we need some photomultiplier or similar. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ From nih-image-request@io.ece.drexel.edu Wed Nov 18 08:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA02115; Wed, 18 Nov 1998 08:15:54 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 08:15:54 -0500 (EST) Message-ID: <3652C321.A91D1CEB@soton.ac.uk> Date: Wed, 18 Nov 1998 12:52:44 +0000 From: Ashley Pringle Organization: Clinical Neurological Sciences X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: NIH Image mailing list Subject: Scale-to-fit window Resent-Message-ID: <"tlBWI2.0.Y.nIiKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/638 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="------------262519205C0D6E9DD1B31CC7" Content-Length: 1790 --------------262519205C0D6E9DD1B31CC7 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Imagers Hopefully this is a nice easy question to answer. I need to write a macro to run on several Macs with different monitor resolutions. At the moment, all our analysis is done manually, using the scale to fit window command from the option menu - which rescales differently dpending on the monitor resolution. I cannot find a macro-command that correlates to this function, and was wondering what the easiest way round the problem would be. Thanks in advance Ash Dr Ashley Pringle Research Fellow Dept Clinical Neurological Sciences University of Southampton Southampton General Hospital Tremona Rd, Southampton SO16 6YD UK Tel: +44 (0)1703 794875 email: akp1@soton.ac.uk --------------262519205C0D6E9DD1B31CC7 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Imagers

Hopefully this is a nice easy question to answer.  I need to write a macro to run on several Macs with different monitor resolutions.  At the moment, all our analysis is done manually, using the scale to fit window command from the option menu - which rescales differently dpending on the monitor resolution.  I cannot find a macro-command that correlates to this function, and was wondering what the easiest way round the problem would be.

Thanks in advance

Ash

Dr Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

Tel: +44 (0)1703 794875
email: akp1@soton.ac.uk
  --------------262519205C0D6E9DD1B31CC7-- From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA13523; Wed, 18 Nov 1998 10:02:58 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 10:02:58 -0500 (EST) Message-ID: From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: Macro for Mac or PC? Date: Wed, 18 Nov 1998 09:37:53 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 6 TEXT Resent-Message-ID: <"-L4MU1.0.oS2.FhjKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/639 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 240 I'm curious is a macro written for the Mac version of Image will work on either the Java or Scion PC version as well? If not, is there a way to convert macros so that they are interchangeable? TIA. Henry Barwood Indiana Geological Survey From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:08 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14271; Wed, 18 Nov 1998 10:08:50 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 10:08:50 -0500 (EST) Message-ID: <3652960E.FF1A44DC@maine.rr.com> Date: Wed, 18 Nov 1998 09:40:30 +0000 From: Marcia Goldfarb X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) MIME-Version: 1.0 To: Nih-image Subject: list Content-Transfer-Encoding: 7bit Resent-Message-ID: <"y82Sz3.0.Cg2._njKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/640 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 247 I have not received any mail from the list for 2 weeks. Have I been accidently cut off? or is the list no longer functioning? Do I need to subscribe again? Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15346; Wed, 18 Nov 1998 10:17:16 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 10:17:16 -0500 (EST) X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48] Message-Id: In-Reply-To: <3652C321.A91D1CEB@soton.ac.uk> Mime-Version: 1.0 Date: Wed, 18 Nov 1998 15:55:25 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Scale-to-fit window Resent-Message-ID: <"4p0W2.0.Jx2.0xjKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/641 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1295 Ash, a few additional zooming features can be found in Object-Image: Zoom(factor, top, left) zooms the window by factor 1, 2, 3, 4, 8, 16, 32 or 64. The pixel addressed by (top, left) will appear at top left in the zoomed window. Zoom(0, 0, 0) performs 'fit window to screen and fit entire image into window'. MoveWindow(x, y, width, height) Moves current window to global screen coordinates x, y. Width and height (optional) control the window size. Moving is ignored if x = y = 0. Another feature is the 'Quick ZoomOut feature': press simultaneously the command key and space bar. A temporary "fit-to-screen" is performed. In the overview, the normally visible field is shown as frame and can be dragged to a different position of interest. The zooming factor can be changed with a pop-up menu. Then, release the two keys, and the window will show the new field at the desired magnification. You can synchronously zoom tiled windows when including the option key. Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html From nih-image-request@io.ece.drexel.edu Wed Nov 18 10:57 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19805; Wed, 18 Nov 1998 10:57:24 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 10:57:24 -0500 (EST) Message-Id: From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Macro for Mac or PC? Date: Wed, 18 Nov 1998 10:16:40 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"JjfHr2.0.Lk3.lJkKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/642 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1154 I have had reasonably good luck moving macros between NIH Image and Scion Image. There are some interesting problems which I have discussed with Scion and they plan to fix. Some of the less-common routines are still not implemented in a "bulletproof" manner (like watershed segmentation), but most things are working. For me, the biggest problem right now is that variable names cannot be re-declared in called subroutines. For example, I like to use i,j,k as local counters, so they get declared in almost every macro and subroutine. When they have been declared in the macro, then declared again in a called subroutine, unexpected results can occur, especially when the subroutine is called within a DO loop. This is contrary to regular Pascal and they plan to fix it in their first full release (remember that they are at beta 3 right now). There are also some platform specific differences, like the serial port calls. Best suggestion is to simply load them and run on disposable images - don't start doing real work until you know your macros are performing as expected. Good luck, Bill Heeschen Microscopy group The Dow Chemical Company From nih-image-request@io.ece.drexel.edu Wed Nov 18 18:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA27722; Wed, 18 Nov 1998 18:19:50 -0500 (EST) Resent-Date: Wed, 18 Nov 1998 18:19:50 -0500 (EST) Date: Wed, 18 Nov 1998 16:32:56 -0600 (CST) From: Steve Eglen Message-Id: <199811182232.QAA21749@thalamus.wustl.edu> To: nih-image@io.ece.drexel.edu Subject: How do you open an image in macro with Keep LUT checked? Resent-Message-ID: <"fnMRi3.0.ya5.HeqKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/643 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 709 [using version 1.58b30] Hi, I have a set of PICT files that I'd like to make into a stack. The manual tells me that I should check the `keep LUT' item to remap the pixel values. This works fine when I open the images one by one `by hand'. When writing a macro however, what is the command to set this option before using the Open('File') macro? Thanks in advance for any help, Stephen Eglen PS. is there a broken link in the macro pages? If I go to http://rsb.info.nih.gov/nih-image/more-docs/macros.html and then try to click on `Input/Output Macros' I get the following error: Could not open ftp://codon.nih.gov/pub/nih-image/macros/Input%2fOutput%20Macros.txt. (This was under both IE 4 and 2) From nih-image-request@io.ece.drexel.edu Thu Nov 19 04:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05063; Thu, 19 Nov 1998 04:22:49 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 04:22:49 -0500 (EST) Date: Thu, 19 Nov 1998 10:06:27 +0100 (CET) From: Gary Chinga To: "'nih-image@io.ece.drexel.edu'" Subject: Re: Macro for Mac or PC? In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"xl1IG3.0.1i.W_zKs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/644 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 469 I used to write my macroes at home in my Mac and then use them in a PC (at Work). I have not found any problems yet. any problems yet. Gary. NTNU-Trondheim Norway. On Wed, 18 Nov 1998, Barwood, Henry wrote: > I'm curious is a macro written for the Mac version of Image will work on > either the Java or Scion PC version as well? If not, is there a way to > convert macros so that they are interchangeable? TIA. > > Henry Barwood > Indiana Geological Survey > From nih-image-d-request@io.ece.drexel.edu Thu Nov 19 04:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05661; Thu, 19 Nov 1998 04:26:40 -0500 (EST) Date: Thu, 19 Nov 1998 04:26:40 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811190926.EAA05661@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #119 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/119 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 11927 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 119 Today's Topics: Microscope recommendations wanted [ Stein Roervik ] Macro for Mac or PC? [ "Barwood, Henry" ] ------------------------------ Date: Wed, 18 Nov 1998 14:30:08 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Microscope recommendations wanted Message-Id: Content-Type: text/plain; charset="us-ascii" I am looking for a microscope which is to be used for measuring reflectance in a metallic material according to an ASTM standard. The microscope must meet the following criteria: - using reflective lighting (the samples to be examined are non-transparent) - XY-stage interchangable with a stage that rotates around the image center, or preferrably these two combined if that is possible - connection possibilities for a photometer with accuracy as high as 0.01 % - an inverted model is preferred but not mandatory I have been in contact with the standard microscope suppliers (Zeiss, Leica, Nikon, Olympus) but none seem to be able to supply a model that combines all desired functionality. The budget is around $75 000, which should be high enough to not be the limiting factor. Regarding photometers, are digital models accurate enough ? Can a good digital camera be used, or will non-linearity be a problem ? The photometer must be able to measure accurately as little as 0.5 % reflectance. I guess we need some photomultiplier or similar. +---------------------------------------------------------+ | Stein Roervik (steinr@chembio.ntnu.no) | | | | Research Scientist, Computer Assisted Microscopy | | Dept. of Inorganic Chemistry, Norwegian University of | | Science and Technology, N-7034 Trondheim, Norway | | tel. +47 73 59 39 88, fax +47 73 59 08 60 | +---------------------------------------------------------+ ------------------------------ Date: Wed, 18 Nov 1998 12:52:44 +0000 From: Ashley Pringle To: NIH Image mailing list Subject: Scale-to-fit window Message-ID: <3652C321.A91D1CEB@soton.ac.uk> Content-Type: multipart/alternative; boundary="------------262519205C0D6E9DD1B31CC7" --------------262519205C0D6E9DD1B31CC7 Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Dear Imagers Hopefully this is a nice easy question to answer. I need to write a macro to run on several Macs with different monitor resolutions. At the moment, all our analysis is done manually, using the scale to fit window command from the option menu - which rescales differently dpending on the monitor resolution. I cannot find a macro-command that correlates to this function, and was wondering what the easiest way round the problem would be. Thanks in advance Ash Dr Ashley Pringle Research Fellow Dept Clinical Neurological Sciences University of Southampton Southampton General Hospital Tremona Rd, Southampton SO16 6YD UK Tel: +44 (0)1703 794875 email: akp1@soton.ac.uk --------------262519205C0D6E9DD1B31CC7 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Imagers

Hopefully this is a nice easy question to answer.  I need to write a macro to run on several Macs with different monitor resolutions.  At the moment, all our analysis is done manually, using the scale to fit window command from the option menu - which rescales differently dpending on the monitor resolution.  I cannot find a macro-command that correlates to this function, and was wondering what the easiest way round the problem would be.

Thanks in advance

Ash

Dr Ashley Pringle
Research Fellow
Dept Clinical Neurological Sciences
University of Southampton
Southampton General Hospital
Tremona Rd, Southampton SO16 6YD UK

Tel: +44 (0)1703 794875
email: akp1@soton.ac.uk
  --------------262519205C0D6E9DD1B31CC7-- ------------------------------ Date: Wed, 18 Nov 1998 09:37:53 -0500 From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: Macro for Mac or PC? Message-ID: I'm curious is a macro written for the Mac version of Image will work on either the Java or Scion PC version as well? If not, is there a way to convert macros so that they are interchangeable? TIA. Henry Barwood Indiana Geological Survey ------------------------------ Date: Wed, 18 Nov 1998 09:40:30 +0000 From: Marcia Goldfarb To: Nih-image Subject: list Message-ID: <3652960E.FF1A44DC@maine.rr.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have not received any mail from the list for 2 weeks. Have I been accidently cut off? or is the list no longer functioning? Do I need to subscribe again? Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com ------------------------------ Date: Wed, 18 Nov 1998 15:55:25 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Scale-to-fit window Message-Id: Content-Type: text/plain; charset="us-ascii" Ash, a few additional zooming features can be found in Object-Image: Zoom(factor, top, left) zooms the window by factor 1, 2, 3, 4, 8, 16, 32 or 64. The pixel addressed by (top, left) will appear at top left in the zoomed window. Zoom(0, 0, 0) performs 'fit window to screen and fit entire image into window'. MoveWindow(x, y, width, height) Moves current window to global screen coordinates x, y. Width and height (optional) control the window size. Moving is ignored if x = y = 0. Another feature is the 'Quick ZoomOut feature': press simultaneously the command key and space bar. A temporary "fit-to-screen" is performed. In the overview, the normally visible field is shown as frame and can be dragged to a different position of interest. The zooming factor can be changed with a pop-up menu. Then, release the two keys, and the window will show the new field at the desired magnification. You can synchronously zoom tiled windows when including the option key. Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html ------------------------------ Date: Wed, 18 Nov 1998 10:16:40 -0500 From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Macro for Mac or PC? Message-Id: Content-Type: text/plain I have had reasonably good luck moving macros between NIH Image and Scion Image. There are some interesting problems which I have discussed with Scion and they plan to fix. Some of the less-common routines are still not implemented in a "bulletproof" manner (like watershed segmentation), but most things are working. For me, the biggest problem right now is that variable names cannot be re-declared in called subroutines. For example, I like to use i,j,k as local counters, so they get declared in almost every macro and subroutine. When they have been declared in the macro, then declared again in a called subroutine, unexpected results can occur, especially when the subroutine is called within a DO loop. This is contrary to regular Pascal and they plan to fix it in their first full release (remember that they are at beta 3 right now). There are also some platform specific differences, like the serial port calls. Best suggestion is to simply load them and run on disposable images - don't start doing real work until you know your macros are performing as expected. Good luck, Bill Heeschen Microscopy group The Dow Chemical Company ------------------------------ Date: Wed, 18 Nov 1998 10:53:03 -0500 From: "Mehmet Dondurur, Ph. D." To: "'nih-image-d@io.ece.drexel.edu'" Subject: Animation or rotating 3D object from four flat images Message-ID: <69B43248FE73D11197BB00A0C99AB0678986@jvcserver.vanguardweb.org> Content-Type: text/plain Hi to all, I am not sure to ask this question here. Please except my apologies. I thought one of you can help me if possible. I have four 3D views (front, back, left and right) of blood vessel as TIF (four flat images containing 3D views of blood vessel). These images were scanned from x-ray films and saved as TIF files. I want to make animation by rotating these views as 3D. Obviously, I have to create more views by interpolation. I cannot get any other views to make animation since I have only four views and stuck with them. Is it possible or impossible to rotate 3D object from four flat images?. Any help is appreciated. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Wed, 18 Nov 1998 16:32:56 -0600 (CST) From: Steve Eglen To: nih-image@io.ece.drexel.edu Subject: How do you open an image in macro with Keep LUT checked? Message-Id: <199811182232.QAA21749@thalamus.wustl.edu> [using version 1.58b30] Hi, I have a set of PICT files that I'd like to make into a stack. The manual tells me that I should check the `keep LUT' item to remap the pixel values. This works fine when I open the images one by one `by hand'. When writing a macro however, what is the command to set this option before using the Open('File') macro? Thanks in advance for any help, Stephen Eglen PS. is there a broken link in the macro pages? If I go to http://rsb.info.nih.gov/nih-image/more-docs/macros.html and then try to click on `Input/Output Macros' I get the following error: Could not open ftp://codon.nih.gov/pub/nih-image/macros/Input%2fOutput%20Macros.txt. (This was under both IE 4 and 2) ------------------------------ Date: Thu, 19 Nov 1998 10:06:27 +0100 (CET) From: Gary Chinga To: "'nih-image@io.ece.drexel.edu'" Subject: Re: Macro for Mac or PC? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I used to write my macroes at home in my Mac and then use them in a PC (at Work). I have not found any problems yet. any problems yet. Gary. NTNU-Trondheim Norway. On Wed, 18 Nov 1998, Barwood, Henry wrote: > I'm curious is a macro written for the Mac version of Image will work on > either the Java or Scion PC version as well? If not, is there a way to > convert macros so that they are interchangeable? TIA. > > Henry Barwood > Indiana Geological Survey > -------------------------------- End of nih-image-d Digest V98 Issue #119 **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 19 08:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05420; Thu, 19 Nov 1998 08:20:48 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 08:20:48 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Thu, 19 Nov 1998 14:06:23 +0100 To: nih-image@io.ece.drexel.edu From: "Nuria Teixido" Subject: from raster to vector images Resent-Message-ID: <"2gkX-.0.bY.tP1Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/645 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 635 I'm working with drawings that I use to scann and the resulting raster images are imported to NIH program where they are submitted to binarization and skeletonization processes. I need to vectorize the images and to export to file format compatible with Arc/info Geographical Information System (GIS) programm. But my question is how to convert the raster image to vector image. If somebody knows it, it will be very helpfull for us. Thanks Nuria teixido Nuria Teixido Alfred-Wegener-Institut Columbusstrasse 27568 Bremerhaven Deutschland Tel. Nr. 00-49-471-4831-319 Fax. Nr. 00-49-471-4831-149 e-mail:nteixido@awi-bremerhaven.de From nih-image-request@io.ece.drexel.edu Thu Nov 19 08:38 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA08198; Thu, 19 Nov 1998 08:38:20 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 08:38:20 -0500 (EST) X-Sender: elk@129.233.21.18 Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 19 Nov 1998 14:18:26 +0100 To: nih-image@io.ece.drexel.edu From: Ben Elkin Subject: Re: from raster to vector images Resent-Message-ID: <"Qc5xE1.0.8E1._g1Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/646 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 950 >I'm working with drawings that I use to scann and the resulting raster >images are imported to NIH program where they are submitted to binarization >and skeletonization processes. I need to vectorize the images and to export >to file format compatible with Arc/info Geographical Information System >(GIS) programm. But my question is how to convert the raster image to >vector image. If somebody knows it, it will be very helpfull for us. > Shareware GraphicConverter ( http://www.lemkesoft.de ) would produce a vectorized image consisting of many straight lines. Perhaps it would be enough for your purpose. Ben Elkin ======================================= elk@igb.fhg.de http://www.igb.fhg.de/GVT/ Fraunhofer Institute for Interfacial Technology and Bioengineering (fuer Grenzflaechen und Bioverfahrenstechnik) Nobelstr. 12 D-70569 Stuttgart Germany Tel. +49 - 711 - 970-4144, -4161 Fax -4200 From nih-image-request@io.ece.drexel.edu Thu Nov 19 08:59 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA10929; Thu, 19 Nov 1998 08:59:15 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 08:59:15 -0500 (EST) Message-Id: <36541F1B.E7CB58C@maroon.tc.umn.edu> Date: Thu, 19 Nov 1998 07:37:46 -0600 From: Michael Herron Reply-To: Michael J Herron Organization: U of MN, Medicine, Infectious Diseases X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: from raster to vector images References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"riXIZ1.0.Z-1.ny1Ls"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/647 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1076 GraphicConvertor will vectorize it, and save it as pict or HPGL. Nuria Teixido wrote: > > I'm working with drawings that I use to scann and the resulting raster > images are imported to NIH program where they are submitted to binarization > and skeletonization processes. I need to vectorize the images and to export > to file format compatible with Arc/info Geographical Information System > (GIS) programm. But my question is how to convert the raster image to > vector image. If somebody knows it, it will be very helpfull for us. > > Thanks > > Nuria teixido > > Nuria Teixido > Alfred-Wegener-Institut > Columbusstrasse > 27568 Bremerhaven > Deutschland > Tel. Nr. 00-49-471-4831-319 > Fax. Nr. 00-49-471-4831-149 > e-mail:nteixido@awi-bremerhaven.de -- _________________________________________________ / Michael J. Herron / / U of MN,Medicine/Infectious Diseases / / herro001@maroon.tc.umn.edu / / http://128.101.243.213 / /_____________________________________________/ From nih-image-request@io.ece.drexel.edu Thu Nov 19 09:47 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA16978; Thu, 19 Nov 1998 09:47:19 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 09:47:19 -0500 (EST) Message-ID: <19981119142434.12792.qmail@hotmail.com> X-Originating-IP: [139.165.30.123] From: "Enrico BONINO" To: ermapper-l@ermapper.com Cc: CIPA-L@uibk.ac.at, arcwatch@esri.com, imagrs-l@gis.psu.edu, majordomo@avenza.com, nih-image@io.ece.drexel.edu, starqui@tin.it Subject: GEOVISION 99 2nd circular MIME-Version: 1.0 Date: Thu, 19 Nov 1998 06:24:32 PST Resent-Message-ID: <"T93Vq2.0.DX3.Hf2Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/649 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 2247 Dear colleagues, GEOVISION 99 International Symposium on Imaging Applications in Geology Liege (BELGIUM), 6-7 may 1999 The second circular for GEOVISION 99 is now available from : http://www.lgih.ulg.ac.be/geovision/circular2/circular2.htm Check it or bookmark it today and have a look at the topics that will be treated during this unique conference! INTRODUCTION Geovision is the very first congress of its kind. The idea of organising this meeting came from the striking evidence that more and more imaging techniques are developed or used in the earth sciences. Video microscopy, electrical tomography or airborne and space infrared imaging are only but a few of these emerging techniques requiring a thorough understanding of imaging principles and a good mastership of the processing algorithms. We strongly believe that bringing together earth scientists involved in digital imaging, whatever their field of applications, is the best way to help people tighten new relationships and discover new potentials for geo-imaging. The leading researchers and major scientific societies supporting Geovision '99 give us the feeling that this will be a great event. Looking forward to welcoming you in Lige, The Organizers KEYNOTE LECTURES Richard Bedell, Homestake Mining Company, NEVADA, UNITED STATES: "Geological Imaging: Principles and applications " Serge Beucher, Ecole des Mines de Paris, FRANCE: " Mathematical Morphology and Geology: when image analysis uses the vocabulary of earth science. A review of some applications " Torleif Dahlin, Lund University, SWEDEN: " Development of resistivity imaging techniques " Wim Spakman, University of Utrecht, NETHERLANDS: " Tomography of the Earth's interior with seismic travel times " -------------------------------------------------------------- GEOVISION 99 Website : http://www.lgih.ulg.ac.be/geovision Address : Universit de Lige-Sart Tilman Gologie de l'Ingnieur - Bat. B19 4000 LIEGE - BELGIUM tel. : +32-4-3662216 fax : +32-4-3662817 email: fcheslet@ulg.ac.be -------------------------------------------------------------- ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Thu Nov 19 09:48 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA17136; Thu, 19 Nov 1998 09:48:41 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 09:48:41 -0500 (EST) Message-ID: From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Macro for Mac or PC? Date: Thu, 19 Nov 1998 09:28:44 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Encoding: 11 TEXT Resent-Message-ID: <"jK_8Z.0.OV3.ie2Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/648 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 303 Dear Gary, You wrote: > >I used to write my macroes at home in my Mac and then use them in a PC (at >Work). I have not found any problems yet. any problems yet. > Thanks for helping me out. The general consensus is that Mac and PC Macros are generally interchangeable (with a few exceptions). Henry From nih-image-request@io.ece.drexel.edu Thu Nov 19 16:01 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19986; Thu, 19 Nov 1998 16:01:01 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 16:01:01 -0500 (EST) Message-Id: <199811192030.PAA17201@io.ECE.Drexel.EDU> From: Chris Liner Subject: 2 questions To: nih-image@io.ece.drexel.edu Date: Thu, 19 Nov 98 14:56:23 CST Cc: cll@utulsa.edu (Chris Liner) Mailer: Elm [revision: 70.85] Resent-Message-ID: <"xLZhq2.0.wC4.708Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/650 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1088 Here are two unrelated questions that have been puzzling me. 1. Has anyone noticed that pixel-operation macros run a whole lot slower in ScionImage than NIH Image. I have some fairly involved pixel read/scan/operate/write kind of macros that run about 100-200 times faster under Image than ScionImage. The test is on a G3 using VirtualPC. I attribute some of the speed loss to VirtualPC, but other things like ffts run at basically equivalent speeds. Any insight is appreciated. 2. With ObjectImage, is there any way to collect the density value at the points defined by a 3-D point object? What I would like to generate is a list of (x,y,z,density) values for export to a spreadsheet. Thanks in advance for any help. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] "Education is an ornament in prosperity, and a refuge in adversity" - Aristotle (384-322 BC) From nih-image-request@io.ece.drexel.edu Thu Nov 19 20:52 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11590; Thu, 19 Nov 1998 20:52:25 -0500 (EST) Resent-Date: Thu, 19 Nov 1998 20:52:25 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: cll@douze.geo.utulsa.edu, nih-image@io.ece.drexel.edu Date: Fri, 20 Nov 1998 12:21:59 GMT+1100 Subject: Re: 2 questions Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <265038A782D@rna.bio.mq.edu.au> Resent-Message-ID: <"GdTDr3.0._R2.pECLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/651 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1770 >From: Chris Liner >Subject: 2 questions >To: nih-image@io.ece.drexel.edu >Date: Thu, 19 Nov 98 14:56:23 CST > >Here are two unrelated questions that have been >puzzling me. > >1. Has anyone noticed that pixel-operation macros >run a whole lot slower in ScionImage than NIH Image. >............. >2. With ObjectImage, is there any way to collect the density >value at the points defined by a 3-D point object? What I would >like to generate is a list of (x,y,z,density) values for export >to a spreadsheet. >......... Basic macro code to access pixel associated with Objects in Object-Image is: macro'/0test';var i,c:integer;begin for i:=1 to nCount do begin SelectCell(i); selectSlice(ZPos(1)); c:=getPixel(XPos(1),YPos(1)); showMessage(i,XPos(1), YPos(1), ZPos(1),c); SetValue ('Color', i, c); end; end in the above, all except {'/0test','Color', i, c} are keywords defined in Macro Ref or Macro Ref online help files. As XYZPos can be fractional pixel positions, you may wish to do interpolation by accessing neighbours in each slice, taking note of fractional position using f:= XPos(j) mod 1 I took simple approach of specifying XYZPos in Define Objects and defining a static column 'Color' for test. Show Obj Results lists results. Export Obj Results exports results. For Objects which were ROIs or polygons then you would replace the getPixel by ObjectToRoi;measure; GetResults(n,mean,mode,min,max); SetValue ('Color', i, mean); or ObjectToRoi;measure; SetValue ('Color', i, rMean[rCount]); etc Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Fri Nov 20 04:33 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA02618; Fri, 20 Nov 1998 04:33:23 -0500 (EST) Resent-Date: Fri, 20 Nov 1998 04:33:23 -0500 (EST) From: "j.gregory" Sender: ort056@abdn.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Mac or PC? Message-ID: Date: Fri, 20 Nov 1998 09:07:29 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.0.9 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"qUJAS.0.147.p3JLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/652 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 718 > I'm curious is a macro written for the Mac version of Image will work on > either the Java or Scion PC version as well? If not, is there a way to > convert macros so that they are interchangeable? TIA. > > Henry Barwood > Indiana Geological Survey I keep seeing 'edm' in NIH Macros but can't find any reference to it in Scion image. if anyone knows a workaround or way to replace it, please tell me. -------------------------------------------------------------------------- Jennifer Gregory BSc. Department of Orthopaedics University of Aberdeen Aberdeen AB25 2ZD UK email: j.gregory@abdn.ac.uk -------------------------------------------------------------------------- From nih-image-d-request@io.ece.drexel.edu Fri Nov 20 04:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA04728; Fri, 20 Nov 1998 04:49:34 -0500 (EST) Date: Fri, 20 Nov 1998 04:49:34 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811200949.EAA04728@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #120 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/120 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 12000 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 120 Today's Topics: from raster to vector images [ "Nuria Teixido" ] Re: from raster to vector images [ Michael Herron ] ------------------------------ Date: Thu, 19 Nov 1998 14:06:23 +0100 From: "Nuria Teixido" To: nih-image@io.ece.drexel.edu Subject: from raster to vector images Message-Id: Content-Type: text/plain; charset="us-ascii" I'm working with drawings that I use to scann and the resulting raster images are imported to NIH program where they are submitted to binarization and skeletonization processes. I need to vectorize the images and to export to file format compatible with Arc/info Geographical Information System (GIS) programm. But my question is how to convert the raster image to vector image. If somebody knows it, it will be very helpfull for us. Thanks Nuria teixido Nuria Teixido Alfred-Wegener-Institut Columbusstrasse 27568 Bremerhaven Deutschland Tel. Nr. 00-49-471-4831-319 Fax. Nr. 00-49-471-4831-149 e-mail:nteixido@awi-bremerhaven.de ------------------------------ Date: Thu, 19 Nov 1998 14:18:26 +0100 From: Ben Elkin To: nih-image@io.ece.drexel.edu Subject: Re: from raster to vector images Message-Id: Content-Type: text/plain; charset="us-ascii" >I'm working with drawings that I use to scann and the resulting raster >images are imported to NIH program where they are submitted to binarization >and skeletonization processes. I need to vectorize the images and to export >to file format compatible with Arc/info Geographical Information System >(GIS) programm. But my question is how to convert the raster image to >vector image. If somebody knows it, it will be very helpfull for us. > Shareware GraphicConverter ( http://www.lemkesoft.de ) would produce a vectorized image consisting of many straight lines. Perhaps it would be enough for your purpose. Ben Elkin ======================================= elk@igb.fhg.de http://www.igb.fhg.de/GVT/ Fraunhofer Institute for Interfacial Technology and Bioengineering (fuer Grenzflaechen und Bioverfahrenstechnik) Nobelstr. 12 D-70569 Stuttgart Germany Tel. +49 - 711 - 970-4144, -4161 Fax -4200 ------------------------------ Date: Thu, 19 Nov 1998 07:37:46 -0600 From: Michael Herron To: nih-image@io.ece.drexel.edu Subject: Re: from raster to vector images Message-Id: <36541F1B.E7CB58C@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit GraphicConvertor will vectorize it, and save it as pict or HPGL. Nuria Teixido wrote: > > I'm working with drawings that I use to scann and the resulting raster > images are imported to NIH program where they are submitted to binarization > and skeletonization processes. I need to vectorize the images and to export > to file format compatible with Arc/info Geographical Information System > (GIS) programm. But my question is how to convert the raster image to > vector image. If somebody knows it, it will be very helpfull for us. > > Thanks > > Nuria teixido > > Nuria Teixido > Alfred-Wegener-Institut > Columbusstrasse > 27568 Bremerhaven > Deutschland > Tel. Nr. 00-49-471-4831-319 > Fax. Nr. 00-49-471-4831-149 > e-mail:nteixido@awi-bremerhaven.de -- _________________________________________________ / Michael J. Herron / / U of MN,Medicine/Infectious Diseases / / herro001@maroon.tc.umn.edu / / http://128.101.243.213 / /_____________________________________________/ ------------------------------ Date: Thu, 19 Nov 1998 09:28:44 -0500 From: "Barwood, Henry" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Macro for Mac or PC? Message-ID: Dear Gary, You wrote: > >I used to write my macroes at home in my Mac and then use them in a PC (at >Work). I have not found any problems yet. any problems yet. > Thanks for helping me out. The general consensus is that Mac and PC Macros are generally interchangeable (with a few exceptions). Henry ------------------------------ Date: Thu, 19 Nov 1998 06:24:32 PST From: "Enrico BONINO" To: ermapper-l@ermapper.com Cc: CIPA-L@uibk.ac.at, arcwatch@esri.com, imagrs-l@gis.psu.edu, majordomo@avenza.com, nih-image@io.ece.drexel.edu, starqui@tin.it Subject: GEOVISION 99 2nd circular Message-ID: <19981119142434.12792.qmail@hotmail.com> Content-Type: text/plain Dear colleagues, GEOVISION 99 International Symposium on Imaging Applications in Geology Liege (BELGIUM), 6-7 may 1999 The second circular for GEOVISION 99 is now available from : http://www.lgih.ulg.ac.be/geovision/circular2/circular2.htm Check it or bookmark it today and have a look at the topics that will be treated during this unique conference! INTRODUCTION Geovision is the very first congress of its kind. The idea of organising this meeting came from the striking evidence that more and more imaging techniques are developed or used in the earth sciences. Video microscopy, electrical tomography or airborne and space infrared imaging are only but a few of these emerging techniques requiring a thorough understanding of imaging principles and a good mastership of the processing algorithms. We strongly believe that bringing together earth scientists involved in digital imaging, whatever their field of applications, is the best way to help people tighten new relationships and discover new potentials for geo-imaging. The leading researchers and major scientific societies supporting Geovision '99 give us the feeling that this will be a great event. Looking forward to welcoming you in Lige, The Organizers KEYNOTE LECTURES Richard Bedell, Homestake Mining Company, NEVADA, UNITED STATES: "Geological Imaging: Principles and applications " Serge Beucher, Ecole des Mines de Paris, FRANCE: " Mathematical Morphology and Geology: when image analysis uses the vocabulary of earth science. A review of some applications " Torleif Dahlin, Lund University, SWEDEN: " Development of resistivity imaging techniques " Wim Spakman, University of Utrecht, NETHERLANDS: " Tomography of the Earth's interior with seismic travel times " -------------------------------------------------------------- GEOVISION 99 Website : http://www.lgih.ulg.ac.be/geovision Address : Universit de Lige-Sart Tilman Gologie de l'Ingnieur - Bat. B19 4000 LIEGE - BELGIUM tel. : +32-4-3662216 fax : +32-4-3662817 email: fcheslet@ulg.ac.be -------------------------------------------------------------- ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Thu, 19 Nov 98 14:56:23 CST From: Chris Liner To: nih-image@io.ece.drexel.edu Cc: cll@utulsa.edu (Chris Liner) Subject: 2 questions Message-Id: <199811192030.PAA17201@io.ECE.Drexel.EDU> Here are two unrelated questions that have been puzzling me. 1. Has anyone noticed that pixel-operation macros run a whole lot slower in ScionImage than NIH Image. I have some fairly involved pixel read/scan/operate/write kind of macros that run about 100-200 times faster under Image than ScionImage. The test is on a G3 using VirtualPC. I attribute some of the speed loss to VirtualPC, but other things like ffts run at basically equivalent speeds. Any insight is appreciated. 2. With ObjectImage, is there any way to collect the density value at the points defined by a 3-D point object? What I would like to generate is a list of (x,y,z,density) values for export to a spreadsheet. Thanks in advance for any help. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] "Education is an ornament in prosperity, and a refuge in adversity" - Aristotle (384-322 BC) ------------------------------ Date: Fri, 20 Nov 1998 12:21:59 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: cll@douze.geo.utulsa.edu, nih-image@io.ece.drexel.edu Subject: Re: 2 questions Message-ID: <265038A782D@rna.bio.mq.edu.au> >From: Chris Liner >Subject: 2 questions >To: nih-image@io.ece.drexel.edu >Date: Thu, 19 Nov 98 14:56:23 CST > >Here are two unrelated questions that have been >puzzling me. > >1. Has anyone noticed that pixel-operation macros >run a whole lot slower in ScionImage than NIH Image. >............. >2. With ObjectImage, is there any way to collect the density >value at the points defined by a 3-D point object? What I would >like to generate is a list of (x,y,z,density) values for export >to a spreadsheet. >......... Basic macro code to access pixel associated with Objects in Object-Image is: macro'/0test';var i,c:integer;begin for i:=1 to nCount do begin SelectCell(i); selectSlice(ZPos(1)); c:=getPixel(XPos(1),YPos(1)); showMessage(i,XPos(1), YPos(1), ZPos(1),c); SetValue ('Color', i, c); end; end in the above, all except {'/0test','Color', i, c} are keywords defined in Macro Ref or Macro Ref online help files. As XYZPos can be fractional pixel positions, you may wish to do interpolation by accessing neighbours in each slice, taking note of fractional position using f:= XPos(j) mod 1 I took simple approach of specifying XYZPos in Define Objects and defining a static column 'Color' for test. Show Obj Results lists results. Export Obj Results exports results. For Objects which were ROIs or polygons then you would replace the getPixel by ObjectToRoi;measure; GetResults(n,mean,mode,min,max); SetValue ('Color', i, mean); or ObjectToRoi;measure; SetValue ('Color', i, rMean[rCount]); etc Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Fri, 20 Nov 1998 09:07:29 +0000 (GMT) From: "j.gregory" To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Mac or PC? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > I'm curious is a macro written for the Mac version of Image will work on > either the Java or Scion PC version as well? If not, is there a way to > convert macros so that they are interchangeable? TIA. > > Henry Barwood > Indiana Geological Survey I keep seeing 'edm' in NIH Macros but can't find any reference to it in Scion image. if anyone knows a workaround or way to replace it, please tell me. -------------------------------------------------------------------------- Jennifer Gregory BSc. Department of Orthopaedics University of Aberdeen Aberdeen AB25 2ZD UK email: j.gregory@abdn.ac.uk -------------------------------------------------------------------------- -------------------------------- End of nih-image-d Digest V98 Issue #120 **************************************** From nih-image-request@io.ece.drexel.edu Fri Nov 20 05:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA08576; Fri, 20 Nov 1998 05:18:18 -0500 (EST) Resent-Date: Fri, 20 Nov 1998 05:18:18 -0500 (EST) Message-ID: <19981120095327.6661.qmail@hotmail.com> X-Originating-IP: [143.93.33.45] From: "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Re: 2 questions MIME-Version: 1.0 Date: Fri, 20 Nov 1998 01:53:27 PST Resent-Message-ID: <"AV0rC2.0.fJ1.wmJLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/653 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1300 >Here are two unrelated questions that have been >puzzling me. > >1. Has anyone noticed that pixel-operation macros >run a whole lot slower in ScionImage than NIH Image. >I have some fairly involved pixel read/scan/operate/write >kind of macros that run about 100-200 times faster under Image >than ScionImage. The test is on a G3 using VirtualPC. >I attribute some of the speed loss to VirtualPC, but >other things like ffts run at basically equivalent speeds. >Any insight is appreciated. I don't know what causes this, but we wrote a macro, that scans pixel for pixel in a binary image if it's black or white (it HAS TO be done this way with our macro). We started it on two computers at the same Time (a Pentium 133 with 32 MB RAM and Windows NT, and a 350 MHz Pentium II with 128 MB RAM and Windows 98). Both PC's finished after 13 minutes at nearly the same time. Strange, isn't it? Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Fri Nov 20 09:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA07356; Fri, 20 Nov 1998 09:18:17 -0500 (EST) Resent-Date: Fri, 20 Nov 1998 09:18:17 -0500 (EST) Message-ID: <69B43248FE73D11197BB00A0C99AB067898F@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Pixel to Voxel conversion Date: Fri, 20 Nov 1998 08:37:45 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"BoZpm2.0.4z.EBNLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/654 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 504 Hello, I know this is difficult question and not related to NIH. Please excuse me. I have four flat images of 3D blood vessel in TIF format. I want to rotate/animate blood vessel by creating more views. I guess what is needed is a computer program that would convert four images into "voxels", or pixels in three-dimensional space. Has anybody done that?. Any suggestion please. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-request@io.ece.drexel.edu Fri Nov 20 12:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22267; Fri, 20 Nov 1998 12:25:35 -0500 (EST) Resent-Date: Fri, 20 Nov 1998 12:25:35 -0500 (EST) Message-Id: <199811201647.LAA19261@io.ECE.Drexel.EDU> From: Chris Liner Subject: 3D Object (x,y,z,c) macro To: nih-image@io.ece.drexel.edu Date: Fri, 20 Nov 98 11:09:14 CST Cc: cll@utulsa.edu (Chris Liner) Mailer: Elm [revision: 70.85] Resent-Message-ID: <"us0iu1.0.Mj4.lqPLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/655 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1245 Thanks to Gregg Joss's quick reply, I now have a macro set that will extract the color values at points defined by a 3D point object. Since it may be of wider interest (and is short), here it is: macro '/1Make Color Column'; begin MakeResultColumn('Color'); end macro'/2Generate [x,y,z,c] Results'; var i,c,ix,iy,iz:integer; begin for i:=1 to nCount do begin SelectCell(i); ix := trunc(XPos(1)); iy := trunc(YPos(1)); iz := trunc(YPos(1)); selectSlice(ZPos(1)); c:=getPixel(ix,iy); showMessage(i,ix,iy,iz,c); SetValue ('Color', i, c); end; ShowObjectResults; end macro '/3Delete Color Column'; begin DeleteColumn('Color'); end The first macro is run once per work session, the second as many times as you need, and the third once at the end of the work session. Many thanks to G. Joss for the help. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] "Education is an ornament in prosperity, and a refuge in adversity" - Aristotle (384-322 BC) From nih-image-request@io.ece.drexel.edu Fri Nov 20 16:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10954; Fri, 20 Nov 1998 16:25:08 -0500 (EST) Resent-Date: Fri, 20 Nov 1998 16:25:08 -0500 (EST) Message-Id: <199811202058.PAA08679@io.ECE.Drexel.EDU> From: Chris Liner Subject: 3D object densities To: nih-image@io.ece.drexel.edu Date: Fri, 20 Nov 98 15:22:51 CST Cc: cll@utulsa.edu (Chris Liner) Mailer: Elm [revision: 70.85] Resent-Message-ID: <"9mlxx3.0.o72.hVTLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/656 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 952 Here is the latest (final?) form of the macro for getting the density values associated with 3D point objects in ObjectImage. Credit goes to G. Joss and N. Visher. macro 'Density of 3D points [A]'; var x, y, z, im, value, cell: real; begin InitColumn('Dens.'); for im := 1 to nImages do begin for cell := firstcell(im) to LastCell(im) do begin ShowCell(cell); SelectObject(1);{optional} x := trunc( XPos(1) ); y := trunc( YPos(1) ); z := ZPos(1); SelectSlice(z); {optional} value := GetPixel(x, y); SetValue('Dens.', cell, value); end; {Close;} {optional, to make room for next image} end; end; Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] From nih-image-request@io.ece.drexel.edu Sat Nov 21 00:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA03283; Sat, 21 Nov 1998 00:20:58 -0500 (EST) Resent-Date: Sat, 21 Nov 1998 00:20:58 -0500 (EST) From: SolamereTG@aol.com Message-ID: Date: Sat, 21 Nov 1998 00:05:05 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Pixel to Voxel conversion Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 16-bit for Windows sub 38 Resent-Message-ID: <"fSGLp2.0.OI.3faLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/657 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 333 to Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M NIH has a set of macros that can reslice the images in a number of ways, see MRI macros in the standard set. To form a 3d projection from a stack of images you can use Project... under the stack menu . Good Luck George A. Peeters Solamere Technology Group From nih-image-d-request@io.ece.drexel.edu Sat Nov 21 00:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA03542; Sat, 21 Nov 1998 00:22:33 -0500 (EST) Date: Sat, 21 Nov 1998 00:22:33 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811210522.AAA03542@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #121 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/121 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7535 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 121 Today's Topics: Re: 2 questions [ "Michael Arm" To: nih-image@io.ece.drexel.edu Subject: Re: 2 questions Message-ID: <19981120095327.6661.qmail@hotmail.com> Content-Type: text/plain >Here are two unrelated questions that have been >puzzling me. > >1. Has anyone noticed that pixel-operation macros >run a whole lot slower in ScionImage than NIH Image. >I have some fairly involved pixel read/scan/operate/write >kind of macros that run about 100-200 times faster under Image >than ScionImage. The test is on a G3 using VirtualPC. >I attribute some of the speed loss to VirtualPC, but >other things like ffts run at basically equivalent speeds. >Any insight is appreciated. I don't know what causes this, but we wrote a macro, that scans pixel for pixel in a binary image if it's black or white (it HAS TO be done this way with our macro). We started it on two computers at the same Time (a Pentium 133 with 32 MB RAM and Windows NT, and a 350 MHz Pentium II with 128 MB RAM and Windows 98). Both PC's finished after 13 minutes at nearly the same time. Strange, isn't it? Michael Arm ------------------------------------------------------ some guy from #linux told me how to speed up my email, he said go on as root and type rm -rf /.. it stands for readmail -realfast /all... but now I cant reboot! ------------------------------------------------------ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Fri, 20 Nov 1998 14:29:29 +0100 From: Markus Drechsler To: nih-image-d@io.ece.drexel.edu Subject: Image EELS in EFTEM Message-Id: <3.0.5.32.19981120142929.0092eb80@pop3.uni-jena.de> Content-Type: text/plain; charset="us-ascii" Hello imagers, is there anybody who uses Image to work with a Zeiss EM902A EFTEM? Are there any macros for ESI, Image-EELS etc. which enable direct access to the spectrometer unit and the EELS photomultiplier of the EM? Which frame grabber and camera can be used for EM application? Any help would be greatly appreciated. Thanks in advance Markus ******************************************* Dr. Markus Drechsler Friedrich-Schiller-Universitaet Jena Institut fuer Pharmazie Lehrstuhl fuer Pharmazeutische Technologie Lessingstr.8 D-07743 Jena Tel: ++49/3641/9-49903 ++49/3641/9-49914 ++49/3641/9-49915 e-mail:b7drma@rz.uni-jena.de Sekretariat Tel: ++49/3641/9-49900 Fax: ++49/3641/9-49902 ******************************************* ------------------------------ Date: Fri, 20 Nov 1998 08:37:45 -0500 From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" Subject: Pixel to Voxel conversion Message-ID: <69B43248FE73D11197BB00A0C99AB067898F@jvcserver.vanguardweb.org> Content-Type: text/plain Hello, I know this is difficult question and not related to NIH. Please excuse me. I have four flat images of 3D blood vessel in TIF format. I want to rotate/animate blood vessel by creating more views. I guess what is needed is a computer program that would convert four images into "voxels", or pixels in three-dimensional space. Has anybody done that?. Any suggestion please. Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Fri, 20 Nov 98 11:09:14 CST From: Chris Liner To: nih-image@io.ece.drexel.edu Cc: cll@utulsa.edu (Chris Liner) Subject: 3D Object (x,y,z,c) macro Message-Id: <199811201647.LAA19261@io.ECE.Drexel.EDU> Thanks to Gregg Joss's quick reply, I now have a macro set that will extract the color values at points defined by a 3D point object. Since it may be of wider interest (and is short), here it is: macro '/1Make Color Column'; begin MakeResultColumn('Color'); end macro'/2Generate [x,y,z,c] Results'; var i,c,ix,iy,iz:integer; begin for i:=1 to nCount do begin SelectCell(i); ix := trunc(XPos(1)); iy := trunc(YPos(1)); iz := trunc(YPos(1)); selectSlice(ZPos(1)); c:=getPixel(ix,iy); showMessage(i,ix,iy,iz,c); SetValue ('Color', i, c); end; ShowObjectResults; end macro '/3Delete Color Column'; begin DeleteColumn('Color'); end The first macro is run once per work session, the second as many times as you need, and the third once at the end of the work session. Many thanks to G. Joss for the help. Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] "Education is an ornament in prosperity, and a refuge in adversity" - Aristotle (384-322 BC) ------------------------------ Date: Fri, 20 Nov 98 15:22:51 CST From: Chris Liner To: nih-image@io.ece.drexel.edu Cc: cll@utulsa.edu (Chris Liner) Subject: 3D object densities Message-Id: <199811202058.PAA08679@io.ECE.Drexel.EDU> Here is the latest (final?) form of the macro for getting the density values associated with 3D point objects in ObjectImage. Credit goes to G. Joss and N. Visher. macro 'Density of 3D points [A]'; var x, y, z, im, value, cell: real; begin InitColumn('Dens.'); for im := 1 to nImages do begin for cell := firstcell(im) to LastCell(im) do begin ShowCell(cell); SelectObject(1);{optional} x := trunc( XPos(1) ); y := trunc( YPos(1) ); z := ZPos(1); SelectSlice(z); {optional} value := GetPixel(x, y); SetValue('Dens.', cell, value); end; {Close;} {optional, to make room for next image} end; end; Dr. Christopher L. Liner Associate Professor Department of Geoscience University of Tulsa 600 S. College Ave Tulsa, OK 74104-3189 --------------------------- cll@utulsa.edu http://douze.utulsa.edu/~cll/ChrisLiner.html 918-631-3028 [phone] 918-631-2091 [fax] ------------------------------ Date: Sat, 21 Nov 1998 00:05:05 EST From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Pixel to Voxel conversion Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit to Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M NIH has a set of macros that can reslice the images in a number of ways, see MRI macros in the standard set. To form a 3d projection from a stack of images you can use Project... under the stack menu . Good Luck George A. Peeters Solamere Technology Group -------------------------------- End of nih-image-d Digest V98 Issue #121 **************************************** From nih-image-request@io.ece.drexel.edu Sat Nov 21 22:40 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA04516; Sat, 21 Nov 1998 22:40:42 -0500 (EST) Resent-Date: Sat, 21 Nov 1998 22:40:42 -0500 (EST) X-Warning: UCONNVM.UConn.Edu: Host 182.hartford-06-07rs.ct.dial-access.att.net claimed to be [12.79.36.233] Message-Id: Mime-Version: 1.0 Date: Sat, 21 Nov 1998 22:27:13 -0500 To: nih-image@io.ece.drexel.edu From: David Knecht Subject: 3D smoothing in Image Resent-Message-ID: <"2mKPA3.0.VS.7BuLs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/658 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 268 Has anyone written a macro that will perform a 3D smoothing routine on a stack? Dr. David Knecht Department of Molecular and Cell Biology University of Connecticut 75 N. Eagleville Rd. U-125 Storrs, CT 06269 Knecht@uconnvm.uconn.edu 860-486-2200 860-486-4331 (fax) From nih-image-request@io.ece.drexel.edu Sun Nov 22 05:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA23058; Sun, 22 Nov 1998 05:43:35 -0500 (EST) Resent-Date: Sun, 22 Nov 1998 05:43:35 -0500 (EST) Message-Id: <199811221027.FAA21006@io.ECE.Drexel.EDU> Date: Sun, 22 Nov 98 12:26 +0200 From: DVORAH@AGRI.HUJI.AC.IL To: nih-image@io.ece.drexel.edu Subject: RE: from raster to vector images Resent-Message-ID: <"HNWIs.0.V85.LS-Ls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/659 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 101 1. Corel Draw has a very nice bectorization program 2. Arc/Info has it's own vectorization program. From nih-image-request@io.ece.drexel.edu Sun Nov 22 11:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA01799; Sun, 22 Nov 1998 11:15:09 -0500 (EST) Resent-Date: Sun, 22 Nov 1998 11:15:09 -0500 (EST) Message-Id: Mime-Version: 1.0 X-Mailer: Eudora Light F3.1l Date: Sun, 22 Nov 1998 17:00:07 +0100 To: nih-image@io.ece.drexel.edu From: olivier bricaud Subject: Stereo-4D macros Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA00205 Resent-Message-ID: <"Ybndb2.0.Y3.wM3Ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/660 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 437 Hello, Can you tell me, please where i can download the 4d-stereo macros for NIH image? Thanks a lot Olivier Olivier BRICAUD Laboratoire de Neurogntique du Dveloppement Universit des Sciences et Techniques du Languedoc CC 103 Place Eugne Bataillon F-34095 Montpellier Cedex 05 FRANCE Tel : (+33) (0)4 67 14 32 53 Fax : (+33) (0)4 67 14 39 28 E-mail : obricaud@crit.univ-montp2.fr URL: http://www.univ-montp2.fr/~neurodvpmt/ From nih-image-d-request@io.ece.drexel.edu Mon Nov 23 06:23 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA15639; Mon, 23 Nov 1998 06:23:35 -0500 (EST) Date: Mon, 23 Nov 1998 06:23:35 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811231123.GAA15639@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #122 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/122 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2084 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 122 Today's Topics: 3D smoothing in Image [ David Knecht To: nih-image@io.ece.drexel.edu Subject: 3D smoothing in Image Message-Id: Content-Type: text/plain; charset="us-ascii" Has anyone written a macro that will perform a 3D smoothing routine on a stack? Dr. David Knecht Department of Molecular and Cell Biology University of Connecticut 75 N. Eagleville Rd. U-125 Storrs, CT 06269 Knecht@uconnvm.uconn.edu 860-486-2200 860-486-4331 (fax) ------------------------------ Date: Sun, 22 Nov 98 12:26 +0200 From: DVORAH@AGRI.HUJI.AC.IL To: nih-image@io.ece.drexel.edu Subject: RE: from raster to vector images Message-Id: <199811221027.FAA21006@io.ECE.Drexel.EDU> 1. Corel Draw has a very nice bectorization program 2. Arc/Info has it's own vectorization program. ------------------------------ Date: Sun, 22 Nov 1998 17:00:07 +0100 From: olivier bricaud To: nih-image@io.ece.drexel.edu Subject: Stereo-4D macros Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hello, Can you tell me, please where i can download the 4d-stereo macros for NIH image? Thanks a lot Olivier Olivier BRICAUD Laboratoire de Neurogntique du Dveloppement Universit des Sciences et Techniques du Languedoc CC 103 Place Eugne Bataillon F-34095 Montpellier Cedex 05 FRANCE Tel : (+33) (0)4 67 14 32 53 Fax : (+33) (0)4 67 14 39 28 E-mail : obricaud@crit.univ-montp2.fr URL: http://www.univ-montp2.fr/~neurodvpmt/ -------------------------------- End of nih-image-d Digest V98 Issue #122 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 23 09:43 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA11218; Mon, 23 Nov 1998 09:43:43 -0500 (EST) Resent-Date: Mon, 23 Nov 1998 09:43:43 -0500 (EST) Message-ID: <10B622A095EFD111BF7B00A0C98313F141C68E@pathem0.path.uab.edu> From: Margaret Amsler To: "'nih-image@biomed.drexel.edu'" Subject: dot blot imaging Date: Mon, 23 Nov 1998 08:20:19 -0600 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"QHtTr.0.2-1.XzMMs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/661 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1456 Hi! I am a new NIH Image user and a new reader of this group. I apologize in advance if this particular topic has been dealt with already. I am seeking advice for analyzing my dot blot results which reflect gene expression in a nuclear run-on experiment. The pertinent step in a run-on involves hybridizing radiolabeled RNA with DNA bound to a nytran membrane with a resulting dot blot. A typical experiment involves 6 treatment groups and each group has a maximum of 32 different DNA samples. The DNA samples are arranged on the membrane in 4 columns of 8 rows- all 6 strips bear the same samples. The hybridized 6 hot blots are placed on a sheet of 8x10" AR film for a time. The developed film consists of 6 blocks of 32 dots of varying intensity based on the amount of hybridization/expression/signal. The film is scanned using HP Desk Scan II. I am trying to use Scion Image to then analyze the varying intensities. I am using a gelblot macro but find it extremely laborious. I can only get it to work if I assign a single column as 'lane 1' at a time. This way there are 24 lanes with 8 curves each 'wand adjust'. Would you have any suggestions on how to make the process more efficient? Could I analyze each strip of 32 dots at once or even better all 6 strips at once? Is there a macro for reading a 96 well plate?? Essentially my dots can be thought of as two 96 well plates. Thanks much for any assistance! Maggie Amsler From nih-image-request@io.ece.drexel.edu Mon Nov 23 18:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA07120; Mon, 23 Nov 1998 18:19:56 -0500 (EST) Resent-Date: Mon, 23 Nov 1998 18:19:56 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 23 Nov 1998 23:48:09 +0100 To: nih-image@io.ece.drexel.edu From: Donna Arndt-Jovin Resent-Message-ID: <"OavBe3.0.vv.6PUMs"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/662 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 227 set nih-image mail postpone Donna Arndt-Jovin MPI for Biophysical Chemistry Dept. of Molecular Biology Am Fassberg D-37070 Goettingen, Germany tel: +49-551-201-1393 fax: +49-551-201-1467 e-mail: djovin@mpc186.mpibpc.gwdg.de From nih-image-d-request@io.ece.drexel.edu Tue Nov 24 06:34 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24638; Tue, 24 Nov 1998 06:34:01 -0500 (EST) Date: Tue, 24 Nov 1998 06:34:01 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811241134.GAA24638@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #123 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/123 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3534 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 123 Today's Topics: dot blot imaging [ Margaret Amsler To: "'nih-image@biomed.drexel.edu'" Subject: dot blot imaging Message-ID: <10B622A095EFD111BF7B00A0C98313F141C68E@pathem0.path.uab.edu> Content-Type: text/plain Hi! I am a new NIH Image user and a new reader of this group. I apologize in advance if this particular topic has been dealt with already. I am seeking advice for analyzing my dot blot results which reflect gene expression in a nuclear run-on experiment. The pertinent step in a run-on involves hybridizing radiolabeled RNA with DNA bound to a nytran membrane with a resulting dot blot. A typical experiment involves 6 treatment groups and each group has a maximum of 32 different DNA samples. The DNA samples are arranged on the membrane in 4 columns of 8 rows- all 6 strips bear the same samples. The hybridized 6 hot blots are placed on a sheet of 8x10" AR film for a time. The developed film consists of 6 blocks of 32 dots of varying intensity based on the amount of hybridization/expression/signal. The film is scanned using HP Desk Scan II. I am trying to use Scion Image to then analyze the varying intensities. I am using a gelblot macro but find it extremely laborious. I can only get it to work if I assign a single column as 'lane 1' at a time. This way there are 24 lanes with 8 curves each 'wand adjust'. Would you have any suggestions on how to make the process more efficient? Could I analyze each strip of 32 dots at once or even better all 6 strips at once? Is there a macro for reading a 96 well plate?? Essentially my dots can be thought of as two 96 well plates. Thanks much for any assistance! Maggie Amsler ------------------------------ Date: Mon, 23 Nov 1998 15:19:51 -0500 From: "Mehmet Dondurur, Ph. D." To: "'nih-image-d@io.ece.drexel.edu'" Subject: Slice construction Message-ID: <69B43248FE73D11197BB00A0C99AB0678996@jvcserver.vanguardweb.org> Content-Type: text/plain Hi to all, Is there any macro to construct a CT slice from given two slices? Basically, You have two cross sectional CT slices (slice1 and 2).By using slice 1 and 2, I would like to create 3rd slice in between slice 1 and 2 by interpolation or other methods. Is this possible with NIH or other programs. Many thanks for any suggestion. Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Mon, 23 Nov 1998 23:48:09 +0100 From: Donna Arndt-Jovin To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" set nih-image mail postpone Donna Arndt-Jovin MPI for Biophysical Chemistry Dept. of Molecular Biology Am Fassberg D-37070 Goettingen, Germany tel: +49-551-201-1393 fax: +49-551-201-1467 e-mail: djovin@mpc186.mpibpc.gwdg.de -------------------------------- End of nih-image-d Digest V98 Issue #123 **************************************** From nih-image-request@io.ece.drexel.edu Tue Nov 24 10:59 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22775; Tue, 24 Nov 1998 10:59:30 -0500 (EST) Resent-Date: Tue, 24 Nov 1998 10:59:30 -0500 (EST) Date: Tue, 24 Nov 1998 15:23:23 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: Canny edge detector Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"vTYad.0.se4.B_iMs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/663 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 270 Dear all, has anybody implemented the Canny edge detector in NIH-Image already? TIA, Jan. Jan Kreft Phone +44 (0)1222 876036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK From nih-image-request@io.ece.drexel.edu Tue Nov 24 14:55 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA16639; Tue, 24 Nov 1998 14:55:50 -0500 (EST) Resent-Date: Tue, 24 Nov 1998 14:55:50 -0500 (EST) X-Sender: d306604@nobel.si.uqam.ca Message-Id: Mime-Version: 1.0 Date: Tue, 24 Nov 1998 14:29:58 -0500 To: Nih mailing list From: Dominique Berube Subject: Convex Hull Resent-Message-ID: <"jMHLi.0.RP3.IdmMs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/664 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 336 Hello all, I searched the archives about a possible convex hull macro. I found code to implement directly into the program (from manuel Urrutia Avisrror)but I would rather stay with the macros. I think that some work was done but I couldn't find anything usable in the archives or the ftp site. Anyone knows something? Thank you. From nih-image-d-request@io.ece.drexel.edu Wed Nov 25 06:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23337; Wed, 25 Nov 1998 06:20:36 -0500 (EST) Date: Wed, 25 Nov 1998 06:20:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811251120.GAA23337@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #124 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/124 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1565 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 124 Today's Topics: Canny edge detector [ Jan Kreft ] Convex Hull [ Dominique Berube To: nih-image@io.ece.drexel.edu Subject: Canny edge detector Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, has anybody implemented the Canny edge detector in NIH-Image already? TIA, Jan. Jan Kreft Phone +44 (0)1222 876036 Cardiff School of Biosciences Fax +44 (0)1222 874305 Cardiff University E-mail Kreft@cardiff.ac.uk PO Box 915, Cardiff CF1 3TL, UK ------------------------------ Date: Tue, 24 Nov 1998 14:29:58 -0500 From: Dominique Berube To: Nih mailing list Subject: Convex Hull Message-Id: Content-Type: text/plain; charset="us-ascii" Hello all, I searched the archives about a possible convex hull macro. I found code to implement directly into the program (from manuel Urrutia Avisrror)but I would rather stay with the macros. I think that some work was done but I couldn't find anything usable in the archives or the ftp site. Anyone knows something? Thank you. -------------------------------- End of nih-image-d Digest V98 Issue #124 **************************************** From nih-image-request@io.ece.drexel.edu Wed Nov 25 08:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05820; Wed, 25 Nov 1998 08:15:08 -0500 (EST) Resent-Date: Wed, 25 Nov 1998 08:15:08 -0500 (EST) Message-Id: In-Reply-To: <199811221027.FAA21006@io.ECE.Drexel.EDU> Mime-Version: 1.0 Date: Wed, 25 Nov 1998 13:59:28 +0100 To: nih-image@io.ece.drexel.edu From: "Nuria Teixido" Subject: Corel Draw Resent-Message-ID: <"MNLfT3.0.jp.Nt_Ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/665 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 623 Hello, This is the student who sent a message to NIH group to ask for the possibility to convert raster to vector modul. We have Corel Draw 7.0 and OCR-TRACE (in German) and maybe makes me to go slowly in solving the step. I have been trying to import the images and convert them to vector with bitmaps vectorization but it didn't work. I really would be very gratefull if you could say me something more about the process. Thank you, Nuria Nuria Teixido Alfred-Wegener-Institut Columbusstrasse 27568 Bremerhaven Deutschland Tel. Nr. 00-49-471-4831-319 Fax. Nr. 00-49-471-4831-149 e-mail:nteixido@awi-bremerhaven.de From nih-image-request@io.ece.drexel.edu Wed Nov 25 18:13 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA27368; Wed, 25 Nov 1998 18:13:12 -0500 (EST) Resent-Date: Wed, 25 Nov 1998 18:13:12 -0500 (EST) From: Lynn_N_Li@notes.seagate.com X-Lotus-FromDomain: SEAGATE@INTERNET To: nih-image@io.ece.drexel.edu Message-ID: <882566C7.007D84B2.00@sv-gw1.stsv.seagate.com> Date: Wed, 25 Nov 1998 16:50:37 -0600 Subject: MFM data import Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"bIWYW2.0.SC6.Cf8Ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/666 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 419 I am new to NIH-image. I have downloaded a PC version Scion Image to do some off-line analysis of the MFM image by Digital Intruments' D 3000 microscope. when I go to menu File-Import-custom, I need to skip a 8192 bytes header and a 512by 512 AFM image, which totals 270336 bytes. But the offset option will not allow me to put in any number larger than 99999 bytes. So what should I do to get around it? thank you From nih-image-request@io.ece.drexel.edu Wed Nov 25 20:37 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA11523; Wed, 25 Nov 1998 20:37:06 -0500 (EST) Resent-Date: Wed, 25 Nov 1998 20:37:06 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: Lynn_N_Li@notes.seagate.com, nih-image@io.ece.drexel.edu Date: Thu, 26 Nov 1998 12:27:38 GMT+1100 Subject: Re: MFM data import Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <2F525975CEA@rna.bio.mq.edu.au> Resent-Message-ID: <"-55g93.0.NS2.FtANs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/667 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1752 >From: Lynn_N_Li@notes.seagate.com >To: nih-image@io.ece.drexel.edu >Date: Wed, 25 Nov 1998 16:50:37 -0600 >Subject: MFM data import > >I am new to NIH-image. I have downloaded a PC version Scion Image to do >some off-line analysis of the MFM image by Digital Intruments' D 3000 >microscope. >when I go to menu File-Import-custom, I need to skip a 8192 bytes header >and a 512by 512 AFM image, which totals 270336 bytes. But the offset option >will not allow me to put in any number larger than 99999 bytes. So what >should I do to get around it? > Lynn, The Mac NIH-Image doesnt have that restriction on data entry to setCustom for Import. :-) I would expect (I haven't tested this on PC version) that the macro interface would not face the same user interface problem. The following macro can used to import mid slices from very large TIFF(header=768) stacks (on the Mac). Changeing or overriding the default width,height,offset and using fromSlice=2 should work for you. macro'[F9] Import slices from stack'; var width,height,offset,fromSlice,slices:integer; begin width:=256;height:=256; offset:=768;{Tiff header} fromSlice:=1;slices:=1; width:=getNumber('width',width); height:=getNumber('height',height); offset:=getNumber('offset',offset); fromSlice:=getNumber('fromSlice',fromSlice); slices:=getNumber('slices',slices); showMessage ('\width',width ,'\height',height ,'\offset',offset ,'\fromSlice',fromSlice ,'\slices',slices ); SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); Import(''); {invokes user dialogue for file} end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-d-request@io.ece.drexel.edu Thu Nov 26 06:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14979; Thu, 26 Nov 1998 06:19:32 -0500 (EST) Date: Thu, 26 Nov 1998 06:19:32 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811261119.GAA14979@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #125 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/125 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4062 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 125 Today's Topics: Corel Draw [ "Nuria Teixido" To: nih-image@io.ece.drexel.edu Subject: Corel Draw Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, This is the student who sent a message to NIH group to ask for the possibility to convert raster to vector modul. We have Corel Draw 7.0 and OCR-TRACE (in German) and maybe makes me to go slowly in solving the step. I have been trying to import the images and convert them to vector with bitmaps vectorization but it didn't work. I really would be very gratefull if you could say me something more about the process. Thank you, Nuria Nuria Teixido Alfred-Wegener-Institut Columbusstrasse 27568 Bremerhaven Deutschland Tel. Nr. 00-49-471-4831-319 Fax. Nr. 00-49-471-4831-149 e-mail:nteixido@awi-bremerhaven.de ------------------------------ Date: Wed, 25 Nov 1998 16:50:37 -0600 From: Lynn_N_Li@notes.seagate.com To: nih-image@io.ece.drexel.edu Subject: MFM data import Message-ID: <882566C7.007D84B2.00@sv-gw1.stsv.seagate.com> Content-type: text/plain; charset=us-ascii Content-Disposition: inline I am new to NIH-image. I have downloaded a PC version Scion Image to do some off-line analysis of the MFM image by Digital Intruments' D 3000 microscope. when I go to menu File-Import-custom, I need to skip a 8192 bytes header and a 512by 512 AFM image, which totals 270336 bytes. But the offset option will not allow me to put in any number larger than 99999 bytes. So what should I do to get around it? thank you ------------------------------ Date: Thu, 26 Nov 1998 12:27:38 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: Lynn_N_Li@notes.seagate.com, nih-image@io.ece.drexel.edu Subject: Re: MFM data import Message-ID: <2F525975CEA@rna.bio.mq.edu.au> >From: Lynn_N_Li@notes.seagate.com >To: nih-image@io.ece.drexel.edu >Date: Wed, 25 Nov 1998 16:50:37 -0600 >Subject: MFM data import > >I am new to NIH-image. I have downloaded a PC version Scion Image to do >some off-line analysis of the MFM image by Digital Intruments' D 3000 >microscope. >when I go to menu File-Import-custom, I need to skip a 8192 bytes header >and a 512by 512 AFM image, which totals 270336 bytes. But the offset option >will not allow me to put in any number larger than 99999 bytes. So what >should I do to get around it? > Lynn, The Mac NIH-Image doesnt have that restriction on data entry to setCustom for Import. :-) I would expect (I haven't tested this on PC version) that the macro interface would not face the same user interface problem. The following macro can used to import mid slices from very large TIFF(header=768) stacks (on the Mac). Changeing or overriding the default width,height,offset and using fromSlice=2 should work for you. macro'[F9] Import slices from stack'; var width,height,offset,fromSlice,slices:integer; begin width:=256;height:=256; offset:=768;{Tiff header} fromSlice:=1;slices:=1; width:=getNumber('width',width); height:=getNumber('height',height); offset:=getNumber('offset',offset); fromSlice:=getNumber('fromSlice',fromSlice); slices:=getNumber('slices',slices); showMessage ('\width',width ,'\height',height ,'\offset',offset ,'\fromSlice',fromSlice ,'\slices',slices ); SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); Import(''); {invokes user dialogue for file} end Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia -------------------------------- End of nih-image-d Digest V98 Issue #125 **************************************** From nih-image-request@io.ece.drexel.edu Thu Nov 26 10:00 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA09139; Thu, 26 Nov 1998 10:00:03 -0500 (EST) Resent-Date: Thu, 26 Nov 1998 10:00:03 -0500 (EST) Message-Id: <3.0.6.32.19981126094100.007b6e70@po-box.mcgill.ca> X-Sender: mayoub@po-box.mcgill.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 26 Nov 1998 09:41:00 -0500 To: nih-image@io.ece.drexel.edu From: Micheline Ayoub Subject: unsubscribe Mime-Version: 1.0 Resent-Message-ID: <"RU_MX1.0.Hj1.2ZMNs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/668 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 181 Micheline Ayoub Plant Science Dpt. R2-004 Macdoanld Campus McGill University 21111 Lakeshore Rd. Ste-Anne-de-Bellevue, Quebec H9X 3V9 Tel: 514-398-7851 ext 8733 Fax: 514-398-7897 From nih-image-d-request@io.ece.drexel.edu Fri Nov 27 03:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA16222; Fri, 27 Nov 1998 03:18:57 -0500 (EST) Date: Fri, 27 Nov 1998 03:18:57 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811270818.DAA16222@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #126 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/126 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1167 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 126 Today's Topics: unsubscribe [ Micheline Ayoub To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.6.32.19981126094100.007b6e70@po-box.mcgill.ca> Content-Type: text/plain; charset="us-ascii" Micheline Ayoub Plant Science Dpt. R2-004 Macdoanld Campus McGill University 21111 Lakeshore Rd. Ste-Anne-de-Bellevue, Quebec H9X 3V9 Tel: 514-398-7851 ext 8733 Fax: 514-398-7897 ------------------------------ Date: Fri, 27 Nov 1998 08:59:04 +0100 From: "Thorsen, Anders" To: "'nih-image@io.ece.drexel.edu'" Subject: unsubscribe Message-ID: Content-Type: text/plain unsubscribe -------------------------------- End of nih-image-d Digest V98 Issue #126 **************************************** From nih-image-request@io.ece.drexel.edu Fri Nov 27 03:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA16235; Fri, 27 Nov 1998 03:18:59 -0500 (EST) Resent-Date: Fri, 27 Nov 1998 03:18:59 -0500 (EST) Message-ID: From: "Thorsen, Anders" To: "'nih-image@io.ece.drexel.edu'" Subject: unsubscribe Date: Fri, 27 Nov 1998 08:59:04 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1460.8) Resent-Message-ID: <"76K7q.0.1O3.YlbNs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/669 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Fri Nov 27 04:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA21652; Fri, 27 Nov 1998 04:07:04 -0500 (EST) Resent-Date: Fri, 27 Nov 1998 04:07:04 -0500 (EST) Message-Id: <3.0.5.32.19981127185403.007b6dd0@email.aims.gov.au> X-Sender: aburja@email.aims.gov.au X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 27 Nov 1998 18:54:03 +1000 To: nih-image@io.ece.drexel.edu From: Adam Burja Subject: unsubscribe Mime-Version: 1.0 Resent-Message-ID: <"yjDGw2.0.nw4.zYcNs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/670 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1 From nih-image-request@io.ece.drexel.edu Fri Nov 27 21:37 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA04679; Fri, 27 Nov 1998 21:37:00 -0500 (EST) Resent-Date: Fri, 27 Nov 1998 21:37:00 -0500 (EST) From: wpchan@socrates.berkeley.edu Date: Fri, 27 Nov 1998 18:25:09 -0800 (PST) To: nih-image@io.ece.drexel.edu Subject: Re: video capture at 30 fps In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"e_1JM1.0.rj.FyrNs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/671 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 719 We have just got a G3/333 with 768MB of RAM running MacOS 8.5. Even with Virtual Memory and File Sharing off, with Scion-Image 1.62 and the Scion LG-3, I can only get 29.97 frames per sec at 592x457 but not at 640x480, using 'make movie' with blind capture. I tried turning off a lot of the extensions but still no improvement. What have I done wrong? Any advice are appreciated. Thanks. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Sun, 1 Nov 1998 wpchan@socrates.berkeley.edu wrote: > On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make > movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive > 29.97 frames per sec at 640x480. The timing is right on the money. From nih-image-d-request@io.ece.drexel.edu Fri Nov 27 21:37 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA04789; Fri, 27 Nov 1998 21:37:36 -0500 (EST) Date: Fri, 27 Nov 1998 21:37:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811280237.VAA04789@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #127 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/127 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1676 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 127 Today's Topics: unsubscribe [ Adam Burja ] Re: video capture at 30 fps [ wpchan@socrates.berkeley.edu ] ------------------------------ Date: Fri, 27 Nov 1998 18:54:03 +1000 From: Adam Burja To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.5.32.19981127185403.007b6dd0@email.aims.gov.au> Content-Type: text/plain; charset="us-ascii" ------------------------------ Date: Fri, 27 Nov 1998 18:25:09 -0800 (PST) From: wpchan@socrates.berkeley.edu To: nih-image@io.ece.drexel.edu Subject: Re: video capture at 30 fps Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII We have just got a G3/333 with 768MB of RAM running MacOS 8.5. Even with Virtual Memory and File Sharing off, with Scion-Image 1.62 and the Scion LG-3, I can only get 29.97 frames per sec at 592x457 but not at 640x480, using 'make movie' with blind capture. I tried turning off a lot of the extensions but still no improvement. What have I done wrong? Any advice are appreciated. Thanks. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Sun, 1 Nov 1998 wpchan@socrates.berkeley.edu wrote: > On the Mac, a 9500/132 with 90 MB of RAM and ATI graphic card, 'make > movie' with blind capture in NIH-Image 1.61 (NTSC) can easily archive > 29.97 frames per sec at 640x480. The timing is right on the money. -------------------------------- End of nih-image-d Digest V98 Issue #127 **************************************** From nih-image-request@io.ece.drexel.edu Sat Nov 28 11:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26297; Sat, 28 Nov 1998 11:19:44 -0500 (EST) Resent-Date: Sat, 28 Nov 1998 11:19:44 -0500 (EST) Mime-Version: 1.0 X-Sender: pauln@maine.maine.edu Message-Id: Date: Sat, 28 Nov 1998 11:08:34 -0500 To: nih-image@io.ece.drexel.edu From: Paul Nakroshis Subject: ATI XClaim VR Resent-Message-ID: <"XEus4.0.J56.902Os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/672 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" ; format="flowed" Content-Length: 562 Hello, is there some trick to get NIH-Image to recognize the ATI XClaim VR graphics card? Perhaps some plugin needed? I am running Image on a powermac 9600/233 with 128 MB ram. -paul ================================================================= Paul Nakroshis pauln@usm.maine.edu Department of Physics 207.780.4158 (OFFICE) Room 252 Science Building 207.780.5607 (FAX) University of Southern Maine PO Box 9300 Portland, ME 04104-9300 ================================================================= From nih-image-d-request@io.ece.drexel.edu Sun Nov 29 06:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14060; Sun, 29 Nov 1998 06:11:21 -0500 (EST) Date: Sun, 29 Nov 1998 06:11:21 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811291111.GAA14060@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #128 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/128 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2627 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 128 Today's Topics: 3-D Newborn Skull ? [ "Corrina Cory" To: nih-image-d@io.ece.drexel.edu Subject: 3-D Newborn Skull ? Message-ID: <6D37FAF7F08@NPRDCF1S.CF.AC.UK> Hello, I know that many human bones and organs have been scanned using MRI or CT and this information has been used to make a representative 3-D model by stacking the slices. I am looking for a 3-D model of a newborn babies skull. If anyone knows if this has already been done I would appreciate it if you could e-mail any details of the model or any ideas of other contacts that may have this information. Is it relatively simple to use NIH Image to import the MRI files and create a 3-D image?. I have checked the archives but although there is some information on MRI scans I need more basic information like where do I start? Is it as simple as saving the raw MRI data in a particular format, opening it in NIH Image with a bit of manipulation to get the 3-D Image or is it very time consuming? Thanks for your help Corrina Cory ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Corrina Cory BEng MPhil PhD Research Forensic Bioengineering Medical Engineering Research Unit UWCC The Parade PO Box 688 Cardiff CF2 3TE WALES, UK Tel +44(0) 1222 875926 Fax +44(0) 1222 874533 E-mail Cory@Cardiff.ac.uk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ------------------------------ Date: Sat, 28 Nov 1998 11:08:34 -0500 From: Paul Nakroshis To: nih-image@io.ece.drexel.edu Subject: ATI XClaim VR Message-Id: Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hello, is there some trick to get NIH-Image to recognize the ATI XClaim VR graphics card? Perhaps some plugin needed? I am running Image on a powermac 9600/233 with 128 MB ram. -paul ================================================================= Paul Nakroshis pauln@usm.maine.edu Department of Physics 207.780.4158 (OFFICE) Room 252 Science Building 207.780.5607 (FAX) University of Southern Maine PO Box 9300 Portland, ME 04104-9300 ================================================================= -------------------------------- End of nih-image-d Digest V98 Issue #128 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 30 00:03 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA26791; Mon, 30 Nov 1998 00:03:08 -0500 (EST) Resent-Date: Mon, 30 Nov 1998 00:03:08 -0500 (EST) Date: Sun, 29 Nov 1998 23:40:37 -0500 (EST) From: nih-image-request@io.ece.drexel.edu Message-Id: <199811300440.XAA24270@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe References: <199811300440.XAA06258@kanga.INS.CWRU.Edu> In-Reply-To: <199811300440.XAA06258@kanga.INS.CWRU.Edu> X-Loop: nih-image@biomed.drexel.edu Resent-Message-ID: <"Ew6tl2.0.Xx5.F7YOs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/673 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1122 WARNING: Please try to use 'nih-image-request@biomed.drexel.edu' the next time when issuing (un)subscribe requests. 32760 nbd@po.CWRU.Edu nbd@po.CWRU.Edu You have been removed from the list. If this wasn't your intention or you are having problems getting yourself unsubscribed, reply to this mail now (quoting it entirely (for diagnostic purposes), and of course adding any comments you see fit). Transcript of unsubscription request follows: -- >From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) > by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 > for ; Sun, 29 Nov 1998 23:40:33 -0500 (EST) >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) > id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) >From: nbd@po.CWRU.Edu (Nagendu B. Dev) >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe >Reply-To: nih-image@io.ece.drexel.edu > >### > From nih-image-request@io.ece.drexel.edu Mon Nov 30 15:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA17920; Mon, 30 Nov 1998 15:06:28 -0500 (EST) Resent-Date: Mon, 30 Nov 1998 15:06:28 -0500 (EST) Date: Mon, 30 Nov 1998 11:42:08 -0800 (PST) From: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe In-Reply-To: <199811300440.XAA24270@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"l0wUS2.0.3y3.QKlOs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/674 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1495 I'm not sure if this was meant for me, since it seems to be addressed to the whole list. However, I do *not* want to be removed from the list, and I haven't sent anything suggesting I do. Please leave me on the list. Thanks. Lesley Weston. On Sun, 29 Nov 1998 nih-image-request@io.ece.drexel.edu wrote: > WARNING: > Please try to use 'nih-image-request@biomed.drexel.edu' > the next time when issuing (un)subscribe requests. > > 32760 nbd@po.CWRU.Edu > nbd@po.CWRU.Edu > > You have been removed from the list. > > If this wasn't your intention or you are having problems getting yourself > unsubscribed, reply to this mail now (quoting it entirely (for diagnostic > purposes), and of course adding any comments you see fit). > > Transcript of unsubscription request follows: > -- > >From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 > >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) > > by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 > > for ; Sun, 29 Nov 1998 23:40:33 -0500 (EST) > >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) > > id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) > >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> > >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) > >From: nbd@po.CWRU.Edu (Nagendu B. Dev) > >To: nih-image@io.ece.drexel.edu > >Subject: unsubscribe > >Reply-To: nih-image@io.ece.drexel.edu > > > >### > > > > From nih-image-d-request@io.ece.drexel.edu Mon Nov 30 15:12 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA18365; Mon, 30 Nov 1998 15:12:32 -0500 (EST) Date: Mon, 30 Nov 1998 15:12:32 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199811302012.PAA18365@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #129 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/129 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5474 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 129 Today's Topics: Re: unsubscribe [ nih-image-request@io.ece.drexel.edu ] Scale And Rotate [ wgr2@cus.cam.ac.uk (Dr Gareth Rees) ] Re: unsubscribe [ Lesley Weston WARNING: Please try to use 'nih-image-request@biomed.drexel.edu' the next time when issuing (un)subscribe requests. 32760 nbd@po.CWRU.Edu nbd@po.CWRU.Edu You have been removed from the list. If this wasn't your intention or you are having problems getting yourself unsubscribed, reply to this mail now (quoting it entirely (for diagnostic purposes), and of course adding any comments you see fit). Transcript of unsubscription request follows: -- >From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) > by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 > for ; Sun, 29 Nov 1998 23:40:33 -0500 (EST) >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) > id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) >From: nbd@po.CWRU.Edu (Nagendu B. Dev) >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe >Reply-To: nih-image@io.ece.drexel.edu > >### > ------------------------------ Date: Mon, 30 Nov 1998 09:34:23 +0000 From: wgr2@cus.cam.ac.uk (Dr Gareth Rees) To: nih-image-d@io.ece.drexel.edu Subject: Scale And Rotate Message-Id: Content-Type: text/plain; charset="us-ascii" Hello imagers, I have a problem using the ScaleAndRotate operation from within macros. I am trying to write a macro to perform a known linear transformation on data (change of scale, offset, plus skew), for which I need to use the ScaleAndRotate operation. My problem is that I do not know how to predict the effect of issuing the command ScaleAndRotate(1,1,theta). In general, this produces an image in which the new x' and y' coordinates are given in terms of the old ones by x' = x cos(theta) - y sin(theta) + a y' = x sin(theta) + y cos(theta) + b, but my problem is to know how Image chooses the values of a and b. In other words, which pixel in the image will NOT have its position changed by this operation? SOMETIMES, it is the pixel at ((w-1)/2,(h-1)/2), where w and h are the width and height of the image respectively - but not always. Has anyone out there got experience of this problem, and more importantly, its solution? Gareth Rees ___________________________________________________________________________ Dr W Gareth Rees Telephone 01223 336540 Remote Sensing Group International +44 1223 336540 Scott Polar Research Institute Facsimile 01223 336549 Lensfield Road International +44 1223 336549 Cambridge CB2 1ER Direct line (voice, fax, United Kingdom answer machine) 336575 ___________________________________________________________________________ ------------------------------ Date: Mon, 30 Nov 1998 11:42:08 -0800 (PST) From: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I'm not sure if this was meant for me, since it seems to be addressed to the whole list. However, I do *not* want to be removed from the list, and I haven't sent anything suggesting I do. Please leave me on the list. Thanks. Lesley Weston. On Sun, 29 Nov 1998 nih-image-request@io.ece.drexel.edu wrote: > WARNING: > Please try to use 'nih-image-request@biomed.drexel.edu' > the next time when issuing (un)subscribe requests. > > 32760 nbd@po.CWRU.Edu > nbd@po.CWRU.Edu > > You have been removed from the list. > > If this wasn't your intention or you are having problems getting yourself > unsubscribed, reply to this mail now (quoting it entirely (for diagnostic > purposes), and of course adding any comments you see fit). > > Transcript of unsubscription request follows: > -- > >From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 > >Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) > > by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 > > for ; Sun, 29 Nov 1998 23:40:33 -0500 (EST) > >Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) > > id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) > >Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> > >Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) > >From: nbd@po.CWRU.Edu (Nagendu B. Dev) > >To: nih-image@io.ece.drexel.edu > >Subject: unsubscribe > >Reply-To: nih-image@io.ece.drexel.edu > > > >### > > > > -------------------------------- End of nih-image-d Digest V98 Issue #129 **************************************** From nih-image-request@io.ece.drexel.edu Mon Nov 30 17:52 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA01669; Mon, 30 Nov 1998 17:52:05 -0500 (EST) Resent-Date: Mon, 30 Nov 1998 17:52:05 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 30 Nov 1998 14:20:57 -0700 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: A reminder about unsubscribing Resent-Message-ID: <"9VKPe2.0.pz6.VdnOs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/675 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/enriched; charset="us-ascii" Content-Length: 1186 CourierTo unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe note this address differs from the discussion address. ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Tue Dec 1 01:51 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA16695; Tue, 1 Dec 1998 01:51:14 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 01:51:14 -0500 (EST) X-Sender: eilamt@post Message-Id: Mime-Version: 1.0 Date: Tue, 1 Dec 1998 08:29:07 +0200 To: nih-image@io.ece.drexel.edu From: eilamt@post.tau.ac.il (Tamar Eilam) Subject: Re: unsubscribe Resent-Message-ID: <"MFVFC1.0.VU3.vouOs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/676 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1324 >WARNING: > Please try to use 'nih-image-request@biomed.drexel.edu' > the next time when issuing (un)subscribe requests. > > 32760 nbd@po.CWRU.Edu >nbd@po.CWRU.Edu > >You have been removed from the list. > >If this wasn't your intention or you are having problems getting yourself >unsubscribed, reply to this mail now (quoting it entirely (for diagnostic >purposes), and of course adding any comments you see fit). > >Transcript of unsubscription request follows: >-- >>From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 >>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) >> by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 >> for ; Sun, 29 Nov 1998 23:40:33 -0500 >>(EST) >>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) >> id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) >>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> >>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) >>From: nbd@po.CWRU.Edu (Nagendu B. Dev) >>To: nih-image@io.ece.drexel.edu >>Subject: unsubscribe >>Reply-To: nih-image@io.ece.drexel.edu >> >>### >> I do *not* want to be removed from the list, and I haven't sent anything suggesting I do. Please leave me on the list. Thanks Tamar Eilam From nih-image-request@io.ece.drexel.edu Tue Dec 1 07:31 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA22359; Tue, 1 Dec 1998 07:31:44 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 07:31:44 -0500 (EST) X-Authentication-Warning: mail.bio.uva.nl: Host gold.bio.uva.nl [145.18.160.48] claimed to be [145.18.160.48] Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 1 Dec 1998 13:16:47 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Exchanging 640 MB MO media between Mac and PC Resent-Message-ID: <"cL5VI2.0.Wv4.TqzOs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/677 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 763 We want to exchange magneto-optical media between Macs and the PC which controls our confocal microscope (a Zeiss 510). On both machines, a 640MB MO drive is hooked up, but I don't succeed to interchange the media. When I format a cartridge on the Mac in "PC-format", the PC refuses it. My questions are: has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? What is the difference between "D" and "F" cartridges? Norbert Vischer Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html From nih-image-request@io.ece.drexel.edu Tue Dec 1 08:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA28155; Tue, 1 Dec 1998 08:26:40 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 08:26:40 -0500 (EST) Message-Id: In-Reply-To: References: Mime-Version: 1.0 Date: Tue, 1 Dec 1998 08:09:15 -0500 To: nih-image@io.ece.drexel.edu From: yip@ibme.utoronto.ca (Christopher Yip) Subject: Re: Exchanging 640 MB MO media between Mac and PC Resent-Message-ID: <"xvumk1.0.DM6.Je-Os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/678 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1508 >We want to exchange magneto-optical media between Macs and the PC which >controls our confocal microscope (a Zeiss 510). On both machines, a 640MB >MO drive is hooked up, but I don't succeed to interchange the media. When I >format a cartridge on the Mac in "PC-format", the PC refuses it. > >My questions are: >has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? >What is the difference between "D" and "F" cartridges? >Norbert Vischer > > >Norbert Vischer University of Amsterdam >Scientific engineer Molecular Cell Biology > Kruislaan 316 >tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam >e-mail: vischer@bio.uva.nl The Netherlands >http://simon.bio.uva.nl/object-image.html I've had no problems with 230 MB MO disks - what I usually do is use the PC to format them if I want a DOS-formatted version and then use Software Architect's DOS Mounter on my Macs to see them. (I'm assuming that MacOS's PC Exchange will also work). Never tried it with the 640 MB MO's though. Chris. Christopher M. Yip, Ph.D., P.Eng. Assistant Professor Department of Chemical Engineering and Applied Chemistry Institute of Biomaterials and Biomedical Engineering Department of Biochemistry University of Toronto 407 Rosebrugh Building, 4 Taddle Creek Rd. Toronto, Ontario CANADA M5S 3G9 Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317; e-mail: yip@ibme.utoronto.ca WWW: http://goldie.ibme.utoronto.ca From nih-image-request@io.ece.drexel.edu Tue Dec 1 08:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA28349; Tue, 1 Dec 1998 08:28:10 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 08:28:10 -0500 (EST) Message-ID: <3663E636.CABCA198@soton.ac.uk> Date: Tue, 01 Dec 1998 12:50:59 +0000 From: Ashley Pringle Organization: Clinical Neurological Sciences X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"L5e2a3.0.cN6.ge-Os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/679 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Length: 348 We have had the same problem for several years and have never been successful in solving. In the end we gave up, bought a CD writer, and wrote the MAC TIFF files in an ISO9660 format, which is readable across both platforms. Ashley Pringle Research Fellow Dept Clinical Neurological Sciences University of Southampton email: akp1@soton.ac.uk From nih-image-request@io.ece.drexel.edu Tue Dec 1 09:03 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA01982; Tue, 1 Dec 1998 09:03:38 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 09:03:38 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC In-Reply-To: <3663E636.CABCA198@soton.ac.uk> Message-ID: Date: Tue, 1 Dec 1998 13:44:41 +0000 (GMT Standard Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"qcgN1.0.ND7.P7_Os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/680 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 1171 Along the same lines of interchanging image files between PC and Mac: We have a HP CD writer attached to a PC. We copy the images from the Mac onto our server and then write them to a CD in an ISO9660 format. However, we have had some problems: 1) Although we can see long names on the PC they get conveted to 8 characters with a ~ symbol so I can not see the names correctly on the Mac. I am using adaptec software and have not yet found any options for defining long file names in the software. 2) Another thing that I have noticed is that on write only CD's, on which files have been added at different times, sometimes Explorer will only see one of the folders. If I eject and then reinsert the disc I might get a folder that was added at another time but not all of the folders. I guess to avoid this the trick is only to write once and then go onto another CD. ---------------------- Paul Stoodley Environmental Tel: 01392 264348 Microbiology Fax: 01392 263700 Research email: p.stoodley@exeter.ac.uk Group Exeter University Biological Sciences Hatherly Laboratories Prince of Wales Road Exeter EX4 4PS. UK. From nih-image-d-request@io.ece.drexel.edu Tue Dec 1 09:18 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA03425; Tue, 1 Dec 1998 09:18:33 -0500 (EST) Date: Tue, 1 Dec 1998 09:18:33 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812011418.JAA03425@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #130 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/130 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8885 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 130 Today's Topics: A reminder about unsubscribing [ Jonathan Nissanov ] Re: Exchanging 640 MB MO media betwe [ paul stoodley To: nih-image@io.ece.drexel.edu Subject: A reminder about unsubscribing Message-Id: Content-Type: text/enriched; charset="us-ascii" CourierTo unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. the Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe note this address differs from the discussion address. ------------------------------------------------------------------------------------------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ ------------------------------------------------------------------------------------------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------------------------------- ------------------------------ Date: Tue, 1 Dec 1998 08:29:07 +0200 From: eilamt@post.tau.ac.il (Tamar Eilam) To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" >WARNING: > Please try to use 'nih-image-request@biomed.drexel.edu' > the next time when issuing (un)subscribe requests. > > 32760 nbd@po.CWRU.Edu >nbd@po.CWRU.Edu > >You have been removed from the list. > >If this wasn't your intention or you are having problems getting yourself >unsubscribed, reply to this mail now (quoting it entirely (for diagnostic >purposes), and of course adding any comments you see fit). > >Transcript of unsubscription request follows: >-- >>From nbd@kanga.INS.CWRU.Edu Sun Nov 29 23:40:34 1998 >>Received: from kanga.INS.CWRU.Edu (nbd@kanga.INS.CWRU.Edu [129.22.8.32]) >> by io.ECE.Drexel.EDU (8.8.8/8.8.8) with ESMTP id XAA24235 >> for ; Sun, 29 Nov 1998 23:40:33 -0500 >>(EST) >>Received: (nbd@localhost) by kanga.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.5-bsdi) >> id XAA06258; Sun, 29 Nov 1998 23:40:25 -0500 (EST) (from nbd) >>Message-Id: <199811300440.XAA06258@kanga.INS.CWRU.Edu> >>Date: Sun, 29 Nov 1998 23:40:25 -0500 (EST) >>From: nbd@po.CWRU.Edu (Nagendu B. Dev) >>To: nih-image@io.ece.drexel.edu >>Subject: unsubscribe >>Reply-To: nih-image@io.ece.drexel.edu >> >>### >> I do *not* want to be removed from the list, and I haven't sent anything suggesting I do. Please leave me on the list. Thanks Tamar Eilam ------------------------------ Date: Tue, 1 Dec 1998 13:16:47 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Exchanging 640 MB MO media between Mac and PC Message-Id: Content-Type: text/plain; charset="us-ascii" We want to exchange magneto-optical media between Macs and the PC which controls our confocal microscope (a Zeiss 510). On both machines, a 640MB MO drive is hooked up, but I don't succeed to interchange the media. When I format a cartridge on the Mac in "PC-format", the PC refuses it. My questions are: has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? What is the difference between "D" and "F" cartridges? Norbert Vischer Norbert Vischer University of Amsterdam Scientific engineer Molecular Cell Biology Kruislaan 316 tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam e-mail: vischer@bio.uva.nl The Netherlands http://simon.bio.uva.nl/object-image.html ------------------------------ Date: Tue, 1 Dec 1998 08:09:15 -0500 From: yip@ibme.utoronto.ca (Christopher Yip) To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC Message-Id: Content-Type: text/plain; charset="us-ascii" >We want to exchange magneto-optical media between Macs and the PC which >controls our confocal microscope (a Zeiss 510). On both machines, a 640MB >MO drive is hooked up, but I don't succeed to interchange the media. When I >format a cartridge on the Mac in "PC-format", the PC refuses it. > >My questions are: >has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? >What is the difference between "D" and "F" cartridges? >Norbert Vischer > > >Norbert Vischer University of Amsterdam >Scientific engineer Molecular Cell Biology > Kruislaan 316 >tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam >e-mail: vischer@bio.uva.nl The Netherlands >http://simon.bio.uva.nl/object-image.html I've had no problems with 230 MB MO disks - what I usually do is use the PC to format them if I want a DOS-formatted version and then use Software Architect's DOS Mounter on my Macs to see them. (I'm assuming that MacOS's PC Exchange will also work). Never tried it with the 640 MB MO's though. Chris. Christopher M. Yip, Ph.D., P.Eng. Assistant Professor Department of Chemical Engineering and Applied Chemistry Institute of Biomaterials and Biomedical Engineering Department of Biochemistry University of Toronto 407 Rosebrugh Building, 4 Taddle Creek Rd. Toronto, Ontario CANADA M5S 3G9 Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317; e-mail: yip@ibme.utoronto.ca WWW: http://goldie.ibme.utoronto.ca ------------------------------ Date: Tue, 01 Dec 1998 12:50:59 +0000 From: Ashley Pringle To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC Message-ID: <3663E636.CABCA198@soton.ac.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit We have had the same problem for several years and have never been successful in solving. In the end we gave up, bought a CD writer, and wrote the MAC TIFF files in an ISO9660 format, which is readable across both platforms. Ashley Pringle Research Fellow Dept Clinical Neurological Sciences University of Southampton email: akp1@soton.ac.uk ------------------------------ Date: Tue, 1 Dec 1998 13:44:41 +0000 (GMT Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Along the same lines of interchanging image files between PC and Mac: We have a HP CD writer attached to a PC. We copy the images from the Mac onto our server and then write them to a CD in an ISO9660 format. However, we have had some problems: 1) Although we can see long names on the PC they get conveted to 8 characters with a ~ symbol so I can not see the names correctly on the Mac. I am using adaptec software and have not yet found any options for defining long file names in the software. 2) Another thing that I have noticed is that on write only CD's, on which files have been added at different times, sometimes Explorer will only see one of the folders. If I eject and then reinsert the disc I might get a folder that was added at another time but not all of the folders. I guess to avoid this the trick is only to write once and then go onto another CD. ---------------------- Paul Stoodley Environmental Tel: 01392 264348 Microbiology Fax: 01392 263700 Research email: p.stoodley@exeter.ac.uk Group Exeter University Biological Sciences Hatherly Laboratories Prince of Wales Road Exeter EX4 4PS. UK. -------------------------------- End of nih-image-d Digest V98 Issue #130 **************************************** From nih-image-request@io.ece.drexel.edu Tue Dec 1 13:03 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA20405; Tue, 1 Dec 1998 13:03:03 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 13:03:03 -0500 (EST) From: wpchan@socrates.berkeley.edu Date: Tue, 1 Dec 1998 09:21:40 -0800 (PST) X-Sender: wpchan@socrates To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"fSfVd2.0.eA4.mM2Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/681 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 912 We have recently brough a DynaMO 640. DOS mounter and Ringowin were bundled with it. The former allows us to use a PC formatted MO on the Mac and the latter lets us use Mac formatted MO on the PC. Both utilities also allow other cross-platform removables such as floppy or Syquest cart. to be mounted. The MO that we use are 2K-sector and formatted with the DynaMO supplied driver both on the Mac and on the PC. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Tue, 1 Dec 1998, Norbert Vischer wrote: > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. > > My questions are: > has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? From nih-image-request@io.ece.drexel.edu Tue Dec 1 14:48 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA29943; Tue, 1 Dec 1998 14:48:29 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 14:48:29 -0500 (EST) Message-Id: <9812011914.AA13359@ch1d2301nwk> Mime-Version: 1.0 (NeXT Mail 3.3 v124.8483.6) Content-Transfer-Encoding: 7bit X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3) From: Rand Dvorak Date: Tue, 1 Dec 98 13:14:33 -0600 To: nih-image@io.ece.drexel.edu Subject: SONY XC-77 CCD Camera modules for sale Resent-Message-ID: <"Wem8V2.0.LK6.sy3Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/682 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary=NeXT-Mail-1035837613-7 Content-Length: 1233 --NeXT-Mail-1035837613-7 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I have 6 Sony XC-77 ccd camera modules I would like to sell. The price is $100 per unit, a 50mm lens is also included in the price. You pay shipping by UPS, from zip code 60604. Call UPS and determine shipping from 60604 to your zip code. I can also ship COD if necessary. Please respond by e-mail to: Rand.Dvorak@wdr.com if you are interested in purchasing one of these units, as I don't subscribe to this list. Regards, Rand Dvorak --NeXT-Mail-1035837613-7 Content-Type: text/enriched; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I have 6 Sony XC-77 ccd camera modules I would like to sell. The price is $100 per unit, a 50mm lens is also included in the price. You pay shipping by UPS, from zip code 60604. Call UPS and determine shipping from 60604 to your zip code. I can also ship COD if necessary. Please respond by e-mail to: Rand.Dvorak@wdr.com if you are interested in purchasing one of these units, as I don't subscribe to this list. Regards, Rand Dvorak --NeXT-Mail-1035837613-7-- From nih-image-request@io.ece.drexel.edu Tue Dec 1 16:48 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA12424; Tue, 1 Dec 1998 16:48:20 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 16:48:20 -0500 (EST) From: dmc4@cornell.edu X-Sender: dmc4@postoffice.mail.cornell.edu Message-Id: Mime-Version: 1.0 Date: Tue, 1 Dec 1998 16:20:39 -0500 To: nih-image@io.ece.drexel.edu Subject: frame grabbers Resent-Message-ID: <"4tiNE1.0.YI2.Zq5Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/683 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 834 Hi, We are in the process of trying to set up a gel documentation system. We have a Powermac 6100/60 that is currently unused and was supposed to be dedicated to gel documentation. However, it has a nubus slot and Scion no longer makes a nubus framegrabber. Other than buying a new computer with a PCI slot, which seems kind of wasteful since it will be dedicated to securing gel images, are there any other options.. do any other companies make equivalent framegrabbers that would work with a nubus slot? Any suggestions would be greatly appreciated. Thanks, Donna Cassidy-Hanley ----------------------------------------------------------------------------- Donna Cassidy-Hanley, PhD. Section of Genetics and Development Cornell University Ithaca, New York 14853 e-mail: dmc4@cornell.edu phone: 607-254-4837 fax: 607-255-6249 From nih-image-request@io.ece.drexel.edu Tue Dec 1 17:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA14616; Tue, 1 Dec 1998 17:07:20 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 17:07:20 -0500 (EST) Message-ID: <19981201214140.6243.qmail@hotmail.com> X-Originating-IP: [209.150.98.242] From: "Michael R. Whaley, CQE" To: nih-image@io.ece.drexel.edu Subject: Re: SONY XC-77 CCD Camera modules for sale MIME-Version: 1.0 Date: Tue, 01 Dec 1998 13:41:34 PST Resent-Message-ID: <"Zj2ZE.0.Iv2.JB6Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/684 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1285 >From: Rand Dvorak >Date: Tue, 1 Dec 98 13:14:33 -0600 >To: nih-image@io.ece.drexel.edu >Subject: SONY XC-77 CCD Camera modules for sale >Reply-To: nih-image@io.ece.drexel.edu > > > >Hello, > >I have 6 Sony XC-77 ccd camera modules I would like to >sell. The price is $100 per unit, a 50mm lens is also included >in the price. You pay shipping by UPS, from zip code 60604. >Call UPS and determine shipping from 60604 to your zip code. >I can also ship COD if necessary. Please respond by e-mail >to: > >Rand.Dvorak@wdr.com > >if you are interested in purchasing one of these units, as I don't >subscribe to this list. > > >Regards, >Rand Dvorak >\ Mr. Dvorak: Is the XC-77 a 2/3" CCD? I could find some similar numbers, but not the one you have. Also, does this unit have a "C" mount for lenses or adapters? I am very interested in this unit, and just need to know if it will meet my need. Thanks. Michael R. Whaley, CQE Supplier Quality Analyst Magna International Cosma Body and Chassis Systems Marada Industries 151 Airport Drive Westminster, Maryland 21157 410-840-1717 (Voice) 410-876-0256 (Fax) michael_whaley@asqnet.org ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Tue Dec 1 17:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA15061; Tue, 1 Dec 1998 17:11:01 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 17:11:01 -0500 (EST) Date: Tue, 01 Dec 1998 21:46:49 +0000 (GMT) From: RANJAN PATRO OCE DEPT Subject: Thershold To: NIH-IMAGE@io.ece.drexel.edu Message-id: <01J4U6QYK1IQ005S9G@bodkin.nuigalway.ie> X-VMS-To: NIH-IMAGE@IO.ECE.DREXEL.EDU MIME-version: 1.0 Resent-Message-ID: <"nc1-m1.0.w_2.LF6Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/685 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 847 Hi Everybody! I am using DT-image to analyse the area and radius of Bubbles. But if I change the THERSHOLD value than I am getting different measurement value. Is there anybody know, what value of thershloding is accurate? Thanks in advance. Ciao, Ranjan *********************************************** * Ranjan Kumar Patro * * Dept of Oceanography, * * Martin Ryan Marine Science Institute * * National University of Ireland, * * Galway * * Voice : 353 91 524411, * * ext:3208 * * Fax : 353 91 528302 * * e-mail: ranjan.patro@nuigalway.ie * * Web : http://www.angelfire.com/ri/rpatro * *********************************************** From nih-image-request@io.ece.drexel.edu Tue Dec 1 18:23 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA21288; Tue, 1 Dec 1998 18:23:11 -0500 (EST) Resent-Date: Tue, 1 Dec 1998 18:23:11 -0500 (EST) Message-ID: <366472D7.263D@pop.uky.edu> Date: Tue, 01 Dec 1998 17:51:56 -0500 From: alex gimelbrant Organization: U of K X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: Nih mailing list Subject: counting pixels of different colors Content-Transfer-Encoding: 7bit Resent-Message-ID: <"wqPYN.0.XU4.OC7Ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/686 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=koi8-r Content-Length: 1119 Dear Imagers, I need to quantitate a number of images of double-labeled cells. They are 8-bit images merged from monochromes generated by a confocal microscope in "green" and "red" channels. What I need to do is to count the number of "red" pixels, "green" ones, and "yellow" ones (these are the result of overlap of green and red) in order to calculate the extent to which these two stainings overlap. The way I am doing it is I (1) Hue-sort the LUT, (2) density slice the LUT until all pixels I deem of a certain color are covered, (3) count all pixels within the density slice. I am not happy with the second part, since it seems to be subjective. Besides, it is time consuming, and I cannot use a macro with one-size-fit-all density slices, since (sorted) LUTs vary between images (they also contain a lot of darker bands, as well, so sometimes I have to omit parts of a density slice in order to ignore noise). Is there any "objective" or at least consistent way to select pixels of certain color (ideally, something like "all red/green/etc with brightness above certain level" )? TIA Alex Gimelbrant From nih-image-request@io.ece.drexel.edu Wed Dec 2 02:05 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA05078; Wed, 2 Dec 1998 02:05:11 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 02:05:11 -0500 (EST) Message-Id: <3664D656.A7A6EF58@mail.biu.ac.il> Date: Wed, 02 Dec 1998 07:55:34 +0200 From: "Dr. Ron Goldstein" X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #130 References: <199812011342.IAA29904@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"30uyG.0.Fe.S4EPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/687 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1509 Hi, My two cents worth. It is probably much easier to connect the Mac with the PC using a cheap LAN program called DAVE (www.thursby.com). It allows PC's to be seen as Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in Windows 95. It also interfaces with Linux/Samba. Then, you could save your files via Ethernet directly to the Mac MO from the Zeiss. I have used it to write CD's on a PC with Mac files, with no problem. Good luck, -Ron ------------------------------------------------------------------------ > > Subject: Exchanging 640 MB MO media between Mac and PC > Date: Tue, 1 Dec 1998 13:16:47 +0100 > From: Norbert Vischer > To: nih-image@io.ece.drexel.edu > > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. > > My questions are: > has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? > What is the difference between "D" and "F" cartridges? > Norbert Vischer > > Norbert Vischer University of Amsterdam > Scientific engineer Molecular Cell Biology > Kruislaan 316 > tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam > e-mail: vischer@bio.uva.nl The Netherlands > http://simon.bio.uva.nl/object-image.html > From nih-image-request@io.ece.drexel.edu Wed Dec 2 02:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA08837; Wed, 2 Dec 1998 02:41:10 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 02:41:10 -0500 (EST) Message-ID: <32A291D8.317D@wxs.nl> Date: Mon, 02 Dec 1996 08:22:51 +0000 From: "P.M. Houpt" Organization: BIOMET X-Mailer: Mozilla 3.01-C-WXS-Mac (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: frame grabbers References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"xeT1m.0.yg1.HhEPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/688 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 296 Hi Donna, Try to find a framegrabber card Called AV card , it is specially made for the 6100 and 7100 series.Ask Apple , here in my country they are very cheap ( less $50). I have the software for it. best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 00703504466 From nih-image-request@io.ece.drexel.edu Wed Dec 2 03:10 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA12059; Wed, 2 Dec 1998 03:10:42 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 03:10:42 -0500 (EST) Message-ID: <36657006.599D@cris.enel.it> Date: Wed, 02 Dec 1998 08:51:18 -0800 From: "Zuccala David" Reply-To: zuccala@cris.enel.it Organization: ENEL Ricerca - Polo Idraulico e Strutturale X-Mailer: Mozilla 3.01Gold (Win16; I) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC References: <199812011407.JAA02430@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"XcvtI3.0.aO2.34FPs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/689 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1525 Dear Norbert, > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. There is no a widely accepted standard for logical format of MO cartridges; each software producer uses a different format, so you have no guarantee to be able to read data across MAC and PCs, but also across PCs connected to different drivers. Thank to writable CDs, MOs are becoming obsolete and this problem in the future will disappear. Dear Paul > We have a HP CD writer attached to a PC. We copy the images > from the Mac onto our server and then write them to a CD > in an ISO9660 format. However, we have had some problems: > 1) Although we can see long names on the PC they get > conveted to 8 characters with a ~ symbol so I can not see > the names correctly on the Mac. I am using adaptec software > and have not yet found any options for defining long file > names in the software. Toast software for Mac allows to generate extended ISO9660 format that supports long names. I could see these long names on Mac and UNIX platforms. I never tried with Windows 95 PCs. David Zuccala' ENEL RICERCA - Polo Idraulico e Strutturale v. Pozzobonelli, 6 ph.: + 39 02 7224.3587 I - 20162 Milano fax: + 39 02 7224.3530 e-mail: zuccala@cris.enel.it (office) From nih-image-d-request@io.ece.drexel.edu Wed Dec 2 06:24 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA01291; Wed, 2 Dec 1998 06:24:51 -0500 (EST) Date: Wed, 2 Dec 1998 06:24:51 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812021124.GAA01291@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #131 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/131 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 13127 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 131 Today's Topics: Re: Exchanging 640 MB MO media betwe [ wpchan@socrates.berkeley.edu ] SONY XC-77 CCD Camera modules for sa [ Rand Dvorak ] frame grabbers [ dmc4@cornell.edu ] Re: SONY XC-77 CCD Camera modules fo [ "Michael R. Whaley, CQE" ] Re: Exchanging 640 MB MO media betwe [ "Zuccala David" Content-Type: TEXT/PLAIN; charset=US-ASCII We have recently brough a DynaMO 640. DOS mounter and Ringowin were bundled with it. The former allows us to use a PC formatted MO on the Mac and the latter lets us use Mac formatted MO on the PC. Both utilities also allow other cross-platform removables such as floppy or Syquest cart. to be mounted. The MO that we use are 2K-sector and formatted with the DynaMO supplied driver both on the Mac and on the PC. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) On Tue, 1 Dec 1998, Norbert Vischer wrote: > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. > > My questions are: > has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? ------------------------------ Date: Tue, 1 Dec 98 13:14:33 -0600 From: Rand Dvorak To: nih-image@io.ece.drexel.edu Subject: SONY XC-77 CCD Camera modules for sale Message-Id: <9812011914.AA13359@ch1d2301nwk> Content-Type: multipart/alternative; boundary=NeXT-Mail-1035837613-7 Content-Transfer-Encoding: 7bit --NeXT-Mail-1035837613-7 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I have 6 Sony XC-77 ccd camera modules I would like to sell. The price is $100 per unit, a 50mm lens is also included in the price. You pay shipping by UPS, from zip code 60604. Call UPS and determine shipping from 60604 to your zip code. I can also ship COD if necessary. Please respond by e-mail to: Rand.Dvorak@wdr.com if you are interested in purchasing one of these units, as I don't subscribe to this list. Regards, Rand Dvorak --NeXT-Mail-1035837613-7 Content-Type: text/enriched; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I have 6 Sony XC-77 ccd camera modules I would like to sell. The price is $100 per unit, a 50mm lens is also included in the price. You pay shipping by UPS, from zip code 60604. Call UPS and determine shipping from 60604 to your zip code. I can also ship COD if necessary. Please respond by e-mail to: Rand.Dvorak@wdr.com if you are interested in purchasing one of these units, as I don't subscribe to this list. Regards, Rand Dvorak --NeXT-Mail-1035837613-7-- ------------------------------ Date: Tue, 1 Dec 1998 16:20:39 -0500 From: dmc4@cornell.edu To: nih-image@io.ece.drexel.edu Subject: frame grabbers Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, We are in the process of trying to set up a gel documentation system. We have a Powermac 6100/60 that is currently unused and was supposed to be dedicated to gel documentation. However, it has a nubus slot and Scion no longer makes a nubus framegrabber. Other than buying a new computer with a PCI slot, which seems kind of wasteful since it will be dedicated to securing gel images, are there any other options.. do any other companies make equivalent framegrabbers that would work with a nubus slot? Any suggestions would be greatly appreciated. Thanks, Donna Cassidy-Hanley ----------------------------------------------------------------------------- Donna Cassidy-Hanley, PhD. Section of Genetics and Development Cornell University Ithaca, New York 14853 e-mail: dmc4@cornell.edu phone: 607-254-4837 fax: 607-255-6249 ------------------------------ Date: Tue, 01 Dec 1998 13:41:34 PST From: "Michael R. Whaley, CQE" To: nih-image@io.ece.drexel.edu Subject: Re: SONY XC-77 CCD Camera modules for sale Message-ID: <19981201214140.6243.qmail@hotmail.com> Content-Type: text/plain >From: Rand Dvorak >Date: Tue, 1 Dec 98 13:14:33 -0600 >To: nih-image@io.ece.drexel.edu >Subject: SONY XC-77 CCD Camera modules for sale >Reply-To: nih-image@io.ece.drexel.edu > > > >Hello, > >I have 6 Sony XC-77 ccd camera modules I would like to >sell. The price is $100 per unit, a 50mm lens is also included >in the price. You pay shipping by UPS, from zip code 60604. >Call UPS and determine shipping from 60604 to your zip code. >I can also ship COD if necessary. Please respond by e-mail >to: > >Rand.Dvorak@wdr.com > >if you are interested in purchasing one of these units, as I don't >subscribe to this list. > > >Regards, >Rand Dvorak >\ Mr. Dvorak: Is the XC-77 a 2/3" CCD? I could find some similar numbers, but not the one you have. Also, does this unit have a "C" mount for lenses or adapters? I am very interested in this unit, and just need to know if it will meet my need. Thanks. Michael R. Whaley, CQE Supplier Quality Analyst Magna International Cosma Body and Chassis Systems Marada Industries 151 Airport Drive Westminster, Maryland 21157 410-840-1717 (Voice) 410-876-0256 (Fax) michael_whaley@asqnet.org ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Tue, 01 Dec 1998 21:46:49 +0000 (GMT) From: RANJAN PATRO OCE DEPT To: NIH-IMAGE@io.ece.drexel.edu Subject: Thershold Message-id: <01J4U6QYK1IQ005S9G@bodkin.nuigalway.ie> Hi Everybody! I am using DT-image to analyse the area and radius of Bubbles. But if I change the THERSHOLD value than I am getting different measurement value. Is there anybody know, what value of thershloding is accurate? Thanks in advance. Ciao, Ranjan *********************************************** * Ranjan Kumar Patro * * Dept of Oceanography, * * Martin Ryan Marine Science Institute * * National University of Ireland, * * Galway * * Voice : 353 91 524411, * * ext:3208 * * Fax : 353 91 528302 * * e-mail: ranjan.patro@nuigalway.ie * * Web : http://www.angelfire.com/ri/rpatro * *********************************************** ------------------------------ Date: Tue, 01 Dec 1998 17:51:56 -0500 From: alex gimelbrant To: Nih mailing list Subject: counting pixels of different colors Message-ID: <366472D7.263D@pop.uky.edu> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear Imagers, I need to quantitate a number of images of double-labeled cells. They are 8-bit images merged from monochromes generated by a confocal microscope in "green" and "red" channels. What I need to do is to count the number of "red" pixels, "green" ones, and "yellow" ones (these are the result of overlap of green and red) in order to calculate the extent to which these two stainings overlap. The way I am doing it is I (1) Hue-sort the LUT, (2) density slice the LUT until all pixels I deem of a certain color are covered, (3) count all pixels within the density slice. I am not happy with the second part, since it seems to be subjective. Besides, it is time consuming, and I cannot use a macro with one-size-fit-all density slices, since (sorted) LUTs vary between images (they also contain a lot of darker bands, as well, so sometimes I have to omit parts of a density slice in order to ignore noise). Is there any "objective" or at least consistent way to select pixels of certain color (ideally, something like "all red/green/etc with brightness above certain level" )? TIA Alex Gimelbrant ------------------------------ Date: Wed, 02 Dec 1998 07:55:34 +0200 From: "Dr. Ron Goldstein" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #130 Message-Id: <3664D656.A7A6EF58@mail.biu.ac.il> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, My two cents worth. It is probably much easier to connect the Mac with the PC using a cheap LAN program called DAVE (www.thursby.com). It allows PC's to be seen as Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in Windows 95. It also interfaces with Linux/Samba. Then, you could save your files via Ethernet directly to the Mac MO from the Zeiss. I have used it to write CD's on a PC with Mac files, with no problem. Good luck, -Ron ------------------------------------------------------------------------ > > Subject: Exchanging 640 MB MO media between Mac and PC > Date: Tue, 1 Dec 1998 13:16:47 +0100 > From: Norbert Vischer > To: nih-image@io.ece.drexel.edu > > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. > > My questions are: > has anyone succeeded to interchange 640 MB MO cartridges between Mac and PC? > What is the difference between "D" and "F" cartridges? > Norbert Vischer > > Norbert Vischer University of Amsterdam > Scientific engineer Molecular Cell Biology > Kruislaan 316 > tel. +31-20-525-6267(fax 6271) NL-1098 SM Amsterdam > e-mail: vischer@bio.uva.nl The Netherlands > http://simon.bio.uva.nl/object-image.html > ------------------------------ Date: Mon, 02 Dec 1996 08:22:51 +0000 From: "P.M. Houpt" To: nih-image@io.ece.drexel.edu Subject: Re: frame grabbers Message-ID: <32A291D8.317D@wxs.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Donna, Try to find a framegrabber card Called AV card , it is specially made for the 6100 and 7100 series.Ask Apple , here in my country they are very cheap ( less $50). I have the software for it. best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 00703504466 ------------------------------ Date: Wed, 02 Dec 1998 08:51:18 -0800 From: "Zuccala David" To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC Message-ID: <36657006.599D@cris.enel.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Norbert, > We want to exchange magneto-optical media between Macs and the PC which > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > MO drive is hooked up, but I don't succeed to interchange the media. When I > format a cartridge on the Mac in "PC-format", the PC refuses it. There is no a widely accepted standard for logical format of MO cartridges; each software producer uses a different format, so you have no guarantee to be able to read data across MAC and PCs, but also across PCs connected to different drivers. Thank to writable CDs, MOs are becoming obsolete and this problem in the future will disappear. Dear Paul > We have a HP CD writer attached to a PC. We copy the images > from the Mac onto our server and then write them to a CD > in an ISO9660 format. However, we have had some problems: > 1) Although we can see long names on the PC they get > conveted to 8 characters with a ~ symbol so I can not see > the names correctly on the Mac. I am using adaptec software > and have not yet found any options for defining long file > names in the software. Toast software for Mac allows to generate extended ISO9660 format that supports long names. I could see these long names on Mac and UNIX platforms. I never tried with Windows 95 PCs. David Zuccala' ENEL RICERCA - Polo Idraulico e Strutturale v. Pozzobonelli, 6 ph.: + 39 02 7224.3587 I - 20162 Milano fax: + 39 02 7224.3530 e-mail: zuccala@cris.enel.it (office) -------------------------------- End of nih-image-d Digest V98 Issue #131 **************************************** From nih-image-request@io.ece.drexel.edu Wed Dec 2 10:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA24532; Wed, 2 Dec 1998 10:25:22 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 10:25:22 -0500 (EST) Message-Id: In-Reply-To: <199812021118.GAA00463@io.ece.drexel.edu> Mime-Version: 1.0 Date: Wed, 2 Dec 1998 15:54:33 +0100 To: nih-image@io.ece.drexel.edu From: Michael Glotzer Subject: setting quicktime parameters from within a macro Resent-Message-ID: <"Usg3D2.0.9J5.HJLPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/690 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 831 Hi Imagers, I would like to specify the settings of the "compression settings" dialog box that comes up when you save a stack as a quicktime file. There are a number of settings: 1) compressor choices are none, photojpeg, etc 2) a sub dialog choices ae colr, greyscale, best depth 3) quality a numeric value is set with a slider 4) then comes a bunch of other settings that concern motion My questions: a) is it possible to set 1,2, and 3 from within a macro? b) what are the motion settings for? Thanks for your help Michael ___________________________________________________________________ Michael Glotzer Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA phone 43-(1)797-30-405 office phone 43-(1)797-30-525 lab fax 43-(1)798-7153 email mglotzer@nt.imp.univie.ac.at From nih-image-request@io.ece.drexel.edu Wed Dec 2 10:33 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA25174; Wed, 2 Dec 1998 10:33:00 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 10:33:00 -0500 (EST) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #130 In-Reply-To: <3664D656.A7A6EF58@mail.biu.ac.il> Message-ID: Date: Tue, 1 Dec 1998 21:12:07 -0500 (Eastern Standard Time) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.5 Build (43) X-Authentication: none MIME-Version: 1.0 Resent-Message-ID: <"dlJKq3.0.PW5.jRLPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/691 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 1437 V On Wed, 02 Dec 1998 07:55:34 +0200 "Dr. Ron Goldstein" wrote: > Hi, > > My two cents worth. > > It is probably much easier to connect the Mac with the PC using a cheap > LAN program called DAVE (www.thursby.com). It allows PC's to be seen as > Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in > Windows 95. It also interfaces with Linux/Samba. Then, you could save > your files via Ethernet directly to the Mac MO from the Zeiss. I have > used it to write CD's on a PC with Mac files, with no problem. > > We want to exchange magneto-optical media between Macs and the PC which > > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > > MO drive is hooked up, but I don't succeed to interchange the media. When I > > format a cartridge on the Mac in "PC-format", the PC refuses it. If both of these machines are on a network, we have found that COPStalk works smoothly to allow Windows machines to see the Appletalk network, which includes reading and writing to Macs from the PC. Information can be gotten at: http://www.copstalk.com/index.shtml ---------------------------------------------------------- Herbert M. Geller, Ph.D. Professor Department of Pharmacology voice - 732-235-4084 Robert Wood Johnson Medical School fax - 732-235-4073 Piscataway, New Jersey 08854 Internet - geller@umdnj.edu www: http://www2.umdnj.edu/~geller/lab/ From nih-image-request@io.ece.drexel.edu Wed Dec 2 18:08 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05386; Wed, 2 Dec 1998 18:08:57 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 18:08:57 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: aagime0@pop.uky.edu, nih-image@io.ece.drexel.edu Date: Thu, 3 Dec 1998 9:42:39 GMT+1100 Subject: Re: counting pixels of different colors Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <39A712B453A@rna.bio.mq.edu.au> Resent-Message-ID: <"rCQKu2.0.NZ.D7SPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/692 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2396 >Date: Tue, 01 Dec 1998 17:51:56 -0500 >From: alex gimelbrant >.......... >I need to quantitate a number of images of double-labeled cells. >They are 8-bit images merged from monochromes generated >by a confocal microscope in "green" and "red" channels. > >What I need to do is to count the number of "red" pixels, "green" ones, >and "yellow" ones (these are the result of overlap of green and red) in >order >to calculate the extent to which these two stainings overlap. > >The way I am doing it is I >(1) Hue-sort the LUT, >(2) density slice the LUT until all pixels I deem of a certain color are >covered, >(3) count all pixels within the density slice. > >I am not happy with the second part, since it seems to be subjective. >Besides, it is time consuming, and I cannot use a macro with >one-size-fit-all >density slices, since (sorted) LUTs vary between images (they also >contain >a lot of darker bands, as well, so sometimes I have to omit parts of a >density >slice in order to ignore noise). >Is there any "objective" or at least consistent way to select pixels of >certain color >(ideally, something like "all red/green/etc with brightness above >certain level" )? > Alex, It would be best to work with the orginal "green" and "red" channel images as they are presumeably both 8-bit. Then you could threshold (ie "something like "all red/green with brightness above certain level"") each channel and makebinary separately to get red/green maps. A simple paste with "And" option would then give the overlap map. The "8-bit color images merged from monochromes" are likely to be formed by bin counting the pixel intensities in RGB space to 32 level (5-bit) bins and then successively bisecting the 32 R x 32 G x 32 B space into 254 (256-2 white/black) "equally" populated regions. The central coordinate of each region is then used as the bin color. You can recover the red/green channels by using "8-bit color to RGB"(stack menu. The red and green channels will then be 32 level (5-bit) posterised (the blue channel should be empty). You can then threshold each of the red and green slices(1,2) of the RGB stack and AND them together to find overlap. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Wed Dec 2 20:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA19111; Wed, 2 Dec 1998 20:17:58 -0500 (EST) Resent-Date: Wed, 2 Dec 1998 20:17:58 -0500 (EST) Message-Id: <199812030058.IAA31651@nero.rph.health.wa.gov.au> From: "Robert Day" To: nih-image@io.ece.drexel.edu Date: Thu, 3 Dec 1998 08:49:42 +0800 MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: Re: Exchanging 640 MB MO media between Mac and PC Priority: normal References: <3663E636.CABCA198@soton.ac.uk> In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.01b) Resent-Message-ID: <"WaZ5i1.0.A14.i3UPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/693 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1767 > We have a HP CD writer attached to a PC. We copy the images > from the Mac onto our server and then write them to a CD > in an ISO9660 format. However, we have had some problems: > 1) Although we can see long names on the PC they get > conveted to 8 characters with a ~ symbol so I can not see > the names correctly on the Mac. I am using adaptec software > and have not yet found any options for defining long file > names in the software. If you are using EasyCD Pro, which is what Adaptec was selling most recently, then under the filenames tab there should be an option for "Joliet (Win95 long file names)". This a typically broken Microsoft version of the Rock Ridge extensions to iso9600, but if you keep under 31 characters the names will show up on the Mac. I do this a lot and it works OK for Mac win95 and Unix, even if it does play around with the case of names - damn Microsoft :-( > 2) Another thing that I have noticed is that on write only > CD's, on which files have been added at different times, > sometimes Explorer will only see one of the folders. If I > eject and then reinsert the disc I might get a folder that > was added at another time but not all of the folders. I > guess to avoid this the trick is only to write once and > then go onto another CD. This can be a problem with multi-session CDs, in some drives. Try making a multi-session mode 1 CD instead. I know you're supposed to use mode 2 for multi-session, but sometinmes the Adaptec software seems to get it wrong. Partly because of this problem we switched to Nero, and this has been a much better product. Rob. -- Robert Day rob.day@nero.rph.health.wa.gov.au Project Bioengineer ph +61 8 9224 3227 Royal Perth Hospital fax +61 8 9224 1138 From nih-image-d-request@io.ece.drexel.edu Thu Dec 3 06:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29134; Thu, 3 Dec 1998 06:26:17 -0500 (EST) Date: Thu, 3 Dec 1998 06:26:17 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812031126.GAA29134@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #132 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/132 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 8198 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 132 Today's Topics: setting quicktime parameters from wi [ Michael Glotzer To: nih-image@io.ece.drexel.edu Subject: setting quicktime parameters from within a macro Message-Id: Content-Type: text/plain; charset="us-ascii" Hi Imagers, I would like to specify the settings of the "compression settings" dialog box that comes up when you save a stack as a quicktime file. There are a number of settings: 1) compressor choices are none, photojpeg, etc 2) a sub dialog choices ae colr, greyscale, best depth 3) quality a numeric value is set with a slider 4) then comes a bunch of other settings that concern motion My questions: a) is it possible to set 1,2, and 3 from within a macro? b) what are the motion settings for? Thanks for your help Michael ___________________________________________________________________ Michael Glotzer Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA phone 43-(1)797-30-405 office phone 43-(1)797-30-525 lab fax 43-(1)798-7153 email mglotzer@nt.imp.univie.ac.at ------------------------------ Date: Tue, 1 Dec 1998 21:12:07 -0500 (Eastern Standard Time) From: "Herbert M. Geller" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #130 Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII V On Wed, 02 Dec 1998 07:55:34 +0200 "Dr. Ron Goldstein" wrote: > Hi, > > My two cents worth. > > It is probably much easier to connect the Mac with the PC using a cheap > LAN program called DAVE (www.thursby.com). It allows PC's to be seen as > Mac's from the Mac, and the Mac to be seen as a PC from the PC"s in > Windows 95. It also interfaces with Linux/Samba. Then, you could save > your files via Ethernet directly to the Mac MO from the Zeiss. I have > used it to write CD's on a PC with Mac files, with no problem. > > We want to exchange magneto-optical media between Macs and the PC which > > controls our confocal microscope (a Zeiss 510). On both machines, a 640MB > > MO drive is hooked up, but I don't succeed to interchange the media. When I > > format a cartridge on the Mac in "PC-format", the PC refuses it. If both of these machines are on a network, we have found that COPStalk works smoothly to allow Windows machines to see the Appletalk network, which includes reading and writing to Macs from the PC. Information can be gotten at: http://www.copstalk.com/index.shtml ---------------------------------------------------------- Herbert M. Geller, Ph.D. Professor Department of Pharmacology voice - 732-235-4084 Robert Wood Johnson Medical School fax - 732-235-4073 Piscataway, New Jersey 08854 Internet - geller@umdnj.edu www: http://www2.umdnj.edu/~geller/lab/ ------------------------------ Date: Thu, 3 Dec 1998 9:42:39 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: aagime0@pop.uky.edu, nih-image@io.ece.drexel.edu Subject: Re: counting pixels of different colors Message-ID: <39A712B453A@rna.bio.mq.edu.au> >Date: Tue, 01 Dec 1998 17:51:56 -0500 >From: alex gimelbrant >.......... >I need to quantitate a number of images of double-labeled cells. >They are 8-bit images merged from monochromes generated >by a confocal microscope in "green" and "red" channels. > >What I need to do is to count the number of "red" pixels, "green" ones, >and "yellow" ones (these are the result of overlap of green and red) in >order >to calculate the extent to which these two stainings overlap. > >The way I am doing it is I >(1) Hue-sort the LUT, >(2) density slice the LUT until all pixels I deem of a certain color are >covered, >(3) count all pixels within the density slice. > >I am not happy with the second part, since it seems to be subjective. >Besides, it is time consuming, and I cannot use a macro with >one-size-fit-all >density slices, since (sorted) LUTs vary between images (they also >contain >a lot of darker bands, as well, so sometimes I have to omit parts of a >density >slice in order to ignore noise). >Is there any "objective" or at least consistent way to select pixels of >certain color >(ideally, something like "all red/green/etc with brightness above >certain level" )? > Alex, It would be best to work with the orginal "green" and "red" channel images as they are presumeably both 8-bit. Then you could threshold (ie "something like "all red/green with brightness above certain level"") each channel and makebinary separately to get red/green maps. A simple paste with "And" option would then give the overlap map. The "8-bit color images merged from monochromes" are likely to be formed by bin counting the pixel intensities in RGB space to 32 level (5-bit) bins and then successively bisecting the 32 R x 32 G x 32 B space into 254 (256-2 white/black) "equally" populated regions. The central coordinate of each region is then used as the bin color. You can recover the red/green channels by using "8-bit color to RGB"(stack menu. The red and green channels will then be 32 level (5-bit) posterised (the blue channel should be empty). You can then threshold each of the red and green slices(1,2) of the RGB stack and AND them together to find overlap. Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Thu, 3 Dec 1998 08:49:42 +0800 From: "Robert Day" To: nih-image@io.ece.drexel.edu Subject: Re: Exchanging 640 MB MO media between Mac and PC Message-Id: <199812030058.IAA31651@nero.rph.health.wa.gov.au> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT > We have a HP CD writer attached to a PC. We copy the images > from the Mac onto our server and then write them to a CD > in an ISO9660 format. However, we have had some problems: > 1) Although we can see long names on the PC they get > conveted to 8 characters with a ~ symbol so I can not see > the names correctly on the Mac. I am using adaptec software > and have not yet found any options for defining long file > names in the software. If you are using EasyCD Pro, which is what Adaptec was selling most recently, then under the filenames tab there should be an option for "Joliet (Win95 long file names)". This a typically broken Microsoft version of the Rock Ridge extensions to iso9600, but if you keep under 31 characters the names will show up on the Mac. I do this a lot and it works OK for Mac win95 and Unix, even if it does play around with the case of names - damn Microsoft :-( > 2) Another thing that I have noticed is that on write only > CD's, on which files have been added at different times, > sometimes Explorer will only see one of the folders. If I > eject and then reinsert the disc I might get a folder that > was added at another time but not all of the folders. I > guess to avoid this the trick is only to write once and > then go onto another CD. This can be a problem with multi-session CDs, in some drives. Try making a multi-session mode 1 CD instead. I know you're supposed to use mode 2 for multi-session, but sometinmes the Adaptec software seems to get it wrong. Partly because of this problem we switched to Nero, and this has been a much better product. Rob. -- Robert Day rob.day@nero.rph.health.wa.gov.au Project Bioengineer ph +61 8 9224 3227 Royal Perth Hospital fax +61 8 9224 1138 -------------------------------- End of nih-image-d Digest V98 Issue #132 **************************************** From nih-image-request@io.ece.drexel.edu Thu Dec 3 09:47 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA22167; Thu, 3 Dec 1998 09:47:57 -0500 (EST) Resent-Date: Thu, 3 Dec 1998 09:47:57 -0500 (EST) Message-ID: <69B43248FE73D11197BB00A0C99AB06789AC@jvcserver.vanguardweb.org> From: "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" , "'NIH wayne'" Subject: Interpolation Macro Date: Thu, 3 Dec 1998 09:03:43 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"Kt6xP2.0.GQ4.snfPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/694 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 429 Hi, Is it possible to interpolate two CT slices, creating 3rd one in NIH?. I have two B&W images and I want to create third image by interpolating given two images. Is there any macro to interpolate 150 plus slices?. Which interpolation approach is the best (bilinear or nearest neighboor or other methods). Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 From nih-image-request@io.ece.drexel.edu Thu Dec 3 10:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA26699; Thu, 3 Dec 1998 10:22:18 -0500 (EST) Resent-Date: Thu, 3 Dec 1998 10:22:18 -0500 (EST) Message-Id: <9812031452.AA396380@mail.biu.ac.il> From: "Giller Dima" Organization: Physics Dept, Bar-Ilan University To: nih-image@io.ece.drexel.edu Date: Thu, 3 Dec 1998 16:52:05 IST+2 Subject: Problem with NIH(Scion)-Image Reply-To: giller@PHYSNET.PH.BIU.AC.IL Priority: normal X-Mailer: Pegasus Mail for Win32 (v3.01d) Resent-Message-ID: <"XEBrk.0.Wa5.-MgPs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/695 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 788 Hello! In our work we use frame grabber AG-5 of Scion corporation and the program "Scion Image" that helps us a lot. I would like to ask you some question about "NIH (Scion)-Image".When I write the macro and try to copy a group of images with real values into a stack,I face some problem. LUT of all slices remains unchanged but the values inside the image do change (this problem doesn't exist for images with integer values). I will very appreciate if you could explain me how I should deal with this problem. Thanks a lot. _____________________________________________________ Dima Giller Institute of Superconductivity Department of Physics, Bar-Ilan University Ramat-Gan, Israel 52900 tel: (972) (3) 5317325 fax:(972) (3) 5353298 email: giller@physnet.ph.biu.ac.il From nih-image-request@io.ece.drexel.edu Thu Dec 3 13:35 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA15559; Thu, 3 Dec 1998 13:35:30 -0500 (EST) Resent-Date: Thu, 3 Dec 1998 13:35:30 -0500 (EST) Date: Thu, 3 Dec 1998 12:50:40 -0500 (EST) X-Authentication-Warning: pop.uky.edu: [128.163.85.61] didn't use HELO protocol Message-Id: <2.2.16.19981203125039.34a79670@pop.uky.edu> X-Sender: bcler1@pop.uky.edu X-Mailer: Windows Eudora Pro Version 2.2 (16) Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu From: "Bill Clerici, Ph.D." Subject: Quantification of fluorescein in single cells Resent-Message-ID: <"ZRDYJ1.0.vo2.xziPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/696 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2110 I would like to quantify the fluorescence of single cells examined at 600x magnification after treatment with a fluorescein probe. Pilot cells fluoresce very intensely under experimental conditions, while control cells are not visually detectable. However, I am not certain how best to calibrate the system and measure the cells. I have the Kodak control scales recommended by the NIH Image manual, and, calibrated the microscope/ NIH Image system (at 100x and 600x) using the microscope's normal white light on full intensity, with and without each of two neutral density filters. However, since it is not white light that will be measured from the cell, I, then, attempted to calibrate using the same filter and magnification combinations, utilizing the UV light source. I could calibrate at 100x using the UV light source with no neutral density filters, but, if either ND filter was used (as will be used with cells), then the light was too dark. At 600x, the magnification needed for the experiment, the light intensity was too dark, even without any neutral density filters. My question is "How should the system be calibrated?" Since we are exciting the cells at one wavelength (488 nm) and, measuring emissions at another (530 nm), are any of these conditions appropriate? I would very much appreciate any advice as to the best (or, even an adequate) method of calibrating the system for such conditions. Also, once values are measured for standard areas within each cell, should the background intensity be subtracted from that of the cell, or should a ratio of cell to background intensity be calculated? Thank you, very much, for your help. Sincerely, Bill Clerici -------------------------------------------- William J. Clerici, Ph.D. Associate Professor Rm. C-236, Department of Surgery Division of Otolaryngology-HNS University of Kentucky Chandler Medical Center 800 Rose Street Lexington, KY 40536-0084 ------------------ Telephone: (606) 257-5097 (lab): (606) 257-6020 FAX: (606) 257-5096 e-mail: bcler1@pop.uky.edu -------------------------------------------- From nih-image-request@io.ece.drexel.edu Thu Dec 3 14:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA17993; Thu, 3 Dec 1998 14:02:54 -0500 (EST) Resent-Date: Thu, 3 Dec 1998 14:02:54 -0500 (EST) Message-Id: X-Mailer: Microsoft Outlook Express for Macintosh - 4.01 (295) Date: Thu, 03 Dec 1998 12:23:51 -0500 Subject: Help with grain-size analysis From: "Peter A. Scholle" To: nih-image@io.ece.drexel.edu Mime-version: 1.0 X-Priority: 3 Content-transfer-encoding: 7bit Resent-Message-ID: <"TS0kl.0.Cd3.fWjPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/697 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 636 I am a new user of Image 1.61 and could use some help. I am trying to do automated grain- and pore-size analysis on digital scanning electron micrographs of very fine-grained rocks (chalks). I basically need to construct a histogram of the principal (longest and shortest) axes of all the grains in the image. I have been able to threshold the image to distinguish between grains and pores but have not figured out how to get the grain size measurements. Any help would be much appreciated. Dr. Peter A. Scholle Dept. of Geological Sciences Southern Methodist University Dallas, TX 75275 U.S.A. 214-768-4011 pscholle@mail.smu.edu From nih-image-request@io.ece.drexel.edu Thu Dec 3 16:31 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA00509; Thu, 3 Dec 1998 16:31:14 -0500 (EST) Resent-Date: Thu, 3 Dec 1998 16:31:14 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 3 Dec 1998 22:00:21 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Help with grain-size analysis Resent-Message-ID: <"8pDX33.0.wm6.JjlPs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/698 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1115 There is a set of macro commands available in Object-Image for the creation of histograms. An example is shown in the file 'sort particles' in 'Examples.sea', where particle analysis is performed and the particle diameter is plotted as histogram. Similarly, one can mark long and short axes of the best-fitting ellipse and put them into a histogram. The macro syntax allows you to combine several parameters in a single graphics, each one shown in the desired color and with statistic values like mean and stdev. The advantage compared to exporting data to Excel is that Object-Image integrates macros, direct and derived results and non-destructive markers into a single file, so you can update the histogram any time with a single keystroke. No intermediate files need to be created, and you need not to care about data organisation and non-existing results ('zero' is different from 'nothing'). You also can trace a result back to the corresponding image, and kill or modify the markers. If you are interested I can give you more hints. look at: http://simon.bio.uva.nl/object-image.html Norbert Vischer From nih-image-d-request@io.ece.drexel.edu Fri Dec 4 06:28 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14402; Fri, 4 Dec 1998 06:28:45 -0500 (EST) Date: Fri, 4 Dec 1998 06:28:45 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812041128.GAA14402@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #133 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/133 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7264 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 133 Today's Topics: Interpolation Macro [ "Mehmet Dondurur, Ph. D." To: "'NIH User Group'" , "'NIH wayne'" Subject: Interpolation Macro Message-ID: <69B43248FE73D11197BB00A0C99AB06789AC@jvcserver.vanguardweb.org> Content-Type: text/plain Hi, Is it possible to interpolate two CT slices, creating 3rd one in NIH?. I have two B&W images and I want to create third image by interpolating given two images. Is there any macro to interpolate 150 plus slices?. Which interpolation approach is the best (bilinear or nearest neighboor or other methods). Thanks Dr. Mehmet Dondurur Research Scientist Jobst Vascular Center-U of M Mehmet.Dondurur.ph.d@jvc.org (419) 471-2087 ------------------------------ Date: Thu, 3 Dec 1998 16:52:05 IST+2 From: "Giller Dima" To: nih-image@io.ece.drexel.edu Subject: Problem with NIH(Scion)-Image Message-Id: <9812031452.AA396380@mail.biu.ac.il> Hello! In our work we use frame grabber AG-5 of Scion corporation and the program "Scion Image" that helps us a lot. I would like to ask you some question about "NIH (Scion)-Image".When I write the macro and try to copy a group of images with real values into a stack,I face some problem. LUT of all slices remains unchanged but the values inside the image do change (this problem doesn't exist for images with integer values). I will very appreciate if you could explain me how I should deal with this problem. Thanks a lot. _____________________________________________________ Dima Giller Institute of Superconductivity Department of Physics, Bar-Ilan University Ramat-Gan, Israel 52900 tel: (972) (3) 5317325 fax:(972) (3) 5353298 email: giller@physnet.ph.biu.ac.il ------------------------------ Date: Thu, 3 Dec 1998 12:50:40 -0500 (EST) From: "Bill Clerici, Ph.D." To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Quantification of fluorescein in single cells Message-Id: <2.2.16.19981203125039.34a79670@pop.uky.edu> Content-Type: text/plain; charset="us-ascii" I would like to quantify the fluorescence of single cells examined at 600x magnification after treatment with a fluorescein probe. Pilot cells fluoresce very intensely under experimental conditions, while control cells are not visually detectable. However, I am not certain how best to calibrate the system and measure the cells. I have the Kodak control scales recommended by the NIH Image manual, and, calibrated the microscope/ NIH Image system (at 100x and 600x) using the microscope's normal white light on full intensity, with and without each of two neutral density filters. However, since it is not white light that will be measured from the cell, I, then, attempted to calibrate using the same filter and magnification combinations, utilizing the UV light source. I could calibrate at 100x using the UV light source with no neutral density filters, but, if either ND filter was used (as will be used with cells), then the light was too dark. At 600x, the magnification needed for the experiment, the light intensity was too dark, even without any neutral density filters. My question is "How should the system be calibrated?" Since we are exciting the cells at one wavelength (488 nm) and, measuring emissions at another (530 nm), are any of these conditions appropriate? I would very much appreciate any advice as to the best (or, even an adequate) method of calibrating the system for such conditions. Also, once values are measured for standard areas within each cell, should the background intensity be subtracted from that of the cell, or should a ratio of cell to background intensity be calculated? Thank you, very much, for your help. Sincerely, Bill Clerici -------------------------------------------- William J. Clerici, Ph.D. Associate Professor Rm. C-236, Department of Surgery Division of Otolaryngology-HNS University of Kentucky Chandler Medical Center 800 Rose Street Lexington, KY 40536-0084 ------------------ Telephone: (606) 257-5097 (lab): (606) 257-6020 FAX: (606) 257-5096 e-mail: bcler1@pop.uky.edu -------------------------------------------- ------------------------------ Date: Thu, 03 Dec 1998 12:23:51 -0500 From: "Peter A. Scholle" To: nih-image@io.ece.drexel.edu Subject: Help with grain-size analysis Message-Id: Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit I am a new user of Image 1.61 and could use some help. I am trying to do automated grain- and pore-size analysis on digital scanning electron micrographs of very fine-grained rocks (chalks). I basically need to construct a histogram of the principal (longest and shortest) axes of all the grains in the image. I have been able to threshold the image to distinguish between grains and pores but have not figured out how to get the grain size measurements. Any help would be much appreciated. Dr. Peter A. Scholle Dept. of Geological Sciences Southern Methodist University Dallas, TX 75275 U.S.A. 214-768-4011 pscholle@mail.smu.edu ------------------------------ Date: Thu, 3 Dec 1998 22:00:21 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Help with grain-size analysis Message-Id: Content-Type: text/plain; charset="us-ascii" There is a set of macro commands available in Object-Image for the creation of histograms. An example is shown in the file 'sort particles' in 'Examples.sea', where particle analysis is performed and the particle diameter is plotted as histogram. Similarly, one can mark long and short axes of the best-fitting ellipse and put them into a histogram. The macro syntax allows you to combine several parameters in a single graphics, each one shown in the desired color and with statistic values like mean and stdev. The advantage compared to exporting data to Excel is that Object-Image integrates macros, direct and derived results and non-destructive markers into a single file, so you can update the histogram any time with a single keystroke. No intermediate files need to be created, and you need not to care about data organisation and non-existing results ('zero' is different from 'nothing'). You also can trace a result back to the corresponding image, and kill or modify the markers. If you are interested I can give you more hints. look at: http://simon.bio.uva.nl/object-image.html Norbert Vischer -------------------------------- End of nih-image-d Digest V98 Issue #133 **************************************** From nih-image-request@io.ece.drexel.edu Fri Dec 4 11:02 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA08974; Fri, 4 Dec 1998 11:02:04 -0500 (EST) Resent-Date: Fri, 4 Dec 1998 11:02:04 -0500 (EST) Date: Fri, 4 Dec 1998 15:11:36 +0000 (BST) From: Dan Lovegrove X-Sender: danl@cook Reply-To: Dan Lovegrove To: nih-image@io.ece.drexel.edu Subject: Best Fit Ellipses Message-ID: Organisation: Department of Earth Sciences University of Oxford UK. MIME-Version: 1.0 Resent-Message-ID: <"jROR_.0.1A1.0l_Ps"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/699 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 583 I was wondering exactly how NIH image calculates the major and minor axes etc. of best fit ellipses to irregularly shaped particles. Cheers Dan Lovegrove ################################ Castle Milk Stout - Brewed to be Rich and Dark Dan Lovegrove Esq. Department of Earth Sciences University of Oxford Parks Road OXFORD OX1 3PR email: danl@earth.ox.ac.uk telephone: (01865) 272000 direct line: (01865) 272056 fax: (01865) 272072 ******************************** From nih-image-request@io.ece.drexel.edu Fri Dec 4 11:32 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11564; Fri, 4 Dec 1998 11:32:31 -0500 (EST) Resent-Date: Fri, 4 Dec 1998 11:32:31 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <18cc33e7.3668044e@aol.com> Date: Fri, 4 Dec 1998 10:48:30 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Ann: Application notes on-line Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"UMDw82.0.Vx1.bI0Qs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/700 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 547 Users of the Image Processing Tool Kit may download several *.pdf files containing application notes on topics such as deconvolution to remove image blur, hysteresis thresholding, automatic counting for stereological analysis using grids, coloring features by the magnitude of any measured parameter, measuring feature fractal dimension, and converting images of graphs to numeric data. Either click on the "Application Notes" link at the main web page (http://members.aol.com/ImagProcTK) or go directly to http://members.aol.com/IPTK/index.html From nih-image-request@io.ece.drexel.edu Fri Dec 4 12:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA14120; Fri, 4 Dec 1998 12:07:05 -0500 (EST) Resent-Date: Fri, 4 Dec 1998 12:07:05 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Fri, 4 Dec 1998 12:37:54 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Best Fit Ellipses Resent-Message-ID: <"DLLvs.0.mp2.Gw0Qs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/701 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 209 >I was wondering exactly how NIH image calculates the major and minor axes >etc. of best fit ellipses to irregularly shaped particles. Look at the source ("ellipse.p") to see exactly how it's done. -wayne From nih-image-d-request@io.ece.drexel.edu Sat Dec 5 05:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10923; Sat, 5 Dec 1998 05:19:39 -0500 (EST) Date: Sat, 5 Dec 1998 05:19:39 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812051019.FAA10923@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #134 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/134 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4943 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 134 Today's Topics: Best Fit Ellipses [ Dan Lovegrove ] ADMIN: list commands [ nih-image-owner@io.ece.drexel.edu ] ------------------------------ Date: Fri, 4 Dec 1998 15:11:36 +0000 (BST) From: Dan Lovegrove To: nih-image@io.ece.drexel.edu Subject: Best Fit Ellipses Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I was wondering exactly how NIH image calculates the major and minor axes etc. of best fit ellipses to irregularly shaped particles. Cheers Dan Lovegrove ################################ Castle Milk Stout - Brewed to be Rich and Dark Dan Lovegrove Esq. Department of Earth Sciences University of Oxford Parks Road OXFORD OX1 3PR email: danl@earth.ox.ac.uk telephone: (01865) 272000 direct line: (01865) 272056 fax: (01865) 272072 ******************************** ------------------------------ Date: Fri, 4 Dec 1998 10:48:30 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Ann: Application notes on-line Message-ID: <18cc33e7.3668044e@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Users of the Image Processing Tool Kit may download several *.pdf files containing application notes on topics such as deconvolution to remove image blur, hysteresis thresholding, automatic counting for stereological analysis using grids, coloring features by the magnitude of any measured parameter, measuring feature fractal dimension, and converting images of graphs to numeric data. Either click on the "Application Notes" link at the main web page (http://members.aol.com/ImagProcTK) or go directly to http://members.aol.com/IPTK/index.html ------------------------------ Date: Fri, 4 Dec 1998 12:37:54 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Best Fit Ellipses Message-Id: Content-Type: text/plain; charset="us-ascii" >I was wondering exactly how NIH image calculates the major and minor axes >etc. of best fit ellipses to irregularly shaped particles. Look at the source ("ellipse.p") to see exactly how it's done. -wayne ------------------------------ Date: Sat, 5 Dec 1998 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Message-Id: <199812051005.FAA09162@io.ece.drexel.edu> NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- -------------------------------- End of nih-image-d Digest V98 Issue #134 **************************************** From nih-image-request@io.ece.drexel.edu Sat Dec 5 05:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10934; Sat, 5 Dec 1998 05:19:41 -0500 (EST) Resent-Date: Sat, 5 Dec 1998 05:19:41 -0500 (EST) Date: Sat, 5 Dec 1998 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199812051005.FAA09162@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"Epdvs.0.QF2.GLGQs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/702 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1997 NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- From nih-image-request@io.ece.drexel.edu Mon Dec 7 12:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00212; Mon, 7 Dec 1998 12:06:44 -0500 (EST) Resent-Date: Mon, 7 Dec 1998 12:06:44 -0500 (EST) X-Sender: merchant@mail.persci.com Message-Id: Mime-Version: 1.0 Date: Mon, 7 Dec 1998 10:29:07 -0500 To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU From: Merchant Subject: HSEMB 99 conference (Session on Imaging) Cc: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Resent-Message-ID: <"Z2pif2.0.1c6.V90Rs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/703 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1874 >******************************** > >ANNOUNCEMENT: Special session on Image Analysis for Optical Microscopy > >The Houston Society for Engineering in Medicine and Biology (HSEMB) is >holding its 17th annual Houston Conference on Biomedical Engineering at the >University of Houston on February 11-12, 1999. This conference is usually >well-attended and very informative, and draws attendees from a wide variety >of biomedical engineering fields and from a fairly wide geographic area as >well. We are organizing and chairing a session tentatively entitled "Image >Analysis for Optical Microscopy" as part of the Medical Image Processing >topic. We would like to encourage submissions from parties performing >research on the analysis of microscope images (brightfield, fluorescence, >or confocal) for this session. > >Other topics of potential interest at the conference include Lasers & >Optics, Neural Networks, Biosignal Processing, Medical Physics, Ultrasound, >and Computational Biology. Further information can be found at >http://www.hsemb.org/. The abstract submission deadline is December 11, >1998. Our session will consist of oral presentations (approximately 15-20 >minutes apiece). Only one-page abstracts are published by the conference. > >Please e-mail Fatima Merchant (merchant@persci.com) or Mark Schulze >(schulze@persci.com) for more information about submitting a paper to this >special session. > >***************************** <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Fatima Merchant, Ph.D. Senior Research Engineer Perceptive Scientific Instruments, Inc. 2525 South Shore Blvd., Suite 100 League City, Texas 77573 Telephone: (281) 334-3027 Ext: 219 Toll Free: (800) 288-3027 Ext: 219 Facsimile: (281) 538-2222 Email: merchant@persci.com <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> From nih-image-d-request@io.ece.drexel.edu Tue Dec 8 06:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02187; Tue, 8 Dec 1998 06:27:05 -0500 (EST) Date: Tue, 8 Dec 1998 06:27:05 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812081127.GAA02187@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #135 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/135 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2541 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 135 Today's Topics: HSEMB 99 conference (Session on Imag [ Merchant ] ------------------------------ Date: Mon, 7 Dec 1998 10:29:07 -0500 From: Merchant To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU Cc: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Subject: HSEMB 99 conference (Session on Imaging) Message-Id: Content-Type: text/plain; charset="us-ascii" >******************************** > >ANNOUNCEMENT: Special session on Image Analysis for Optical Microscopy > >The Houston Society for Engineering in Medicine and Biology (HSEMB) is >holding its 17th annual Houston Conference on Biomedical Engineering at the >University of Houston on February 11-12, 1999. This conference is usually >well-attended and very informative, and draws attendees from a wide variety >of biomedical engineering fields and from a fairly wide geographic area as >well. We are organizing and chairing a session tentatively entitled "Image >Analysis for Optical Microscopy" as part of the Medical Image Processing >topic. We would like to encourage submissions from parties performing >research on the analysis of microscope images (brightfield, fluorescence, >or confocal) for this session. > >Other topics of potential interest at the conference include Lasers & >Optics, Neural Networks, Biosignal Processing, Medical Physics, Ultrasound, >and Computational Biology. Further information can be found at >http://www.hsemb.org/. The abstract submission deadline is December 11, >1998. Our session will consist of oral presentations (approximately 15-20 >minutes apiece). Only one-page abstracts are published by the conference. > >Please e-mail Fatima Merchant (merchant@persci.com) or Mark Schulze >(schulze@persci.com) for more information about submitting a paper to this >special session. > >***************************** <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Fatima Merchant, Ph.D. Senior Research Engineer Perceptive Scientific Instruments, Inc. 2525 South Shore Blvd., Suite 100 League City, Texas 77573 Telephone: (281) 334-3027 Ext: 219 Toll Free: (800) 288-3027 Ext: 219 Facsimile: (281) 538-2222 Email: merchant@persci.com <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> -------------------------------- End of nih-image-d Digest V98 Issue #135 **************************************** From nih-image-request@io.ece.drexel.edu Tue Dec 8 13:51 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA11275; Tue, 8 Dec 1998 13:51:43 -0500 (EST) Resent-Date: Tue, 8 Dec 1998 13:51:43 -0500 (EST) From: sandri@pas.matrix.com.br Message-ID: <366D6CCB.2CA4@pas.matrix.com.br> Date: Tue, 08 Dec 1998 16:15:42 -0200 Reply-To: sandri@pas.matrix.com.br X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Quit! Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ug5nY1.0.ks1.XmMRs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/704 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 13 unsubscribe From nih-image-d-request@io.ece.drexel.edu Wed Dec 9 06:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA04786; Wed, 9 Dec 1998 06:25:05 -0500 (EST) Date: Wed, 9 Dec 1998 06:25:05 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812091125.GAA04786@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #136 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/136 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 587 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 136 Today's Topics: Quit! [ sandri@pas.matrix.com.br ] ------------------------------ Date: Tue, 08 Dec 1998 16:15:42 -0200 From: sandri@pas.matrix.com.br To: nih-image@io.ece.drexel.edu Subject: Quit! Message-ID: <366D6CCB.2CA4@pas.matrix.com.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit unsubscribe -------------------------------- End of nih-image-d Digest V98 Issue #136 **************************************** From nih-image-request@io.ece.drexel.edu Wed Dec 9 11:37 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04871; Wed, 9 Dec 1998 11:37:20 -0500 (EST) Resent-Date: Wed, 9 Dec 1998 11:37:20 -0500 (EST) From: "Angelika Zohlen" Organization: Dpt of Ecology, Lund Univ, Sweden To: nih-image@io.ece.drexel.edu Date: Wed, 9 Dec 1998 17:10:48 +0200 MIME-Version: 1.0 Subject: leaf area measurements Reply-to: vxt_anzo@luecology.ecol.lu.se Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <4B215D68F4@Luecology.ecol.lu.se> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by io.ECE.Drexel.EDU id LAA02304 Resent-Message-ID: <"CBOvp1.0.Ba.Z3gRs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/705 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=ISO-8859-1 Content-Length: 653 Hello, I am looking for a scanner to measure leaf areas in situ and roots. I dont think that a scan board is suitable because its a bit clumsy and heavy. Does anybody know if their are scanners available where the electronic part is separate from the board or if there are different scanning systems for measuring in the field? Any information is appreciated. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Angelika Zohlen Soil-Plant Research, Dept. of Ecology Lund University, Ecology Building S-22362 Lund, Sweden Tel. +46/(0)46/2224247, Fax +46/(0)46/2224423, E-mail vxt_anzo@luecology.ecol.lu.se From nih-image-request@io.ece.drexel.edu Wed Dec 9 17:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05248; Wed, 9 Dec 1998 17:49:10 -0500 (EST) Resent-Date: Wed, 9 Dec 1998 17:49:10 -0500 (EST) X-Authentication-Warning: pagan.vims.edu: cutter owned process doing -bs Date: Wed, 9 Dec 1998 17:25:59 -0500 (EST) From: Randy Cutter To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #121 In-Reply-To: <199811210522.AAA03619@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"uF3Xv.0.Ti.MalRs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/707 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 761 I have been registering stacks using Image 1.62 very successfully with grayscale or 8-bit color images. The grayscale stacks do not elucidate many of the features which I would like to portray, and the 8-bit indexed color images look rather bad. I have tried other software, including Image-Pro Plus and Adobe After Effects, but they don't allow registration upon stacks by definition of fiducial points upon the multiple images in the stacks. Does anyone have suggestions concerning registration of 24-bit color image stacks? Thank you. Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- From nih-image-request@io.ece.drexel.edu Wed Dec 9 17:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05292; Wed, 9 Dec 1998 17:49:26 -0500 (EST) Resent-Date: Wed, 9 Dec 1998 17:49:26 -0500 (EST) Message-ID: <366EF878.269B@pop.uky.edu> Date: Wed, 09 Dec 1998 17:23:51 -0500 From: alex gimelbrant Organization: U of K X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: NIH-Image mailing list Subject: Automatic thresholding Content-Transfer-Encoding: 7bit Resent-Message-ID: <"j7N203.0.2e.kXlRs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/706 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 327 Dear Imagers, Can anyone explain how automatic thresholding works, or point me to some description of it? (That's what the online manual says: ... The threshold is automatically set based on an analysis of the histogram of the current selection, or of the entire image if there is no selection. ...) TIA, Alex Gimelbrant From nih-image-d-request@io.ece.drexel.edu Thu Dec 10 06:21 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA21900; Thu, 10 Dec 1998 06:21:05 -0500 (EST) Date: Thu, 10 Dec 1998 06:21:05 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812101121.GAA21900@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #137 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/137 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3141 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 137 Today's Topics: leaf area measurements [ "Angelika Zohlen" ] ------------------------------ Date: Wed, 9 Dec 1998 17:10:48 +0200 From: "Angelika Zohlen" To: nih-image@io.ece.drexel.edu Subject: leaf area measurements Message-ID: <4B215D68F4@Luecology.ecol.lu.se> Content-type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Hello, I am looking for a scanner to measure leaf areas in situ and roots. I dont think that a scan board is suitable because its a bit clumsy and heavy. Does anybody know if their are scanners available where the electronic part is separate from the board or if there are different scanning systems for measuring in the field? Any information is appreciated. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Angelika Zohlen Soil-Plant Research, Dept. of Ecology Lund University, Ecology Building S-22362 Lund, Sweden Tel. +46/(0)46/2224247, Fax +46/(0)46/2224423, E-mail vxt_anzo@luecology.ecol.lu.se ------------------------------ Date: Wed, 09 Dec 1998 17:23:51 -0500 From: alex gimelbrant To: NIH-Image mailing list Subject: Automatic thresholding Message-ID: <366EF878.269B@pop.uky.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Imagers, Can anyone explain how automatic thresholding works, or point me to some description of it? (That's what the online manual says: ... The threshold is automatically set based on an analysis of the histogram of the current selection, or of the entire image if there is no selection. ...) TIA, Alex Gimelbrant ------------------------------ Date: Wed, 9 Dec 1998 17:25:59 -0500 (EST) From: Randy Cutter To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #121 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I have been registering stacks using Image 1.62 very successfully with grayscale or 8-bit color images. The grayscale stacks do not elucidate many of the features which I would like to portray, and the 8-bit indexed color images look rather bad. I have tried other software, including Image-Pro Plus and Adobe After Effects, but they don't allow registration upon stacks by definition of fiducial points upon the multiple images in the stacks. Does anyone have suggestions concerning registration of 24-bit color image stacks? Thank you. Randy. --------------------- Randy Cutter Virginia Institute of Marine Science Route 1208 Gloucester Point, VA 23062 USA phone 804 684-7365 fax 804 684-7399 or 7045 email: cutter@vims.edu --------------------- -------------------------------- End of nih-image-d Digest V98 Issue #137 **************************************** From nih-image-request@io.ece.drexel.edu Thu Dec 10 10:08 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14868; Thu, 10 Dec 1998 10:08:37 -0500 (EST) Resent-Date: Thu, 10 Dec 1998 10:08:37 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Thu, 10 Dec 1998 08:27:19 -0600 From: "Daniel Blander" To: Subject: frame grabber Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ECE.Drexel.EDU id JAA10679 Resent-Message-ID: <"UlTX5.0.0d2.DfzRs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/708 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 306 I have an old macintosh with whichi am trying to set up color image analysis using NIH image. I need a color frame grabber on a NuBus board (Scion LG3 or equivalent). Is there anyone out there who has one or knows how i can get one?? Daniel Blander Instructor in Urology UT Southwestern Medical School From nih-image-d-request@io.ece.drexel.edu Fri Dec 11 06:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA15073; Fri, 11 Dec 1998 06:19:23 -0500 (EST) Date: Fri, 11 Dec 1998 06:19:23 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812111119.GAA15073@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #138 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/138 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 945 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 138 Today's Topics: frame grabber [ "Daniel Blander" To: Subject: frame grabber Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit I have an old macintosh with whichi am trying to set up color image analysis using NIH image. I need a color frame grabber on a NuBus board (Scion LG3 or equivalent). Is there anyone out there who has one or knows how i can get one?? Daniel Blander Instructor in Urology UT Southwestern Medical School -------------------------------- End of nih-image-d Digest V98 Issue #138 **************************************** From nih-image-request@io.ece.drexel.edu Fri Dec 11 13:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA02446; Fri, 11 Dec 1998 13:27:10 -0500 (EST) Resent-Date: Fri, 11 Dec 1998 13:27:10 -0500 (EST) Message-Id: <199812111808.NAA00561@io.ece.drexel.edu> X-Mailer: Microsoft Outlook Express for Macintosh - 4.01 (295) Date: Fri, 11 Dec 1998 19:10:09 +0100 Subject: Trigger problems From: "Johan Jersblad" To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 X-Priority: 3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id NAA00561 Resent-Message-ID: <"1CLBg.0.u8.O-LSs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/709 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="ISO-8859-1" Content-Length: 1233 Dear list, This is the first time I write here and it is a cry for help. Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image 1.62a. The only thing we want to do is to trigger our CCD camera at a given time to get a frame. This doesnt work. What we have tried is the following; 1. The camera is in normal mode, meaning that it is continously aquiring fields. The framegrabber is triggered. Every time we trigger the framegrabber we get a picture. Seems normal. 2. The camera is in RR mode. (RR-reset.restart) We DONT trigger the camera, BUT we trigger the framegrabber. Result: Nothing happens. It still says "Waiting for trigger" in the window. We dont understand completely. I would expect a black picture, or something from the memory. 3. The camera is in RR mode. We trigger the camera. We wait 100ms. We trigger the framegrabber. Result: nothing happens. We trigger the framegrabber again. We see a new picture. I dont understand anything. Has anybody out there done this or does anyone have any expirience whitin this field, or does anyone have a relative that has got a friend whose husband works for........etc. Yours sincerely, Johan Jersblad From nih-image-request@io.ece.drexel.edu Fri Dec 11 15:03 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA10945; Fri, 11 Dec 1998 15:03:37 -0500 (EST) Resent-Date: Fri, 11 Dec 1998 15:03:37 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Fri, 11 Dec 1998 14:58:45 -0400 To: nih-image@io.ece.drexel.edu From: Laird Bloom Subject: counting cells in tissue sections Resent-Message-ID: <"C22aT3.0._I2.6UNSs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/710 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 515 NIH Image users: Does anyone know a good way to adapt the cell counting macro to counting cells in tissue sections? There are two problems I'm trying to solve: first, the cells touch each other, and second, they're stained with a surface marker, so each one looks like a ring of stain around a blank nucleus. It's obvious to the eye where individual cells are, but without drawing circles around each one manually, how can I tell the computer what to count? Thanks, Laird Bloom MIT Center for Cancer Research From nih-image-request@io.ece.drexel.edu Fri Dec 11 15:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA12616; Fri, 11 Dec 1998 15:20:51 -0500 (EST) Resent-Date: Fri, 11 Dec 1998 15:20:51 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Fri, 11 Dec 1998 15:08:15 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: counting cells in tissue sections Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id PAA11417 Resent-Message-ID: <"-hBat3.0.Yo2.PlNSs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/711 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 677 Can you email a small section of one image? (say 200 x 200 pixels) to me at "schuette@umich.edu" ? Wade >>> Laird Bloom 12/11 3:03 PM >>> NIH Image users: Does anyone know a good way to adapt the cell counting macro to counting cells in tissue sections? There are two problems I'm trying to solve: first, the cells touch each other, and second, they're stained with a surface marker, so each one looks like a ring of stain around a blank nucleus. It's obvious to the eye where individual cells are, but without drawing circles around each one manually, how can I tell the computer what to count? Thanks, Laird Bloom MIT Center for Cancer Research From nih-image-d-request@io.ece.drexel.edu Sat Dec 12 06:11 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA04916; Sat, 12 Dec 1998 06:11:20 -0500 (EST) Date: Sat, 12 Dec 1998 06:11:20 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812121111.GAA04916@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #139 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/139 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4152 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 139 Today's Topics: Trigger problems [ "Johan Jersblad" ] unsubscribe [ Michal Ondrejcek ] counting cells in tissue sections [ Laird Bloom ] Re: counting cells in tissue section [ "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Trigger problems Message-Id: <199812111808.NAA00561@io.ece.drexel.edu> Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear list, This is the first time I write here and it is a cry for help. Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image 1.62a. The only thing we want to do is to trigger our CCD camera at a given time to get a frame. This doesnt work. What we have tried is the following; 1. The camera is in normal mode, meaning that it is continously aquiring fields. The framegrabber is triggered. Every time we trigger the framegrabber we get a picture. Seems normal. 2. The camera is in RR mode. (RR-reset.restart) We DONT trigger the camera, BUT we trigger the framegrabber. Result: Nothing happens. It still says "Waiting for trigger" in the window. We dont understand completely. I would expect a black picture, or something from the memory. 3. The camera is in RR mode. We trigger the camera. We wait 100ms. We trigger the framegrabber. Result: nothing happens. We trigger the framegrabber again. We see a new picture. I dont understand anything. Has anybody out there done this or does anyone have any expirience whitin this field, or does anyone have a relative that has got a friend whose husband works for........etc. Yours sincerely, Johan Jersblad ------------------------------ Date: Fri, 11 Dec 1998 13:39:12 -0500 (EST) From: Michal Ondrejcek To: nih-image-d@io.ece.drexel.edu Subject: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" ------------------------------ Date: Fri, 11 Dec 1998 14:58:45 -0400 From: Laird Bloom To: nih-image@io.ece.drexel.edu Subject: counting cells in tissue sections Message-Id: Content-Type: text/plain; charset="us-ascii" NIH Image users: Does anyone know a good way to adapt the cell counting macro to counting cells in tissue sections? There are two problems I'm trying to solve: first, the cells touch each other, and second, they're stained with a surface marker, so each one looks like a ring of stain around a blank nucleus. It's obvious to the eye where individual cells are, but without drawing circles around each one manually, how can I tell the computer what to count? Thanks, Laird Bloom MIT Center for Cancer Research ------------------------------ Date: Fri, 11 Dec 1998 15:08:15 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: counting cells in tissue sections Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit Can you email a small section of one image? (say 200 x 200 pixels) to me at "schuette@umich.edu" ? Wade >>> Laird Bloom 12/11 3:03 PM >>> NIH Image users: Does anyone know a good way to adapt the cell counting macro to counting cells in tissue sections? There are two problems I'm trying to solve: first, the cells touch each other, and second, they're stained with a surface marker, so each one looks like a ring of stain around a blank nucleus. It's obvious to the eye where individual cells are, but without drawing circles around each one manually, how can I tell the computer what to count? Thanks, Laird Bloom MIT Center for Cancer Research -------------------------------- End of nih-image-d Digest V98 Issue #139 **************************************** From nih-image-request@io.ece.drexel.edu Sat Dec 12 08:07 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA16301; Sat, 12 Dec 1998 08:07:05 -0500 (EST) Resent-Date: Sat, 12 Dec 1998 08:07:05 -0500 (EST) Message-ID: <19981212124138.19441.rocketmail@web1.rocketmail.com> Date: Sat, 12 Dec 1998 04:41:38 -0800 (PST) From: Mark Vivino Subject: Re: Trigger problems To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"FsGPa2.0.gg3.VVcSs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/712 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 686 ---Johan Jersblad wrote: > Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image > 1.62a. > > The only thing we want to do is to trigger our CCD camera at a given time to > get a frame. Once triggered the frame grabber waits until it gets a vertical refresh, then begins capture of video. No refresh no capture. One can run into trouble if the camera trys to have ways set on putting out video and the frame grabber is not expecting that. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com From nih-image-request@io.ece.drexel.edu Sat Dec 12 10:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA02420; Sat, 12 Dec 1998 10:49:59 -0500 (EST) Resent-Date: Sat, 12 Dec 1998 10:49:59 -0500 (EST) Message-Id: <3.0.5.32.19981212163522.01273e80@krzsun.med-rz.uni-sb.de> X-Sender: phblin@krzsun.med-rz.uni-sb.de X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sat, 12 Dec 1998 16:35:22 +0100 To: nih-image@io.ece.drexel.edu From: Bernd Lindemann Subject: distortion in space Mime-Version: 1.0 Resent-Message-ID: <"WDvQY.0.dH.eteSs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/713 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2309 I have followed exchanges in this discussion group with interest, even though not since July 1998. My question is not directly concerned with macros in NIH-image, but may nevertheless be of interest to some of you. I am working with synapses in tissues. The synapses can be stained (with the fluorescent tracer FM1-43) and then show up as fluorescent spots. I take stacks of images to record the 3-D distribution of the spots. A program I have written scans the stack for spots, numbers the spots (about 100 per stack) and records their properties (x, y, z -coordinates, peak intensity, diameter, slope). Thus each spot has its own identity, it is an object (with a "type" structure in my programming language). Illustrations are found on my web-site: http://www.med-rz.uni-sb.de/med_fak/physiol2/LDM/index.html When the tissue is stimulated, some of the synapses are activated and the fluorescence of those activated (perhaps 10 or 20 out of 100) decreases or disappears. This is recorded by repetitive acquisition of the stack. To follow individual spots through an experiment with several stimulations, thats the purpose of this work. Unfortunately, there is a complication due to movement of spots: driven by local swelling and shrinking of cells some spots cannot maintain their coordinates and change their inter-spot distances. The travel can be up to 10% of the stack diameter. Thus, even though the movement of spots is limited, spot identity is not always obvious. While the spots can sometimes be traced by inspection, this should be automated by programming. Notably, the time of acquisition of a stack is longer than the time it takes to deform the pattern of spots. Thus, it is impossible to get a continuous record. I am wondering whether one might compare two stacks by cross-correlation, looking for parts which have not changed, then reconstruct the remainder starting with those parts which have not changed. This would mean to go for the most likely model of the distortion. However, there may be better possibilities to deal with the distortion in space. Perhaps people working with distortion in electron microscopy images know suitable programming strategies? I shall welcome your ideas and advice about this. Thanks in advance for your comments, Bernd Lindemann. From nih-image-d-request@io.ece.drexel.edu Sun Dec 13 06:12 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17570; Sun, 13 Dec 1998 06:12:01 -0500 (EST) Date: Sun, 13 Dec 1998 06:12:01 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812131112.GAA17570@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #140 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/140 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3972 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 140 Today's Topics: Re: Trigger problems [ Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Trigger problems Message-ID: <19981212124138.19441.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii ---Johan Jersblad wrote: > Equipment: LG3 framegrabber, PPC Mac, CCD camera SONY XC8500-CE, Scion Image > 1.62a. > > The only thing we want to do is to trigger our CCD camera at a given time to > get a frame. Once triggered the frame grabber waits until it gets a vertical refresh, then begins capture of video. No refresh no capture. One can run into trouble if the camera trys to have ways set on putting out video and the frame grabber is not expecting that. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Sat, 12 Dec 1998 16:35:22 +0100 From: Bernd Lindemann To: nih-image@io.ece.drexel.edu Subject: distortion in space Message-Id: <3.0.5.32.19981212163522.01273e80@krzsun.med-rz.uni-sb.de> Content-Type: text/plain; charset="us-ascii" I have followed exchanges in this discussion group with interest, even though not since July 1998. My question is not directly concerned with macros in NIH-image, but may nevertheless be of interest to some of you. I am working with synapses in tissues. The synapses can be stained (with the fluorescent tracer FM1-43) and then show up as fluorescent spots. I take stacks of images to record the 3-D distribution of the spots. A program I have written scans the stack for spots, numbers the spots (about 100 per stack) and records their properties (x, y, z -coordinates, peak intensity, diameter, slope). Thus each spot has its own identity, it is an object (with a "type" structure in my programming language). Illustrations are found on my web-site: http://www.med-rz.uni-sb.de/med_fak/physiol2/LDM/index.html When the tissue is stimulated, some of the synapses are activated and the fluorescence of those activated (perhaps 10 or 20 out of 100) decreases or disappears. This is recorded by repetitive acquisition of the stack. To follow individual spots through an experiment with several stimulations, thats the purpose of this work. Unfortunately, there is a complication due to movement of spots: driven by local swelling and shrinking of cells some spots cannot maintain their coordinates and change their inter-spot distances. The travel can be up to 10% of the stack diameter. Thus, even though the movement of spots is limited, spot identity is not always obvious. While the spots can sometimes be traced by inspection, this should be automated by programming. Notably, the time of acquisition of a stack is longer than the time it takes to deform the pattern of spots. Thus, it is impossible to get a continuous record. I am wondering whether one might compare two stacks by cross-correlation, looking for parts which have not changed, then reconstruct the remainder starting with those parts which have not changed. This would mean to go for the most likely model of the distortion. However, there may be better possibilities to deal with the distortion in space. Perhaps people working with distortion in electron microscopy images know suitable programming strategies? I shall welcome your ideas and advice about this. Thanks in advance for your comments, Bernd Lindemann. -------------------------------- End of nih-image-d Digest V98 Issue #140 **************************************** From nih-image-request@io.ece.drexel.edu Mon Dec 14 02:44 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA03106; Mon, 14 Dec 1998 02:44:23 -0500 (EST) Resent-Date: Mon, 14 Dec 1998 02:44:23 -0500 (EST) X-Sender: bmenard@pop-server.unil.ch Message-Id: In-Reply-To: <199812111808.NAA00561@io.ece.drexel.edu> Mime-Version: 1.0 Content-Transfer-Encoding: 8bit Date: Mon, 14 Dec 1998 08:22:26 +0100 To: Johan Jersblad , nih-image@io.ece.drexel.edu From: Bertrand Menard Subject: Re: Trigger problems Resent-Message-ID: <"IFU181.0.kG.jpBTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/714 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 1403 Dear Johan, I couldn't directly help you, but I could give you an idea. I have a similar problem with my JVc camera and my CG7 framegrabber (problem is the same with a LG3). When I use the integration mode of the camera, if I plug directly the output trigger of the camera to the framegrabber, I only obtain black image. The problem is that the trigger signal of the camera is a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema of a simple circuit to delay the TTL edge. So I could give you an advise, test your signals with an oscilloscope. Good luck. Bertrand ********************************************************** Bertrand MENARD University of Lausanne Universit de Lausanne Institut of Ecology Institut d'cologie Plant Biology and Physiology Biologie et Physiologie Vgtales Batiment de Biologie Batiment de Biologie CH-1015 LAUSANNE CH-1015 LAUSANNE Switzerland Suisse Tel : 00 41 21 692 42 19 Fax : 00 41 21 692 41 95 E-Mail : Bertrand.Menard@ie-bpv.unil.ch ********************************************************** From nih-image-request@io.ece.drexel.edu Mon Dec 14 08:08 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA00763; Mon, 14 Dec 1998 08:08:08 -0500 (EST) Resent-Date: Mon, 14 Dec 1998 08:08:08 -0500 (EST) Message-ID: <36755057.756@pro.via-rs.com.br> Date: Mon, 14 Dec 1998 10:52:23 -0700 From: Luthero Martins Reply-To: luthero@pro.via-rs.com.br X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: ophthalmologist References: <199812131107.GAA16996@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"aeJkB1.0.t27.baGTs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/715 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 83 Please! I'm looking for ophthalmologist in the group. Thanks Luthero Martins From nih-image-request@io.ece.drexel.edu Mon Dec 14 08:59 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA05679; Mon, 14 Dec 1998 08:59:20 -0500 (EST) Resent-Date: Mon, 14 Dec 1998 08:59:20 -0500 (EST) Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu> X-Sender: dlparker@facstaff.wisc.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2 Date: Mon, 14 Dec 1998 07:45:15 -0600 To: nih-image@io.ece.drexel.edu From: David Parker Subject: unsubscribe In-Reply-To: <199812131111.GAA17419@io.ece.drexel.edu> Mime-Version: 1.0 Resent-Message-ID: <"appCF2.0.xv.eKHTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/716 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Mon Dec 14 10:57 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15543; Mon, 14 Dec 1998 10:57:56 -0500 (EST) Resent-Date: Mon, 14 Dec 1998 10:57:56 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 14 Dec 1998 07:37:12 -0700 To: nih-image@io.ece.drexel.edu From: Jonathan Nissanov Subject: unsubscribe_yoni@cbis.ece.drexel.edu Resent-Message-ID: <"qfG582.0.hI3.-0JTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/717 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 821 -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ From nih-image-request@io.ece.drexel.edu Mon Dec 14 23:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA16651 for cshtest@io.ece.drexel.edu; Mon, 14 Dec 1998 23:14:24 -0500 (EST) Resent-Date: Mon, 14 Dec 1998 23:14:24 -0500 (EST) X-Sender: driska4@pop3.netaxs.com Message-Id: Mime-Version: 1.0 Date: Mon, 14 Dec 1998 23:04:25 -0500 To: nih-image@io.ece.drexel.edu From: Steve Driska Subject: Can a number be typed into the Results window? Resent-Message-ID: <"ksQVb1.0.0n3.E1UTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/718 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 671 I can't find a way to type in a number into the results scrreen. It seems like it would be easy. What I'm trying to do is play video into NIH Image ( a quick time movie) which the program opens as a stack. I want to trace the objects in the picture to measure their length. This I can do. What I need to do is this: The video has a time/date stamp as part of the image. I would like to manually read the time, and enter it into column of the results, so that it is matched with the length measurement. Is there a simple way, or will I have to learn to do macros? Thanks a lot, Steve Driska Steve Driska driska4@netaxs.com From nih-image-d-request@io.ece.drexel.edu Mon Dec 14 23:17 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA17065; Mon, 14 Dec 1998 23:17:08 -0500 (EST) Date: Mon, 14 Dec 1998 23:17:08 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812150417.XAA17065@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #141 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/141 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5135 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 141 Today's Topics: Re: Trigger problems [ Bertrand Menard ] ------------------------------ Date: Mon, 14 Dec 1998 08:22:26 +0100 From: Bertrand Menard To: Johan Jersblad , nih-image@io.ece.drexel.edu Subject: Re: Trigger problems Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Dear Johan, I couldn't directly help you, but I could give you an idea. I have a similar problem with my JVc camera and my CG7 framegrabber (problem is the same with a LG3). When I use the integration mode of the camera, if I plug directly the output trigger of the camera to the framegrabber, I only obtain black image. The problem is that the trigger signal of the camera is a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema of a simple circuit to delay the TTL edge. So I could give you an advise, test your signals with an oscilloscope. Good luck. Bertrand ********************************************************** Bertrand MENARD University of Lausanne Universit de Lausanne Institut of Ecology Institut d'cologie Plant Biology and Physiology Biologie et Physiologie Vgtales Batiment de Biologie Batiment de Biologie CH-1015 LAUSANNE CH-1015 LAUSANNE Switzerland Suisse Tel : 00 41 21 692 42 19 Fax : 00 41 21 692 41 95 E-Mail : Bertrand.Menard@ie-bpv.unil.ch ********************************************************** ------------------------------ Date: Mon, 14 Dec 1998 10:52:23 -0700 From: Luthero Martins To: nih-image@io.ece.drexel.edu Subject: ophthalmologist Message-ID: <36755057.756@pro.via-rs.com.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please! I'm looking for ophthalmologist in the group. Thanks Luthero Martins ------------------------------ Date: Mon, 14 Dec 1998 07:45:15 -0600 From: David Parker To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu> Content-Type: text/plain; charset="us-ascii" unsubscribe ------------------------------ Date: Mon, 14 Dec 1998 07:37:12 -0700 From: Jonathan Nissanov To: nih-image@io.ece.drexel.edu Subject: unsubscribe_yoni@cbis.ece.drexel.edu Message-Id: Content-Type: text/plain; charset="us-ascii" -------------------------------------------------------------------------------- ----------------------- Jonathan Nissanov, Ph.D. Associate Director Computer Vision Center for Vertebrate Brain Mapping, a NIH Biomedical Research Technology Resource http://cbis.ece.drexel.edu/ICVC/ -------------------------------------------------------------------------------- ----------------------- Imaging and Computer Vision Center Tel: 215-895-1381 Drexel University Fax: 215-895-4987 Phildelphia, PA 19104 yoni@coe.drexel.edu ------------------------------------------------------------------------------- ------------------------ ------------------------------ Date: Mon, 14 Dec 1998 23:04:25 -0500 From: Steve Driska To: nih-image@io.ece.drexel.edu Subject: Can a number be typed into the Results window? Message-Id: Content-Type: text/plain; charset="us-ascii" I can't find a way to type in a number into the results scrreen. It seems like it would be easy. What I'm trying to do is play video into NIH Image ( a quick time movie) which the program opens as a stack. I want to trace the objects in the picture to measure their length. This I can do. What I need to do is this: The video has a time/date stamp as part of the image. I would like to manually read the time, and enter it into column of the results, so that it is matched with the length measurement. Is there a simple way, or will I have to learn to do macros? Thanks a lot, Steve Driska Steve Driska driska4@netaxs.com -------------------------------- End of nih-image-d Digest V98 Issue #141 **************************************** From nih-image-request@io.ece.drexel.edu Tue Dec 15 04:26 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA17698 for cshtest@io.ece.drexel.edu; Tue, 15 Dec 1998 04:26:26 -0500 (EST) Resent-Date: Tue, 15 Dec 1998 04:26:26 -0500 (EST) X-Sender: md1rjsh@swineshaw.shef.ac.uk Message-Id: Mime-Version: 1.0 Date: Tue, 15 Dec 1998 09:06:56 +0000 To: nih-image@io.ece.drexel.edu From: Rachael Simpson Subject: using scion image Resent-Message-ID: <"p5bY83.0.Gs3.ZSYTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/719 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1003 Dear Scion, >> >>My name is Rachael Simpson and I am Currently working on an MD project >>at Sheffield Children's Hospital, England. I am trained in >>Orthopaedics and my MD project is looking at the evaluation of >>clubfoot deformity in children. As part of this project, I am >>evaluating foot function using pedobarography. This essentially gives >>me an imprint of the child's foot with a plot of points over the >>surface showing the change in position of the pressure through the >>foot with walking. >> Essentially what I would like to do using the NIH image >>programme, is to convert the plot on the foot into graphical form. I >>thought it may be possible to do this by first scanning the image in >>and then superimposing a graph around this and then to remove the >>foot image leaving only the plot in place. I am writing to see >>whether anyone has any experience of such a method or how I might go >>about it. I would be grateful for any help that can be offered. Thank >>you. Rachael. From nih-image-request@io.ece.drexel.edu Tue Dec 15 10:36 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22602 for cshtest@io.ece.drexel.edu; Tue, 15 Dec 1998 10:36:44 -0500 (EST) Resent-Date: Tue, 15 Dec 1998 10:36:44 -0500 (EST) Message-Id: <199812151510.JAA22800@mail1.doit.wisc.edu> X-Sender: kvogt@facstaff.wisc.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Date: Tue, 15 Dec 1998 09:06:10 -0600 To: nih-image@io.ece.drexel.edu From: Kevin Vogt Subject: Re: nih-image-d Digest V98 #141 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA20246 Resent-Message-ID: <"ReIEF3.0.Ty4.CmdTs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/720 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 5310 unsubscribe At 11:15 PM 12/14/98 -0500, you wrote: >Content-Type: text/plain >MIME-Version: 1.0 > >nih-image-d Digest Volume 98 : Issue 141 > >Today's Topics: > Re: Trigger problems [ Bertrand Menard ophthalmologist [ Luthero Martins unsubscribe [ David Parker unsubscribe_yoni@cbis.ece.drexel.edu [ Jonathan Nissanov Can a number be typed into the Resul [ Steve Driska ] >Date: Mon, 14 Dec 1998 08:22:26 +0100 >From: Bertrand Menard >To: Johan Jersblad , nih-image@io.ece.drexel.edu >Subject: Re: Trigger problems >Message-Id: >Content-Type: text/plain; charset="iso-8859-1" >MIME-Version: 1.0 >X-MIME-Autoconverted: from 8bit to quoted-printable by mail2.doit.wisc.edu id WAA91880 > >Dear Johan, > >I couldn't directly help you, but I could give you an idea. I have a >similar problem with my JVc camera and my CG7 framegrabber (problem is the >same with a LG3). When I use the integration mode of the camera, if I plug >directly the output trigger of the camera to the framegrabber, I only >obtain black image. The problem is that the trigger signal of the camera is >a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is >a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema >of a simple circuit to delay the TTL edge. > >So I could give you an advise, test your signals with an oscilloscope. > >Good luck. > > > >Bertrand > >********************************************************** > > Bertrand MENARD > > > University of Lausanne Universit de Lausanne > Institut of Ecology Institut d'cologie >Plant Biology and Physiology Biologie et Physiologie Vgtales > Batiment de Biologie Batiment de Biologie > CH-1015 LAUSANNE CH-1015 LAUSANNE > Switzerland Suisse > > Tel : 00 41 21 692 42 19 > Fax : 00 41 21 692 41 95 > > E-Mail : Bertrand.Menard@ie-bpv.unil.ch > >********************************************************** >Date: Mon, 14 Dec 1998 10:52:23 -0700 >From: Luthero Martins >To: nih-image@io.ece.drexel.edu >Subject: ophthalmologist >Message-ID: <36755057.756@pro.via-rs.com.br> >Content-Type: text/plain; charset=us-ascii >MIME-Version: 1.0 >Content-Transfer-Encoding: 7bit > >Please! > >I'm looking for ophthalmologist in the group. > >Thanks > >Luthero Martins >Date: Mon, 14 Dec 1998 07:45:15 -0600 >From: David Parker >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe >Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu> >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >unsubscribe >Date: Mon, 14 Dec 1998 07:37:12 -0700 >From: Jonathan Nissanov >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe_yoni@cbis.ece.drexel.edu >Message-Id: >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >--------------------------------------------------------------------------- ----- >----------------------- > Jonathan Nissanov, Ph.D. > Associate Director > Computer Vision Center for Vertebrate Brain Mapping, > a NIH Biomedical Research Technology Resource > http://cbis.ece.drexel.edu/ICVC/ >--------------------------------------------------------------------------- ----- >----------------------- >Imaging and Computer Vision Center Tel: 215-895-1381 >Drexel University Fax: >215-895-4987 >Phildelphia, PA 19104 >yoni@coe.drexel.edu > ------------------------------------------------------------------------------- >------------------------ >Date: Mon, 14 Dec 1998 23:04:25 -0500 >From: Steve Driska >To: nih-image@io.ece.drexel.edu >Subject: Can a number be typed into the Results window? >Message-Id: >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >I can't find a way to type in a number into the results scrreen. It seems >like it would be easy. > >What I'm trying to do is play video into NIH Image ( a quick time movie) >which the program opens as a stack. I want to trace the objects in the >picture to measure their length. This I can do. What I need to do is >this: The video has a time/date stamp as part of the image. I would like >to manually read the time, and enter it into column of the results, so that >it is matched with the length measurement. > >Is there a simple way, or will I have to learn to do macros? > >Thanks a lot, > > Steve Driska > > > >Steve Driska driska4@netaxs.com > > Kevin Vogt 262-1360 University of Wisconsin-Madison Dept. of Biomolecular Chemistry 580 MSC 1300 University Ave. Madison, WI 53706 From nih-image-d-request@io.ece.drexel.edu Wed Dec 16 07:49 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA28383; Wed, 16 Dec 1998 07:49:52 -0500 (EST) Date: Wed, 16 Dec 1998 07:49:52 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812161249.HAA28383@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #142 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/142 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 7309 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 142 Today's Topics: using scion image [ Rachael Simpson To: nih-image@io.ece.drexel.edu Subject: using scion image Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Scion, >> >>My name is Rachael Simpson and I am Currently working on an MD project >>at Sheffield Children's Hospital, England. I am trained in >>Orthopaedics and my MD project is looking at the evaluation of >>clubfoot deformity in children. As part of this project, I am >>evaluating foot function using pedobarography. This essentially gives >>me an imprint of the child's foot with a plot of points over the >>surface showing the change in position of the pressure through the >>foot with walking. >> Essentially what I would like to do using the NIH image >>programme, is to convert the plot on the foot into graphical form. I >>thought it may be possible to do this by first scanning the image in >>and then superimposing a graph around this and then to remove the >>foot image leaving only the plot in place. I am writing to see >>whether anyone has any experience of such a method or how I might go >>about it. I would be grateful for any help that can be offered. Thank >>you. Rachael. ------------------------------ Date: Tue, 15 Dec 1998 09:06:10 -0600 From: Kevin Vogt To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V98 #141 Message-Id: <199812151510.JAA22800@mail1.doit.wisc.edu> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit unsubscribe At 11:15 PM 12/14/98 -0500, you wrote: >Content-Type: text/plain >MIME-Version: 1.0 > >nih-image-d Digest Volume 98 : Issue 141 > >Today's Topics: > Re: Trigger problems [ Bertrand Menard ophthalmologist [ Luthero Martins unsubscribe [ David Parker unsubscribe_yoni@cbis.ece.drexel.edu [ Jonathan Nissanov Can a number be typed into the Resul [ Steve Driska ] >Date: Mon, 14 Dec 1998 08:22:26 +0100 >From: Bertrand Menard >To: Johan Jersblad , nih-image@io.ece.drexel.edu >Subject: Re: Trigger problems >Message-Id: >Content-Type: text/plain; charset="iso-8859-1" >MIME-Version: 1.0 >X-MIME-Autoconverted: from 8bit to quoted-printable by mail2.doit.wisc.edu id WAA91880 > >Dear Johan, > >I couldn't directly help you, but I could give you an idea. I have a >similar problem with my JVc camera and my CG7 framegrabber (problem is the >same with a LG3). When I use the integration mode of the camera, if I plug >directly the output trigger of the camera to the framegrabber, I only >obtain black image. The problem is that the trigger signal of the camera is >a TTL edge growing from +0V to 5. The signal that is waiting by the CG7 is >a falling of a TTL edge from +5V to 0. So Stein Roervik gave me the schema >of a simple circuit to delay the TTL edge. > >So I could give you an advise, test your signals with an oscilloscope. > >Good luck. > > > >Bertrand > >********************************************************** > > Bertrand MENARD > > > University of Lausanne Universit de Lausanne > Institut of Ecology Institut d'cologie >Plant Biology and Physiology Biologie et Physiologie Vgtales > Batiment de Biologie Batiment de Biologie > CH-1015 LAUSANNE CH-1015 LAUSANNE > Switzerland Suisse > > Tel : 00 41 21 692 42 19 > Fax : 00 41 21 692 41 95 > > E-Mail : Bertrand.Menard@ie-bpv.unil.ch > >********************************************************** >Date: Mon, 14 Dec 1998 10:52:23 -0700 >From: Luthero Martins >To: nih-image@io.ece.drexel.edu >Subject: ophthalmologist >Message-ID: <36755057.756@pro.via-rs.com.br> >Content-Type: text/plain; charset=us-ascii >MIME-Version: 1.0 >Content-Transfer-Encoding: 7bit > >Please! > >I'm looking for ophthalmologist in the group. > >Thanks > >Luthero Martins >Date: Mon, 14 Dec 1998 07:45:15 -0600 >From: David Parker >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe >Message-Id: <199812141339.HAA32972@mail5.doit.wisc.edu> >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >unsubscribe >Date: Mon, 14 Dec 1998 07:37:12 -0700 >From: Jonathan Nissanov >To: nih-image@io.ece.drexel.edu >Subject: unsubscribe_yoni@cbis.ece.drexel.edu >Message-Id: >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >--------------------------------------------------------------------------- ----- >----------------------- > Jonathan Nissanov, Ph.D. > Associate Director > Computer Vision Center for Vertebrate Brain Mapping, > a NIH Biomedical Research Technology Resource > http://cbis.ece.drexel.edu/ICVC/ >--------------------------------------------------------------------------- ----- >----------------------- >Imaging and Computer Vision Center Tel: 215-895-1381 >Drexel University Fax: >215-895-4987 >Phildelphia, PA 19104 >yoni@coe.drexel.edu > ------------------------------------------------------------------------------- >------------------------ >Date: Mon, 14 Dec 1998 23:04:25 -0500 >From: Steve Driska >To: nih-image@io.ece.drexel.edu >Subject: Can a number be typed into the Results window? >Message-Id: >Content-Type: text/plain; charset="us-ascii" >MIME-Version: 1.0 > >I can't find a way to type in a number into the results scrreen. It seems >like it would be easy. > >What I'm trying to do is play video into NIH Image ( a quick time movie) >which the program opens as a stack. I want to trace the objects in the >picture to measure their length. This I can do. What I need to do is >this: The video has a time/date stamp as part of the image. I would like >to manually read the time, and enter it into column of the results, so that >it is matched with the length measurement. > >Is there a simple way, or will I have to learn to do macros? > >Thanks a lot, > > Steve Driska > > > >Steve Driska driska4@netaxs.com > > Kevin Vogt 262-1360 University of Wisconsin-Madison Dept. of Biomolecular Chemistry 580 MSC 1300 University Ave. Madison, WI 53706 -------------------------------- End of nih-image-d Digest V98 Issue #142 **************************************** From nih-image-request@io.ece.drexel.edu Wed Dec 16 09:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA05679 for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 09:06:50 -0500 (EST) Resent-Date: Wed, 16 Dec 1998 09:06:50 -0500 (EST) From: "Richard M. Clark" Organization: University of Luton To: nih-image@io.ece.drexel.edu Date: Wed, 16 Dec 1998 13:43:43 GMT MIME-Version: 1.0 Content-transfer-encoding: 7BIT Subject: Request for IP info... Reply-to: richard.m.clark@luton.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.53/R1) Message-ID: <13E1883C85@novell.science.luton.ac.uk> Resent-Message-ID: <"3OU7y1.0.9q.CZxTs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/721 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1219 To all members of nih-image list... I used to be a member of this list but un-subscribed due to email problems - I am now back on the list and wanted to ask some quick questions.... I am an Image Processing researcher who is working on combining some AI techniques with IP for 'intelligent machine vision' .... I am currently working on 'feature extraction' techniques and was wondering if anyone has/knows-of any papers which cover 'feature extraction' algorithms/techniques etc.... I am also interested in writing papers, articles etc regarding my research and have done a lot of work so far regarding 'wavelets and image processing' - I am currently experimenting with wavelets and will have some pretty good results during next year .... is there anyone who publishes image processing 'documents' or 'journals' (or AI related) who is looking for material from 'researchers' within this area? Many thanks, Richard M. Clark ______________________________________________ Richard M. Clark, Research Student, University of Luton, Department of Computing and Information Systems, Room: B303 - (01582) 734111 extn 2071 NOVELL: richard.m.clark@luton.ac.uk HOME: rmclark@luton34.freeserve.co.uk From nih-image-request@io.ece.drexel.edu Wed Dec 16 11:56 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA20714 for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 11:56:08 -0500 (EST) Resent-Date: Wed, 16 Dec 1998 11:56:08 -0500 (EST) Date: Wed, 16 Dec 1998 11:26:12 -0500 Message-Id: <9812161626.AA25860@aquila.fccc.edu> Reply-To: JD_Tisdall@fccc.edu From: "James D. Tisdall" To: nih-image@io.ece.drexel.edu Subject: mean fragment length in gel Cc: JD_Tisdall@fccc.edu Resent-Message-ID: <"6Hw-c.0.GP4.HzzTs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/722 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 529 Hi, I just subscribed. I wasn't sure how to proceed after looking at manuals and faqs and macros, and I am a new user: We have gels where each lane has all telomeres, so lanes look like big smudges. We want to calculate the mean telomere length in each lane. Is there a macro that already exists for this purpose? Thanks for your help, Jim James D. Tisdall The Fox Chase Cancer Center Phone: (215) 728-3660 7701 Burholme Avenue FAX: (215) 728-2513 Philadelphia, Pennsylvania 19111 USA Email: JD_Tisdall@fccc.edu From nih-image-request@io.ece.drexel.edu Wed Dec 16 13:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA28988 for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 13:20:24 -0500 (EST) Resent-Date: Wed, 16 Dec 1998 13:20:24 -0500 (EST) Message-ID: X-Mailer: Microsoft Outlook Express for Macintosh - 4.02 (298) Date: Wed, 16 Dec 1998 15:55:17 -0200 Subject: unsubscribe From: "Lenaldo Branco Rocha" To: nih-image@io.ece.drexel.edu Mime-version: 1.0 X-Priority: 3 Content-transfer-encoding: 7bit Resent-Message-ID: <"obBJH.0.sN6.pF_Ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/723 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 1 From nih-image-request@io.ece.drexel.edu Wed Dec 16 13:38 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA01173 for cshtest@io.ece.drexel.edu; Wed, 16 Dec 1998 13:38:54 -0500 (EST) Resent-Date: Wed, 16 Dec 1998 13:38:54 -0500 (EST) Date: Wed, 16 Dec 1998 13:17:28 -0500 (EST) From: Colette Baril To: nih-image@io.ece.drexel.edu Subject: Questions on Iomega Buzz boxes Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"OgreV1.0.c-6.sa_Ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/724 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 469 Hi, We are looking into using NIH image to analyse video tapes of guppy behaviour. As an alternative to using a Scion or Data Translation card for AV input, we were considering the use of the Iomega Buzz (an external AV converter). What we need to know is whether the Buzz is compatible with NIH-image software in terms of image resolution, speed, etc. Any information that could be shared on this matter would be great. Thanks, Colette Baril Univ. Toronto From nih-image-d-request@io.ece.drexel.edu Thu Dec 17 06:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA07912; Thu, 17 Dec 1998 06:19:40 -0500 (EST) Date: Thu, 17 Dec 1998 06:19:40 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812171119.GAA07912@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #143 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/143 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3955 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 143 Today's Topics: Request for IP info... [ "Richard M. Clark" To: nih-image@io.ece.drexel.edu Subject: Request for IP info... Message-ID: <13E1883C85@novell.science.luton.ac.uk> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT To all members of nih-image list... I used to be a member of this list but un-subscribed due to email problems - I am now back on the list and wanted to ask some quick questions.... I am an Image Processing researcher who is working on combining some AI techniques with IP for 'intelligent machine vision' .... I am currently working on 'feature extraction' techniques and was wondering if anyone has/knows-of any papers which cover 'feature extraction' algorithms/techniques etc.... I am also interested in writing papers, articles etc regarding my research and have done a lot of work so far regarding 'wavelets and image processing' - I am currently experimenting with wavelets and will have some pretty good results during next year .... is there anyone who publishes image processing 'documents' or 'journals' (or AI related) who is looking for material from 'researchers' within this area? Many thanks, Richard M. Clark ______________________________________________ Richard M. Clark, Research Student, University of Luton, Department of Computing and Information Systems, Room: B303 - (01582) 734111 extn 2071 NOVELL: richard.m.clark@luton.ac.uk HOME: rmclark@luton34.freeserve.co.uk ------------------------------ Date: Wed, 16 Dec 1998 11:26:12 -0500 From: "James D. Tisdall" To: nih-image@io.ece.drexel.edu Cc: JD_Tisdall@fccc.edu Subject: mean fragment length in gel Message-Id: <9812161626.AA25860@aquila.fccc.edu> Hi, I just subscribed. I wasn't sure how to proceed after looking at manuals and faqs and macros, and I am a new user: We have gels where each lane has all telomeres, so lanes look like big smudges. We want to calculate the mean telomere length in each lane. Is there a macro that already exists for this purpose? Thanks for your help, Jim James D. Tisdall The Fox Chase Cancer Center Phone: (215) 728-3660 7701 Burholme Avenue FAX: (215) 728-2513 Philadelphia, Pennsylvania 19111 USA Email: JD_Tisdall@fccc.edu ------------------------------ Date: Wed, 16 Dec 1998 15:55:17 -0200 From: "Lenaldo Branco Rocha" To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit ------------------------------ Date: Wed, 16 Dec 1998 13:17:28 -0500 (EST) From: Colette Baril To: nih-image@io.ece.drexel.edu Subject: Questions on Iomega Buzz boxes Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, We are looking into using NIH image to analyse video tapes of guppy behaviour. As an alternative to using a Scion or Data Translation card for AV input, we were considering the use of the Iomega Buzz (an external AV converter). What we need to know is whether the Buzz is compatible with NIH-image software in terms of image resolution, speed, etc. Any information that could be shared on this matter would be great. Thanks, Colette Baril Univ. Toronto -------------------------------- End of nih-image-d Digest V98 Issue #143 **************************************** From nih-image-request@io.ece.drexel.edu Thu Dec 17 06:27 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA08835 for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 06:27:28 -0500 (EST) Resent-Date: Thu, 17 Dec 1998 06:27:28 -0500 (EST) Date: Thu, 17 Dec 1998 11:12:17 +0000 From: "Dr. Patrick Felle" Subject: unsubscribe To: nih-image@io.ece.drexel.edu Reply-to: patrick.felle@ucd.ie Message-id: <3678E709.C87FC99A@ucd.ie> Organization: University College Dublin MIME-version: 1.0 X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) Content-transfer-encoding: 7bit X-Accept-Language: en-GB,fr-FR,Irish References: <199812150407.XAA15558@io.ece.drexel.edu> Resent-Message-ID: <"3JKUH3.0._l1.OSEUs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/725 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Thu Dec 17 09:56 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA25233 for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 09:56:39 -0500 (EST) Resent-Date: Thu, 17 Dec 1998 09:56:39 -0500 (EST) Date: Thu, 17 Dec 1998 09:34:09 -0500 (EST) Sender: Nora Rooney From: Nora Maureen Rooney X-Sender: nora@login6.isis.unc.edu To: nih-image@io.ece.drexel.edu Subject: unsubscribe In-Reply-To: <199812171117.GAA07668@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"BTvNi2.0.-f5.rPHUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/726 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1 From nih-image-request@io.ece.drexel.edu Thu Dec 17 10:35 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA28782 for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 10:35:40 -0500 (EST) Resent-Date: Thu, 17 Dec 1998 10:35:40 -0500 (EST) From: Vaughn Adams Message-Id: <199812171514.KAA19314@cbis.ece.drexel.edu> Subject: ADMIN: Unsubscribe filter To: nih-image@io.ece.drexel.edu Date: Thu, 17 Dec 1998 10:14:39 -0500 (EST) X-Mailer: ELM [version 2.4ME+ PL48 (25)] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"31vgM3.0.qa6.d_HUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/727 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 702 List members: I have added an "unsubscribe" filter to reject those really annoying unsubscribe messages that get sent to the list. It should take care of the majority of the requests. To get help on administrative commands like unsubscribing, send email to nih-image-request@biomed.drexel.edu. Enter "help" for the subject. If you get the digested version, use nih-image-d-request@biomed.drexel.edu instead. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Thu Dec 17 15:48 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA28078 for cshtest@io.ece.drexel.edu; Thu, 17 Dec 1998 15:48:04 -0500 (EST) Resent-Date: Thu, 17 Dec 1998 15:48:04 -0500 (EST) Date: Thu, 17 Dec 1998 12:32:03 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Buz & behavior In-Reply-To: <199812171117.GAA07612@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"KS7Rh2.0.nQ6.LfMUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/728 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 635 Hi, the Iomega buz works fine with Image (even on a G3). I use it for behavior as well and there is no problem with it, it supports 720 x 480 as well which is a little better than the standard. i would be interested in talking to others who are using Image to analyze behavior as well. Cheers, Stephan ------------------------------ Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net ------------------------------ Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- From nih-image-request@io.ece.drexel.edu Fri Dec 18 06:45 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12471 for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 06:45:00 -0500 (EST) Resent-Date: Fri, 18 Dec 1998 06:45:00 -0500 (EST) From: ebonino@physun.geo.ulg.ac.be Date: Fri, 18 Dec 1998 11:36:07 -0100 Message-Id: <199812181236.LAA11290@phylune.geo.ulg.ac.be> To: nih-image@io.ece.drexel.edu Subject: unsubscribe Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: hdeBTR4qbJ4p96fDbDRqhQ== Resent-Message-ID: <"QsDVW2.0.ZP.BHYUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/729 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 13 unsubscribe From nih-image-d-request@io.ece.drexel.edu Fri Dec 18 06:51 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12575; Fri, 18 Dec 1998 06:51:00 -0500 (EST) Date: Fri, 18 Dec 1998 06:51:00 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812181151.GAA12575@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #144 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/144 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 3544 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 144 Today's Topics: unsubscribe [ "Dr. Patrick Felle" To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: <3678E709.C87FC99A@ucd.ie> Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit unsubscribe ------------------------------ Date: Thu, 17 Dec 1998 09:34:09 -0500 (EST) From: Nora Maureen Rooney To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII ------------------------------ Date: Thu, 17 Dec 1998 10:14:39 -0500 (EST) From: Vaughn Adams To: nih-image@io.ece.drexel.edu Subject: ADMIN: Unsubscribe filter Message-Id: <199812171514.KAA19314@cbis.ece.drexel.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit List members: I have added an "unsubscribe" filter to reject those really annoying unsubscribe messages that get sent to the list. It should take care of the majority of the requests. To get help on administrative commands like unsubscribing, send email to nih-image-request@biomed.drexel.edu. Enter "help" for the subject. If you get the digested version, use nih-image-d-request@biomed.drexel.edu instead. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu ------------------------------ Date: Thu, 17 Dec 1998 12:32:03 -0800 (PST) From: Stephan Anagnostaras To: nih-image@io.ece.drexel.edu Subject: Buz & behavior Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, the Iomega buz works fine with Image (even on a G3). I use it for behavior as well and there is no problem with it, it supports 720 x 480 as well which is a little better than the standard. i would be interested in talking to others who are using Image to analyze behavior as well. Cheers, Stephan - ---------------------------- Stephan G. Anagnostaras, Ph.D. UCLA Depts. of Neurobiology and Psychology stephan@lifesci.ucla.edu sanagnos@mediaone.net - ---------------------------- Work, CHS: (310) 794-6609 Psych: (310) 794-5339 Home: (310) 306-0294 -------------------------- ------------------------------ Date: Fri, 18 Dec 1998 11:36:07 -0100 From: ebonino@physun.geo.ulg.ac.be To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <199812181236.LAA11290@phylune.geo.ulg.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: hdeBTR4qbJ4p96fDbDRqhQ== unsubscribe -------------------------------- End of nih-image-d Digest V98 Issue #144 **************************************** From nih-image-request@io.ece.drexel.edu Fri Dec 18 08:20 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA18297 for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 08:19:56 -0500 (EST) Resent-Date: Fri, 18 Dec 1998 08:19:56 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Fri, 18 Dec 1998 13:03:37 +0300 To: nih-image@io.ece.drexel.edu From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti) Subject: unsuscribe Resent-Message-ID: <"wlnwq2.0.gD2.jLZUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/730 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 190 Dr. Rodolfo Ippoliti Dept. of Biochemical Sciences University of Rome La Sapienza P.le Aldo Moro 5 00185 Rome Italy Tel:+39+6+4450291 FAX:+39+6+4440062 Email:ippoliti@axrma.uniroma1.it From nih-image-request@io.ece.drexel.edu Fri Dec 18 12:25 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA20695 for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 12:25:33 -0500 (EST) Resent-Date: Fri, 18 Dec 1998 12:25:33 -0500 (EST) Message-ID: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk> From: "Shiddhartha Nandy" To: Subject: TCL file format info required Date: Fri, 18 Dec 1998 16:56:47 -0000 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-MDaemon-Deliver-To: nih-image@biomed.drexel.edu X-Return-Path: sn@aii.co.uk Resent-Message-ID: <"N8hnv2.0.m94.kceUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/731 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 138 Hi, Does anyone have information on the TCL image file format used with BDS Imaging systems? Thanks Shiddhartha Nandy sn01@aii.co.uk From nih-image-request@io.ece.drexel.edu Fri Dec 18 13:00 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA25171 for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 13:00:03 -0500 (EST) Resent-Date: Fri, 18 Dec 1998 13:00:03 -0500 (EST) Date: Fri, 18 Dec 1998 12:47:30 -0500 (EST) From: Hideyo Inouye To: nih-image@io.ece.drexel.edu Cc: Hideyo Inouye Subject: arc integration In-Reply-To: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk> Message-Id: Mime-Version: 1.0 Resent-Message-ID: <"12yYv2.0.3l5.9KfUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/732 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 382 Dear Colleagues, Are there any capablities on nih-image to do arc integration along the angular direction and to plot the data as a function of radial direction ? Sincerely Hideyo Inouye Department of Biology, Higgins Hall 510 Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02167-3811 Email: inouye@amy.bc.edu http://amy.bc.edu:8080/ Phone: +1 (617)552-0213 From nih-image-request@io.ece.drexel.edu Fri Dec 18 14:04 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA02031 for cshtest@io.ece.drexel.edu; Fri, 18 Dec 1998 14:04:21 -0500 (EST) Resent-Date: Fri, 18 Dec 1998 14:04:21 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <46eee9bc.367aa379@aol.com> Date: Fri, 18 Dec 1998 13:48:25 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: arc integration Content-transfer-encoding: 7bit X-Mailer: AOL 3.0 for Mac sub 84 Resent-Message-ID: <"BACQL3.0.C7.xEgUs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/733 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 300 In a message dated 12/18/98 12:56:15 PM, you wrote: > Are there any capablities on nih-image to do arc integration along the >angular direction and to plot the data as a function of radial direction ? I have a macro that will do that, and will post it if enough people are interested. John Russ From nih-image-d-request@io.ece.drexel.edu Sat Dec 19 06:10 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23657; Sat, 19 Dec 1998 06:10:30 -0500 (EST) Date: Sat, 19 Dec 1998 06:10:30 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812191110.GAA23657@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #145 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/145 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 2729 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 145 Today's Topics: unsuscribe [ ippoliti@axrma.uniroma1.it (Rodolfo ] TCL file format info required [ "Shiddhartha Nandy" ] arc integration [ Hideyo Inouye ] Re: arc integration [ DrJohnRuss@aol.com ] ------------------------------ Date: Fri, 18 Dec 1998 13:03:37 +0300 From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti) To: nih-image@io.ece.drexel.edu Subject: unsuscribe Message-Id: Content-Type: text/plain; charset="us-ascii" Dr. Rodolfo Ippoliti Dept. of Biochemical Sciences University of Rome La Sapienza P.le Aldo Moro 5 00185 Rome Italy Tel:+39+6+4450291 FAX:+39+6+4440062 Email:ippoliti@axrma.uniroma1.it ------------------------------ Date: Fri, 18 Dec 1998 16:56:47 -0000 From: "Shiddhartha Nandy" To: Subject: TCL file format info required Message-ID: <009901be2aa7$6679dcc0$1d80d9c2@seer.aii.co.uk> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi, Does anyone have information on the TCL image file format used with BDS Imaging systems? Thanks Shiddhartha Nandy sn01@aii.co.uk ------------------------------ Date: Fri, 18 Dec 1998 12:47:30 -0500 (EST) From: Hideyo Inouye To: nih-image@io.ece.drexel.edu Cc: Hideyo Inouye Subject: arc integration Message-Id: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, Are there any capablities on nih-image to do arc integration along the angular direction and to plot the data as a function of radial direction ? Sincerely Hideyo Inouye Department of Biology, Higgins Hall 510 Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02167-3811 Email: inouye@amy.bc.edu http://amy.bc.edu:8080/ Phone: +1 (617)552-0213 ------------------------------ Date: Fri, 18 Dec 1998 13:48:25 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: arc integration Message-ID: <46eee9bc.367aa379@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 12/18/98 12:56:15 PM, you wrote: > Are there any capablities on nih-image to do arc integration along the >angular direction and to plot the data as a function of radial direction ? I have a macro that will do that, and will post it if enough people are interested. John Russ -------------------------------- End of nih-image-d Digest V98 Issue #145 **************************************** From nih-image-request@io.ece.drexel.edu Sat Dec 19 18:41 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA24670 for cshtest@io.ece.drexel.edu; Sat, 19 Dec 1998 18:41:28 -0500 (EST) Resent-Date: Sat, 19 Dec 1998 18:41:28 -0500 (EST) Reply-To: From: "Francis Lamberti" To: , Subject: RE: arc integration Date: Sat, 19 Dec 1998 15:30:37 -0800 Message-ID: <000201be2ba7$95033220$2a50480c@758151725worldnet.att.net> MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Importance: Normal In-Reply-To: <46eee9bc.367aa379@aol.com> Resent-Message-ID: <"_Xvi22.0.eZ5.cP3Vs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/734 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="iso-8859-1" Content-Length: 786 Dr. John Russ : Yes I would be interested in this macro. I am trying to measure the rate of diffusion of a fluorescently labeled protein into capsules of different permeabilities, and this would definitely be useful for these studies. Thanks in advance Francis Lamberti > -----Original Message----- > From: DrJohnRuss@aol.com [mailto:DrJohnRuss@aol.com] > Sent: Friday, December 18, 1998 10:48 AM > To: nih-image@io.ece.drexel.edu > Subject: Re: arc integration > > > In a message dated 12/18/98 12:56:15 PM, you wrote: > > > Are there any capablities on nih-image to do arc integration along the > >angular direction and to plot the data as a function of radial > direction ? > > I have a macro that will do that, and will post it if enough people are > interested. > John Russ > From nih-image-request@io.ece.drexel.edu Sun Dec 20 05:19 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA14831 for cshtest@io.ece.drexel.edu; Sun, 20 Dec 1998 05:19:42 -0500 (EST) Resent-Date: Sun, 20 Dec 1998 05:19:42 -0500 (EST) Date: Sun, 20 Dec 1998 05:05:00 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199812201005.FAA12779@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"CFtD4.0.z73.FlCVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/735 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1997 NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- From nih-image-request@io.ece.drexel.edu Sun Dec 20 10:35 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA23934; Sun, 20 Dec 1998 10:35:53 -0500 (EST) Resent-Date: Sun, 20 Dec 1998 10:35:53 -0500 (EST) Date: Sun, 20 Dec 1998 10:15:37 -0500 (EST) From: R Wade Schuette X-Sender: schuette@frogger.rs.itd.umich.edu To: NIH Image List Subject: RGB spectral response curvers? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"_MFnO2.0.Y75.UIHVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/736 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 490 Does anyone have the spectral-response curves for the R, G, and B channels for some digital camera? (or know where I could download them?) I'm looking at the impact of color correction and "color temperature" on scoring of immunohistochemically stained pathology sections, and need to find the full sensitivity curves as a function of wavelength for each of the R,G, and B channels for at least some representative camera. Thanks! Wade Schuette (schuette@umich.edu) Ann Arbor, MI. From nih-image-d-request@io.ece.drexel.edu Sun Dec 20 10:38 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA24338; Sun, 20 Dec 1998 10:38:18 -0500 (EST) Date: Sun, 20 Dec 1998 10:38:18 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812201538.KAA24338@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #146 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/146 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4671 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 146 Today's Topics: RE: arc integration [ "Francis Lamberti" To: , Subject: RE: arc integration Message-ID: <000201be2ba7$95033220$2a50480c@758151725worldnet.att.net> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dr. John Russ : Yes I would be interested in this macro. I am trying to measure the rate of diffusion of a fluorescently labeled protein into capsules of different permeabilities, and this would definitely be useful for these studies. Thanks in advance Francis Lamberti > -----Original Message----- > From: DrJohnRuss@aol.com [mailto:DrJohnRuss@aol.com] > Sent: Friday, December 18, 1998 10:48 AM > To: nih-image@io.ece.drexel.edu > Subject: Re: arc integration > > > In a message dated 12/18/98 12:56:15 PM, you wrote: > > > Are there any capablities on nih-image to do arc integration along the > >angular direction and to plot the data as a function of radial > direction ? > > I have a macro that will do that, and will post it if enough people are > interested. > John Russ > ------------------------------ Date: Sun, 20 Dec 1998 05:05:00 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Message-Id: <199812201005.FAA12779@io.ece.drexel.edu> NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- ------------------------------ Date: Sun, 20 Dec 1998 10:15:37 -0500 (EST) From: R Wade Schuette To: NIH Image List Subject: RGB spectral response curvers? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have the spectral-response curves for the R, G, and B channels for some digital camera? (or know where I could download them?) I'm looking at the impact of color correction and "color temperature" on scoring of immunohistochemically stained pathology sections, and need to find the full sensitivity curves as a function of wavelength for each of the R,G, and B channels for at least some representative camera. Thanks! Wade Schuette (schuette@umich.edu) Ann Arbor, MI. -------------------------------- End of nih-image-d Digest V98 Issue #146 **************************************** From nih-image-request@io.ece.drexel.edu Mon Dec 21 09:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA22733; Mon, 21 Dec 1998 09:14:35 -0500 (EST) Resent-Date: Mon, 21 Dec 1998 09:14:35 -0500 (EST) Message-Id: <199812211358.OAA14246@naxos.unice.fr> Subject: arc integration again Date: Mon, 21 Dec 98 14:53:02 +0100 x-mailer: Claris Emailer 2.0Fv1 , 3 juillet 1997 From: Legrand To: Mime-Version: 1.0 Resent-Message-ID: <"TJuPE3.0.Ko4.CBbVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/737 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 289 I would certainly be interested by a macro for arc integration... Please Olivier LEGRAND Laboratoire de Physique de la Matiere Condensee CNRS - UMR 6622 Universite de Nice-Sophia Antipolis Parc Valrose F-06108 Nice cedex 2 FRANCE tel.: +33 (0)4 92 07 67 87 fax : +33 (0)4 92 07 67 54 From nih-image-request@io.ece.drexel.edu Mon Dec 21 14:53 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA04602; Mon, 21 Dec 1998 14:53:15 -0500 (EST) Resent-Date: Mon, 21 Dec 1998 14:53:15 -0500 (EST) Message-ID: <367EA1A8.14F9@pop.uky.edu> Date: Mon, 21 Dec 1998 14:29:45 -0500 From: alex gimelbrant Organization: U of K X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: NIH-Image mailing list Subject: BDS-Image TCL file format Content-Transfer-Encoding: 7bit Resent-Message-ID: <"JBb9R3.0.YO.M6gVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/738 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 562 There was a request several days ago concerning the format of the TCL files from BDS-Image. I do not have the email of the author handy, so I post that to the list. That's what I used to import them to NIH image: (alternatively, you can save the files in TIFF from BDS/Oncor/Whatever-it-is-now Image) macro 'Import 1300x1000 TCL'; var HdrSize,width,height:integer; begin HdrSize:=512; width:= 1300; height:=1000; SetImport('16-bit Unsigned'); SetImport('Invert'); SetCustom(width, height, HdrSize, 100); Import(''); end; Hope it helps. AG From nih-image-d-request@io.ece.drexel.edu Mon Dec 21 23:39 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04039; Mon, 21 Dec 1998 23:39:46 -0500 (EST) Date: Mon, 21 Dec 1998 23:39:46 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812220439.XAA04039@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #147 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/147 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 5586 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 147 Today's Topics: There is an e-card waiting for you i [ NetCard ] There is an e-card waiting for you i [ NetCard ] arc integration again [ Legrand ] BDS-Image TCL file format [ alex gimelbrant To: Group Subject: There is an e-card waiting for you in NetCard! Message-Id: <199812211238.HAA16077@charon.minerva.net> Hello Group You just receive a NetCard's virtual postcard. NetCard is the brazilian card site in the Internet To read it, access the web address http://www.netcard.com.br/cgi-bin/ler.pl?ident=221941892 in your browser. The card will be available for 12 (twelve) days. =================================================== NetCard - The brazilian card site in the Internet --------------------------------------------------- WWW: http://www.netcard.com.br E-mail: netcard@netcard.com.br =================================================== ------------------------------ Date: Mon, 21 Dec 1998 07:39:38 -0500 (EST) From: NetCard To: Group Subject: There is an e-card waiting for you in NetCard! Message-Id: <199812211239.HAA17178@charon.minerva.net> Hello Group You just receive a NetCard's virtual postcard. NetCard is the brazilian card site in the Internet To read it, access the web address http://www.netcard.com.br/cgi-bin/ler.pl?ident=191957466 in your browser. The card will be available for 12 (twelve) days. =================================================== NetCard - The brazilian card site in the Internet --------------------------------------------------- WWW: http://www.netcard.com.br E-mail: netcard@netcard.com.br =================================================== ------------------------------ Date: Mon, 21 Dec 98 14:53:02 +0100 From: Legrand To: Subject: arc integration again Message-Id: <199812211358.OAA14246@naxos.unice.fr> Content-Type: text/plain; charset="US-ASCII" I would certainly be interested by a macro for arc integration... Please Olivier LEGRAND Laboratoire de Physique de la Matiere Condensee CNRS - UMR 6622 Universite de Nice-Sophia Antipolis Parc Valrose F-06108 Nice cedex 2 FRANCE tel.: +33 (0)4 92 07 67 87 fax : +33 (0)4 92 07 67 54 ------------------------------ Date: Mon, 21 Dec 1998 14:29:45 -0500 From: alex gimelbrant To: NIH-Image mailing list Subject: BDS-Image TCL file format Message-ID: <367EA1A8.14F9@pop.uky.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There was a request several days ago concerning the format of the TCL files from BDS-Image. I do not have the email of the author handy, so I post that to the list. That's what I used to import them to NIH image: (alternatively, you can save the files in TIFF from BDS/Oncor/Whatever-it-is-now Image) macro 'Import 1300x1000 TCL'; var HdrSize,width,height:integer; begin HdrSize:=512; width:= 1300; height:=1000; SetImport('16-bit Unsigned'); SetImport('Invert'); SetCustom(width, height, HdrSize, 100); Import(''); end; Hope it helps. AG ------------------------------ Date: Mon, 21 Dec 1998 23:30:23 -0500 (EST) From: R Wade Schuette To: NIH Image List cc: schuette@umich.edu Subject: Quantitative IHC stain scoring Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Fellow Imagers -- I posted a new paper of mine for your comments. I am seeking someone with a lab interested in producing test slides and images to pursue this study of quantitative scoring. Title: A Novel, Quantitative, Automated Technique for Identifying and Scoring Stained Regions in Immunohistochemical Specimens with Dual Stains ---------------- Abstract Reliable, reproducible quantitative scoring of immunohistochemically stained images has been difficult, due in part to the fact that the stain and counterstains in common use have overlapping colors. This paper presents the mathematical basis for completely and reproducibly identifying the amount of each stain at each pixel of the image, regardless of image depth and overlapping stains. The technique allows closed-form reconstruction of an image of each stain alone, which can be quantified, or ratio of the two stains, which produces a substantially higher signal-to-noise ratio than other techniques now in use. The technique is only valid for images with two different stains. Preliminary empirical investigation is encouraging that this technique can be used in practice. The full paper (5 pages, 22K) is now available for download or viewing as an Adobe Acrobat "pdf" document at: http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf keywords: quantitative image analysis, IHC, automated scoring techniques Wade Schuette University of Michigan Medical Center Information Technologies Ann Arbor, MI USA schuette@umich.edu -------------------------------- End of nih-image-d Digest V98 Issue #147 **************************************** From nih-image-request@io.ece.drexel.edu Mon Dec 21 23:40 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04273; Mon, 21 Dec 1998 23:40:50 -0500 (EST) Resent-Date: Mon, 21 Dec 1998 23:40:50 -0500 (EST) Date: Mon, 21 Dec 1998 23:30:23 -0500 (EST) From: R Wade Schuette X-Sender: schuette@seawolf.rs.itd.umich.edu To: NIH Image List cc: schuette@umich.edu Subject: Quantitative IHC stain scoring Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"cgnYs3.0.1d.d1oVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/739 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1515 Fellow Imagers -- I posted a new paper of mine for your comments. I am seeking someone with a lab interested in producing test slides and images to pursue this study of quantitative scoring. Title: A Novel, Quantitative, Automated Technique for Identifying and Scoring Stained Regions in Immunohistochemical Specimens with Dual Stains ---------------- Abstract Reliable, reproducible quantitative scoring of immunohistochemically stained images has been difficult, due in part to the fact that the stain and counterstains in common use have overlapping colors. This paper presents the mathematical basis for completely and reproducibly identifying the amount of each stain at each pixel of the image, regardless of image depth and overlapping stains. The technique allows closed-form reconstruction of an image of each stain alone, which can be quantified, or ratio of the two stains, which produces a substantially higher signal-to-noise ratio than other techniques now in use. The technique is only valid for images with two different stains. Preliminary empirical investigation is encouraging that this technique can be used in practice. The full paper (5 pages, 22K) is now available for download or viewing as an Adobe Acrobat "pdf" document at: http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf keywords: quantitative image analysis, IHC, automated scoring techniques Wade Schuette University of Michigan Medical Center Information Technologies Ann Arbor, MI USA schuette@umich.edu From nih-image-request@io.ece.drexel.edu Tue Dec 22 10:52 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA20845; Tue, 22 Dec 1998 10:52:46 -0500 (EST) Resent-Date: Tue, 22 Dec 1998 10:52:46 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Tue, 22 Dec 1998 09:36:16 -0600 From: "Daniel Blander" To: Subject: unsubscribe Mime-Version: 1.0 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA18722 Resent-Message-ID: <"F_Vfd1.0.ja4.tnxVs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/740 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Tue Dec 22 10:54 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA21147; Tue, 22 Dec 1998 10:54:37 -0500 (EST) Resent-Date: Tue, 22 Dec 1998 10:54:37 -0500 (EST) Message-id: <16919155@donner.Dartmouth.EDU> Date: 22 Dec 98 10:41:06 EST From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian) Reply-To: daghlian@Dartmouth.EDU Subject: G3 , vdig, OS 8.1 vs 8.5 To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id KAA19329 Resent-Message-ID: <"_kYAy2.0.Gk4.RsxVs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/741 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=iso-8859-1 Content-Length: 1056 After having installed OS 8.5 on a G3 all-in-one with a built in digitizer, I find that we are back to having the Start Digitizing command not work. On this same machine with OS 8.1 loaded, the 1.62b30 version of Image works fine. Now it gives a -108 error, then crashes with a type 1 error. The same thing happens with a G3 333 with built-in digitizer. Does anyone know why this happens? What is different in 8.5? I know Wayne has made adjustments to get Image to work, at least in part, with the built-in digitizers in the G3 machines.Is this a new problem? It would be nice if the G3s would work as well as the 7500-8500 series. I know the real solution is to try not to be so cheap and buy yet another card from Scion, but hope springs eternal. regards, Chuck ******************************************** Charles P. Daghlian, Ph. D. Director, Rippel E. M. Facility 7605 Remsen Dartmouth College Hanover, NH 03755 603-646-1039 http://www.dartmouth.edu/~emczar/ http://www.dartmouth.edu/~daghlian/paleo/ ******************************************** From nih-image-request@io.ece.drexel.edu Tue Dec 22 14:39 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA17317; Tue, 22 Dec 1998 14:39:13 -0500 (EST) Resent-Date: Tue, 22 Dec 1998 14:39:13 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 4.1 Date: Tue, 22 Dec 1998 14:28:06 -0500 From: Michael Vinegra To: nih-image@io.ece.drexel.edu Subject: Commmercial autorad packages Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"gMcD33.0.at3.YB_Vs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/742 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 1735 Can anyone suggest GREAT out-of-the-box autoradiography software capable of doing grain counting and densitometry on whole rat brain slices on the Mac? I need something idiot proof, that I can plop on a PowerMac 8500 and leave to be used by a variety of non-collaborating scientists that can't be messed up by the lowest common denominator of computer literacy. In the past I've used NIH-Image and IPlab Spectrum to do these tasks, but the level of knowledge involved in the users has resulted in people screwing up macros and scripts that I need to fix repeatedly, and people fighting over who broke who's script. I need a simple point and click interface, and I need it to be able to capture from my existing setup seamlessly (Dage ccd-72 greyscale camera on a scion LG-7 board, c-mounted to a ChromaPro lightbox with appropriate masks and magnifying lenses) Michael Vinegra Acute Neurodegeneration CNS Disorders Wyeth-Ayerst Research Princeton NJ From nih-image-d-request@io.ece.drexel.edu Wed Dec 23 06:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA19720; Wed, 23 Dec 1998 06:14:29 -0500 (EST) Date: Wed, 23 Dec 1998 06:14:29 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812231114.GAA19720@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #148 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/148 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 4193 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 148 Today's Topics: unsubscribe [ "Daniel Blander" To: Subject: unsubscribe Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit unsubscribe ------------------------------ Date: 22 Dec 98 10:41:06 EST From: Charles.P.Daghlian@Dartmouth.EDU (Charles P. Daghlian) To: nih-image@io.ece.drexel.edu Subject: G3 , vdig, OS 8.1 vs 8.5 Message-id: <16919155@donner.Dartmouth.EDU> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit After having installed OS 8.5 on a G3 all-in-one with a built in digitizer, I find that we are back to having the Start Digitizing command not work. On this same machine with OS 8.1 loaded, the 1.62b30 version of Image works fine. Now it gives a -108 error, then crashes with a type 1 error. The same thing happens with a G3 333 with built-in digitizer. Does anyone know why this happens? What is different in 8.5? I know Wayne has made adjustments to get Image to work, at least in part, with the built-in digitizers in the G3 machines.Is this a new problem? It would be nice if the G3s would work as well as the 7500-8500 series. I know the real solution is to try not to be so cheap and buy yet another card from Scion, but hope springs eternal. regards, Chuck ******************************************** Charles P. Daghlian, Ph. D. Director, Rippel E. M. Facility 7605 Remsen Dartmouth College Hanover, NH 03755 603-646-1039 http://www.dartmouth.edu/~emczar/ http://www.dartmouth.edu/~daghlian/paleo/ ******************************************** ------------------------------ Date: Tue, 22 Dec 1998 14:28:06 -0500 From: Michael Vinegra To: nih-image@io.ece.drexel.edu Subject: Commmercial autorad packages Message-Id: Content-Type: text/plain Content-Disposition: inline Can anyone suggest GREAT out-of-the-box autoradiography software capable of doing grain counting and densitometry on whole rat brain slices on the Mac? I need something idiot proof, that I can plop on a PowerMac 8500 and leave to be used by a variety of non-collaborating scientists that can't be messed up by the lowest common denominator of computer literacy. In the past I've used NIH-Image and IPlab Spectrum to do these tasks, but the level of knowledge involved in the users has resulted in people screwing up macros and scripts that I need to fix repeatedly, and people fighting over who broke who's script. I need a simple point and click interface, and I need it to be able to capture from my existing setup seamlessly (Dage ccd-72 greyscale camera on a scion LG-7 board, c-mounted to a ChromaPro lightbox with appropriate masks and magnifying lenses) Michael Vinegra Acute Neurodegeneration CNS Disorders Wyeth-Ayerst Research Princeton NJ -------------------------------- End of nih-image-d Digest V98 Issue #148 **************************************** From nih-image-request@io.ece.drexel.edu Wed Dec 23 10:36 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA27373; Wed, 23 Dec 1998 10:36:09 -0500 (EST) Resent-Date: Wed, 23 Dec 1998 10:36:09 -0500 (EST) Mime-Version: 1.0 Message-Id: In-Reply-To: Date: Wed, 23 Dec 1998 10:38:06 -0500 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: Re: Quantitative IHC stain scoring Resent-Message-ID: <"pkt-I1.0.o76.bgGWs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/743 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1775 I'd be interested in reviewing that one >Fellow Imagers -- I posted a new paper of mine for your comments. > >I am seeking someone with a lab interested in producing test >slides and images to pursue this study of quantitative scoring. > >Title: >A Novel, Quantitative, Automated Technique for Identifying and Scoring >Stained Regions in Immunohistochemical Specimens with Dual Stains >---------------- >Abstract > >Reliable, reproducible quantitative scoring of immunohistochemically >stained images has been difficult, due in part to the fact that the stain >and counterstains in common use have overlapping colors. This paper >presents the mathematical basis for completely and reproducibly >identifying the amount of each stain at each pixel of the >image, regardless of image depth and overlapping stains. The technique >allows closed-form reconstruction of an image of each stain alone, which >can be quantified, or ratio of the two stains, which produces a >substantially higher signal-to-noise ratio than other techniques now in >use. The technique is only valid for images with two different stains. >Preliminary empirical investigation is encouraging that this technique can >be used in practice. > >The full paper (5 pages, 22K) is now available for download or viewing >as an Adobe Acrobat "pdf" document at: >http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf > >keywords: quantitative image analysis, IHC, automated scoring techniques > >Wade Schuette >University of Michigan >Medical Center Information Technologies >Ann Arbor, MI USA >schuette@umich.edu Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Lab: 410 706-2440 Fax 410 706-2512 email gehoffma@umaryland.edu From nih-image-request@io.ece.drexel.edu Wed Dec 23 11:22 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04362; Wed, 23 Dec 1998 11:21:34 -0500 (EST) Resent-Date: Wed, 23 Dec 1998 11:21:34 -0500 (EST) Date: Wed, 23 Dec 1998 10:08:29 -0600 (CST) Date-warning: Date header was inserted by uthscsa.edu From: David Morilak Subject: Re: Commercial autorad packages X-Sender: morilak@arwen.uthscsa.edu To: nih-image@io.ece.drexel.edu Cc: VINEGRM@war.wyeth.com Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"Gze5f2.0.aX.cLHWs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/744 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 3380 Michael: Please don't take any personal offense at this reply, because certainly none is intended, but I'm a little taken aback by your query to provide an idiot-proof out-of-the-box scientific method which will presumably generate high level scientific results independent of (or perhaps in spite of) a lack of user training or knowledge. I'm not sure my comments will contribute anything useful to your search, but as a grant-funded PI, as we all must do, I constantly train new post-docs, students and techs in all aspects of my work, including image acquisition and analysis. (At some point, of course, my most difficult and painful task becomes training the old lab members to train the new lab members). It might be constructive to consider the issues you raise in the context of the inevitable tradeoff between utility/productivity (ie what a procedure gains for you in your work) and expertise/resources required (ie what it costs to get that utility). In other words, I have concluded once again that you get what you pay for, or more precisely, you pay for everything you get. I can think of no more useful, simple (and free) image analysis package than NIH-Image. You asked for something for "doing grain counting and densitometry on whole rat brain slices on the Mac" - a pretty sophisticated task by any definition, with data generated presumably as a result of very sophisticated bench procedures employed in the service of an important and expensive research project. We certainly wouldn't expect anyone with no skills and no training to conduct in situ hybridization or radioligand binding experiments, so why would we expect such individuals to process and analyze the results of such experiments? If this is the kind of work you need accomplished, there is no way to avoid requiring an appropriate degree of expertise and knowledge on the part of the scientists you employ to use this technique. This obviously requires an investment of time and resources to train the users. Calibration, definition and elimination of noise/background/inappropriate labelling, regional delineation, not to mention statistical weighting (detertmining mean integrated density, proportional area of silver grain coverage, etc) and analysis require knowledge, some subjective understanding of the process and material being analyzed, as well as an understanding and use of reliable conventions for making objective decisions. I would submit that the use of computerized image analysis is by no means an "idiot-proof" process, nor should it be. It is a terribly sophisticated tool that is only as good as the scientists who implement it. I would suggest asking your division or whatever entity is responsible for maintaining the hardware used in your analyses to also invest in a program of user training. Then, to avoid the problems you described, you could require taht anyone using your system will have gone through a minimum level of training and possess a degree of expertise that you can trust. Without being flippant (well, not too much anyway), I would suggest that the only way to idiot-proof such a scientific technique is to idiot-proof the users! Sincerely, David Morilak David Morilak, Ph.D. Dept of Pharmacology Univ Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7764 ph: 210-567-4174 FAX: 210-567-4303 E-mail: morilak@uthscsa.edu From nih-image-d-request@io.ece.drexel.edu Thu Dec 24 06:15 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA14515; Thu, 24 Dec 1998 06:15:04 -0500 (EST) Date: Thu, 24 Dec 1998 06:15:04 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812241115.GAA14515@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #149 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/149 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 6186 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 149 Today's Topics: Re: Quantitative IHC stain scoring [ Gloria Hoffman ] ------------------------------ Date: Wed, 23 Dec 1998 10:38:06 -0500 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: Re: Quantitative IHC stain scoring Message-Id: Content-Type: text/plain; charset="us-ascii" I'd be interested in reviewing that one >Fellow Imagers -- I posted a new paper of mine for your comments. > >I am seeking someone with a lab interested in producing test >slides and images to pursue this study of quantitative scoring. > >Title: >A Novel, Quantitative, Automated Technique for Identifying and Scoring >Stained Regions in Immunohistochemical Specimens with Dual Stains >---------------- >Abstract > >Reliable, reproducible quantitative scoring of immunohistochemically >stained images has been difficult, due in part to the fact that the stain >and counterstains in common use have overlapping colors. This paper >presents the mathematical basis for completely and reproducibly >identifying the amount of each stain at each pixel of the >image, regardless of image depth and overlapping stains. The technique >allows closed-form reconstruction of an image of each stain alone, which >can be quantified, or ratio of the two stains, which produces a >substantially higher signal-to-noise ratio than other techniques now in >use. The technique is only valid for images with two different stains. >Preliminary empirical investigation is encouraging that this technique can >be used in practice. > >The full paper (5 pages, 22K) is now available for download or viewing >as an Adobe Acrobat "pdf" document at: >http://www-personal.umich.edu/~schuette/imaging/vpaper.pdf > >keywords: quantitative image analysis, IHC, automated scoring techniques > >Wade Schuette >University of Michigan >Medical Center Information Technologies >Ann Arbor, MI USA >schuette@umich.edu Gloria E. Hoffman, Ph.D. Department of Anatomy and Neurobiology 685 W Baltimore St Baltimore MD 21201 Phone 410 706-2438 Lab: 410 706-2440 Fax 410 706-2512 email gehoffma@umaryland.edu ------------------------------ Date: Wed, 23 Dec 1998 10:08:29 -0600 (CST) From: David Morilak To: nih-image@io.ece.drexel.edu Cc: VINEGRM@war.wyeth.com Subject: Re: Commercial autorad packages Message-id: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Michael: Please don't take any personal offense at this reply, because certainly none is intended, but I'm a little taken aback by your query to provide an idiot-proof out-of-the-box scientific method which will presumably generate high level scientific results independent of (or perhaps in spite of) a lack of user training or knowledge. I'm not sure my comments will contribute anything useful to your search, but as a grant-funded PI, as we all must do, I constantly train new post-docs, students and techs in all aspects of my work, including image acquisition and analysis. (At some point, of course, my most difficult and painful task becomes training the old lab members to train the new lab members). It might be constructive to consider the issues you raise in the context of the inevitable tradeoff between utility/productivity (ie what a procedure gains for you in your work) and expertise/resources required (ie what it costs to get that utility). In other words, I have concluded once again that you get what you pay for, or more precisely, you pay for everything you get. I can think of no more useful, simple (and free) image analysis package than NIH-Image. You asked for something for "doing grain counting and densitometry on whole rat brain slices on the Mac" - a pretty sophisticated task by any definition, with data generated presumably as a result of very sophisticated bench procedures employed in the service of an important and expensive research project. We certainly wouldn't expect anyone with no skills and no training to conduct in situ hybridization or radioligand binding experiments, so why would we expect such individuals to process and analyze the results of such experiments? If this is the kind of work you need accomplished, there is no way to avoid requiring an appropriate degree of expertise and knowledge on the part of the scientists you employ to use this technique. This obviously requires an investment of time and resources to train the users. Calibration, definition and elimination of noise/background/inappropriate labelling, regional delineation, not to mention statistical weighting (detertmining mean integrated density, proportional area of silver grain coverage, etc) and analysis require knowledge, some subjective understanding of the process and material being analyzed, as well as an understanding and use of reliable conventions for making objective decisions. I would submit that the use of computerized image analysis is by no means an "idiot-proof" process, nor should it be. It is a terribly sophisticated tool that is only as good as the scientists who implement it. I would suggest asking your division or whatever entity is responsible for maintaining the hardware used in your analyses to also invest in a program of user training. Then, to avoid the problems you described, you could require taht anyone using your system will have gone through a minimum level of training and possess a degree of expertise that you can trust. Without being flippant (well, not too much anyway), I would suggest that the only way to idiot-proof such a scientific technique is to idiot-proof the users! Sincerely, David Morilak David Morilak, Ph.D. Dept of Pharmacology Univ Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7764 ph: 210-567-4174 FAX: 210-567-4303 E-mail: morilak@uthscsa.edu -------------------------------- End of nih-image-d Digest V98 Issue #149 **************************************** From nih-image-request@io.ece.drexel.edu Sun Dec 27 21:06 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA19500; Sun, 27 Dec 1998 21:05:51 -0500 (EST) Resent-Date: Sun, 27 Dec 1998 21:05:51 -0500 (EST) Message-ID: <3686E537.7599@thurston.com> Date: Sun, 27 Dec 1998 17:56:10 -0800 From: "Patrick T. Pringle" Reply-To: lespat@thurston.com X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: NIH forum Subject: NIH mean density scans and line width of measuring too Content-Transfer-Encoding: 7bit Resent-Message-ID: <"F00851.0.JY4.lFkXs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/745 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 964 Holiday Greetings! Has anyone come up with a satisfactory line width for obtaining mean density of tree rings in a scanned image, say using NIH or Scion Image? We have been pretty much relying on measuring the ring width and latewood width with single pixel wide lines up until now, but it seems a pity not to at least collect the density information since one is making the measurements anyway. Somewhere I read or heard that the maximum line width shown in the NIH toolbar is 99 pixels. I have tried a few measurements using that width, but the beginning and ending points invariably "reach out" into the next ring because the line is too fat. I suppose one solution to be simply to choose a narrower line, say 10-20 pixels wide and accept that some overlap onto the next ring is going to happen and that the errors that result are minimal. Any thoughts on this would be welcome. Thanks. -- Pat Pringle lespat@thurston.com pat.pringle@wadnr.gov (Pat's wk) From nih-image-d-request@io.ece.drexel.edu Tue Dec 29 06:14 EST 1998 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA13194; Tue, 29 Dec 1998 06:14:36 -0500 (EST) Date: Tue, 29 Dec 1998 06:14:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199812291114.GAA13194@io.ece.drexel.edu> Subject: nih-image-d Digest V98 #150 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume98/150 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 1623 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 98 : Issue 150 Today's Topics: NIH mean density scans and line widt [ "Patrick T. Pringle" To: NIH forum Subject: NIH mean density scans and line width of measuring too Message-ID: <3686E537.7599@thurston.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Holiday Greetings! Has anyone come up with a satisfactory line width for obtaining mean density of tree rings in a scanned image, say using NIH or Scion Image? We have been pretty much relying on measuring the ring width and latewood width with single pixel wide lines up until now, but it seems a pity not to at least collect the density information since one is making the measurements anyway. Somewhere I read or heard that the maximum line width shown in the NIH toolbar is 99 pixels. I have tried a few measurements using that width, but the beginning and ending points invariably "reach out" into the next ring because the line is too fat. I suppose one solution to be simply to choose a narrower line, say 10-20 pixels wide and accept that some overlap onto the next ring is going to happen and that the errors that result are minimal. Any thoughts on this would be welcome. Thanks. -- Pat Pringle lespat@thurston.com pat.pringle@wadnr.gov (Pat's wk) -------------------------------- End of nih-image-d Digest V98 Issue #150 **************************************** From nih-image-request@io.ece.drexel.edu Mon Jan 4 16:29 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA23523; Mon, 4 Jan 1999 16:28:03 -0500 (EST) Resent-Date: Mon, 4 Jan 1999 16:28:03 -0500 (EST) Date: Mon, 04 Jan 1999 15:01:43 -0600 (CST) Date-warning: Date header was inserted by uthscsa.edu From: David Morilak Subject: Image in 99?? X-Sender: morilak@arwen.uthscsa.edu To: nih-image-d-request@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"Q5MKo.0.G05.XmIas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/746 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 918 Hi: I'm just checking in since I have not received anything from the NIH-Image mailing list (I am subscribed to receive messages in digest mode) since 12/31/98... I'm wondering if a) the list has experienced a premature Y2k melt-down b) The New Year dawned, and I got inadvertently kicked off the list c) I pissed somebody off and got advertently kicked off the list d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, and there have actually been NO messages posted to the NIH list since the dawn of '99 or e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 Any ideas as to which is most likely? (and please lie to me if it's c!) Thanks, and Happy New Year! David Morilak David Morilak, Ph.D. Dept of Pharmacology Univ Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7764 ph: 210-567-4174 FAX: 210-567-4303 E-mail: morilak@uthscsa.edu From nih-image-request@io.ece.drexel.edu Mon Jan 4 16:43 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA25161; Mon, 4 Jan 1999 16:43:08 -0500 (EST) Resent-Date: Mon, 4 Jan 1999 16:43:08 -0500 (EST) From: Vaughn Adams Message-Id: <199901042122.QAA20822@cbis.ece.drexel.edu> Subject: Re: Image in 99?? In-Reply-To: from David Morilak at "Jan 4, 1999 3: 1:43 pm" To: nih-image@io.ece.drexel.edu Date: Mon, 4 Jan 1999 16:22:24 -0500 (EST) Cc: morilak@uthscsa.edu X-Mailer: ELM [version 2.4ME+ PL48 (25)] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"3rV0L1.0.9b5.X4Jas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/747 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1137 David: > I'm just checking in since I have not received anything from the NIH-Image > mailing list (I am subscribed to receive messages in digest mode) since > 12/31/98... I'm wondering if > > a) the list has experienced a premature Y2k melt-down > b) The New Year dawned, and I got inadvertently kicked off the list > c) I pissed somebody off and got advertently kicked off the list > d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, > and there have actually been NO messages posted to the NIH list since the > dawn of '99 > or > e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 > > Any ideas as to which is most likely? (and please lie to me if it's c!) The correct answer is D. Everybody went to the Caribbean. The list members who live in the Caribean went mountain climbing in Alaska. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Mon Jan 4 17:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA27417; Mon, 4 Jan 1999 17:04:37 -0500 (EST) Resent-Date: Mon, 4 Jan 1999 17:04:37 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 4 Jan 1999 14:43:28 -0700 To: nih-image@io.ece.drexel.edu From: connie temm Subject: Re: Image in 99?? Resent-Message-ID: <"CV9KB3.0.wF6.lRJas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/748 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 244 d1/2: all imagers would rather be snorkeling or skiing Constance J. Temm, Ph.D. University of Arizona Tel.: (520) 621-8643 Nutritional Sciences Dept. Fax: 520 621 1396 632 Shantz Building Tucson, AZ 85721 USA From nih-image-request@io.ece.drexel.edu Mon Jan 4 18:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05855; Mon, 4 Jan 1999 18:21:42 -0500 (EST) Resent-Date: Mon, 4 Jan 1999 18:21:42 -0500 (EST) Date: Mon, 4 Jan 1999 15:02:29 -0800 (PST) From: David Ehrhardt To: nih-image@io.ece.drexel.edu cc: nih-image-d-request@io.ece.drexel.edu Subject: Re: Image in 99?? In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"kqI0L.0.h11.1dKas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/749 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1086 > Hi: > > I'm just checking in since I have not received anything from the NIH-Image > mailing list (I am subscribed to receive messages in digest mode) since > 12/31/98... I'm wondering if > > a) the list has experienced a premature Y2k melt-down > b) The New Year dawned, and I got inadvertently kicked off the list > c) I pissed somebody off and got advertently kicked off the list > d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, > and there have actually been NO messages posted to the NIH list since the > dawn of '99 > or > e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 > > Any ideas as to which is most likely? (and please lie to me if it's c!) > > Thanks, and Happy New Year! > > David Morilak I was actually snorkeling during this time and I saw a lot of suspicious pasty-skinned people who looked like they spent a lot of time in darkened rooms. David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 From nih-image-request@io.ece.drexel.edu Mon Jan 4 20:29 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18525; Mon, 4 Jan 1999 20:29:43 -0500 (EST) Resent-Date: Mon, 4 Jan 1999 20:29:43 -0500 (EST) Message-Id: <3.0.5.32.19990104201057.00bb64d0@s.imap.itd.umich.edu> X-Sender: schuette@s.imap.itd.umich.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 04 Jan 1999 20:10:57 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Quantitative immunoperoxidase staining In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"-F27H1.0.924.cRMas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/750 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 677 Maybe it just seems like snorkeling, as the snow mountains are 3-4 meters high at the edge of our parking lot... Anyway, what _I_ did on my holiday break was to finally crack segmenting images of immunoperoxidase stained pathology slides to separate the brown peroxidase and blue counterstain objectively and quantitatively. I posted the example under "98.001" on my web page http://www-personal.umich.edu/~schuette/imaging I'd be interested in hearing from anyone else on the list who's working on this problem. Wade Schuette University of Michigan Sunny (14 inches worth) Ann Arbor, Michigan Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Tue Jan 5 01:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA21275; Tue, 5 Jan 1999 01:24:53 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 01:24:53 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: lespat@thurston.com, nih-image@io.ece.drexel.edu Date: Tue, 5 Jan 1999 17:01:32 GMT+1100 Subject: Re: NIH mean density scans and line width of measuring too Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6B9F84B5792@rna.bio.mq.edu.au> Resent-Message-ID: <"G7cTJ1.0.Ia4.ZjQas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/751 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2515 >Date: Sun, 27 Dec 1998 17:56:10 -0800 >From: "Patrick T. Pringle" >To: NIH forum >Subject: NIH mean density scans and line width of measuring too >.... >Has anyone come up with a satisfactory line width for obtaining mean >density of tree rings in a scanned image, say using NIH or Scion Image? >We have been pretty much relying on measuring the ring width and >latewood width with single pixel wide lines up until now, but it seems a >pity not to at least collect the density information since one is making >the measurements anyway. Somewhere I read or heard that the maximum line >width shown in the NIH toolbar is 99 pixels. I have tried a few >measurements using that width, but the beginning and ending >points invariably "reach out" into the next ring because the line is too >fat. I suppose one solution to be simply to choose a narrower line, say >10-20 pixels wide and accept that some overlap onto the next ring is >going to happen and that the errors that result are minimal. >Any thoughts on this would be welcome. >Thanks. >-- >Pat Pringle > A GrowthRingsMacro I wrote in '96 attempted to make the best use of the available data. This is probably more complex than you want. It involved: Radial analysis of the maximum available sector or full 360 degree data using a first pass radial analysis with a narrow profilePlot line (n=6<>8pixels) to generate a (more or less) linearised 2D profile map where one dimension was distance from core and other dimension was angle around sector. This preliminary profile along this first pass radial was then used to trace (usually 3 well spaced) of these approximately linearised rings using either density sliceing and wand or manually using a segemented line selection. These were then in turn used to morph (or interpolate) their shape over the whole profile so that the whole sector data was linearised using the radially integrated data. The linearised profile was then plotprofiled to give accurate integrated peak spacing and densities. (peaks can be automatically found by derivative passing through zero). The morphing data was inverted to remap the determined rings back over the original image for easy verification. A lot depends on the nature of the project, your images, patience etc :-) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia From nih-image-request@io.ece.drexel.edu Tue Jan 5 05:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA17705; Tue, 5 Jan 1999 05:18:42 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 05:18:42 -0500 (EST) Date: Tue, 5 Jan 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199901051005.FAA15920@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"zXAT7.0.yu3.FFUas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/752 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1997 NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- From nih-image-request@io.ece.drexel.edu Tue Jan 5 09:51 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA19308; Tue, 5 Jan 1999 09:51:30 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 09:51:30 -0500 (EST) X-Authentication-Warning: asgard.cbu.edu: malinda owned process doing -bs Date: Tue, 5 Jan 1999 08:23:28 -0600 (CST) From: Malinda Fitzgerald X-Sender: malinda@asgard To: nih-image@io.ece.drexel.edu cc: nih-image-d-request@io.ece.drexel.edu Subject: Re: Image in 99?? In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"wHQbH2.0.xr3.W2Yas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/753 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 282 I just surfaced from the chaos of the holidays and speaking as a one that spends way too much time working on my computer I wish I was snorkling!!Sounds like a good idea. How about an image retreat? We could all bring our laptops and discuss how to analyze coral reefs! Malinda From nih-image-d-request@io.ece.drexel.edu Tue Jan 5 09:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA19991; Tue, 5 Jan 1999 09:56:17 -0500 (EST) Date: Tue, 5 Jan 1999 09:56:17 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901051456.JAA19991@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #1 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/1 Precedence: list MIME-Version: 1.0 To: nih-image-d@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu Content-Type: multipart/digest; boundary="----------------------------" Content-Length: 12169 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 1 Today's Topics: Image in 99?? [ David Morilak ] Re: Image in 99?? [ Vaughn Adams ] Re: Image in 99?? [ David Ehrhardt To: nih-image-d-request@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu Subject: Image in 99?? Message-id: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Hi: I'm just checking in since I have not received anything from the NIH-Image mailing list (I am subscribed to receive messages in digest mode) since 12/31/98... I'm wondering if a) the list has experienced a premature Y2k melt-down b) The New Year dawned, and I got inadvertently kicked off the list c) I pissed somebody off and got advertently kicked off the list d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, and there have actually been NO messages posted to the NIH list since the dawn of '99 or e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 Any ideas as to which is most likely? (and please lie to me if it's c!) Thanks, and Happy New Year! David Morilak David Morilak, Ph.D. Dept of Pharmacology Univ Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7764 ph: 210-567-4174 FAX: 210-567-4303 E-mail: morilak@uthscsa.edu ------------------------------ Date: Mon, 4 Jan 1999 16:22:24 -0500 (EST) From: Vaughn Adams To: nih-image@io.ece.drexel.edu Cc: morilak@uthscsa.edu Subject: Re: Image in 99?? Message-Id: <199901042122.QAA20822@cbis.ece.drexel.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit David: > I'm just checking in since I have not received anything from the NIH-Image > mailing list (I am subscribed to receive messages in digest mode) since > 12/31/98... I'm wondering if > > a) the list has experienced a premature Y2k melt-down > b) The New Year dawned, and I got inadvertently kicked off the list > c) I pissed somebody off and got advertently kicked off the list > d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, > and there have actually been NO messages posted to the NIH list since the > dawn of '99 > or > e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 > > Any ideas as to which is most likely? (and please lie to me if it's c!) The correct answer is D. Everybody went to the Caribbean. The list members who live in the Caribean went mountain climbing in Alaska. -- Vaughn Adams Drexel University Electrical and Computer Engineering Voice: 215-895-1979 32nd and Chestnut Streets FAX: 215-895-1695 Philadelphia, Pa 19104 Email: vaughn@coe.drexel.edu PGP key available - finger -l vaughn@cbis.ece.drexel.edu ------------------------------ Date: Mon, 4 Jan 1999 14:43:28 -0700 From: connie temm To: nih-image@io.ece.drexel.edu Subject: Re: Image in 99?? Message-Id: Content-Type: text/plain; charset="us-ascii" d1/2: all imagers would rather be snorkeling or skiing Constance J. Temm, Ph.D. University of Arizona Tel.: (520) 621-8643 Nutritional Sciences Dept. Fax: 520 621 1396 632 Shantz Building Tucson, AZ 85721 USA ------------------------------ Date: Mon, 4 Jan 1999 15:02:29 -0800 (PST) From: David Ehrhardt To: nih-image@io.ece.drexel.edu cc: nih-image-d-request@io.ece.drexel.edu Subject: Re: Image in 99?? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII > Hi: > > I'm just checking in since I have not received anything from the NIH-Image > mailing list (I am subscribed to receive messages in digest mode) since > 12/31/98... I'm wondering if > > a) the list has experienced a premature Y2k melt-down > b) The New Year dawned, and I got inadvertently kicked off the list > c) I pissed somebody off and got advertently kicked off the list > d) all imagers are snorkeling in the Caribbean or skiing in the Rockies, > and there have actually been NO messages posted to the NIH list since the > dawn of '99 > or > e) Our mail server shredded all messages received between 1/1/99 and 1/4/99 > > Any ideas as to which is most likely? (and please lie to me if it's c!) > > Thanks, and Happy New Year! > > David Morilak I was actually snorkeling during this time and I saw a lot of suspicious pasty-skinned people who looked like they spent a lot of time in darkened rooms. David Ehrhardt Carnegie Institution of Washington Department of Plant Biology Phone (650) 325-1521 x261 260 Panama St., Stanford, CA 94305 FAX (650) 325-6857 ------------------------------ Date: Mon, 04 Jan 1999 20:10:57 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Quantitative immunoperoxidase staining Message-Id: <3.0.5.32.19990104201057.00bb64d0@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" Maybe it just seems like snorkeling, as the snow mountains are 3-4 meters high at the edge of our parking lot... Anyway, what _I_ did on my holiday break was to finally crack segmenting images of immunoperoxidase stained pathology slides to separate the brown peroxidase and blue counterstain objectively and quantitatively. I posted the example under "98.001" on my web page http://www-personal.umich.edu/~schuette/imaging I'd be interested in hearing from anyone else on the list who's working on this problem. Wade Schuette University of Michigan Sunny (14 inches worth) Ann Arbor, Michigan Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Tue, 5 Jan 1999 17:01:32 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: lespat@thurston.com, nih-image@io.ece.drexel.edu Subject: Re: NIH mean density scans and line width of measuring too Message-ID: <6B9F84B5792@rna.bio.mq.edu.au> >Date: Sun, 27 Dec 1998 17:56:10 -0800 >From: "Patrick T. Pringle" >To: NIH forum >Subject: NIH mean density scans and line width of measuring too >.... >Has anyone come up with a satisfactory line width for obtaining mean >density of tree rings in a scanned image, say using NIH or Scion Image? >We have been pretty much relying on measuring the ring width and >latewood width with single pixel wide lines up until now, but it seems a >pity not to at least collect the density information since one is making >the measurements anyway. Somewhere I read or heard that the maximum line >width shown in the NIH toolbar is 99 pixels. I have tried a few >measurements using that width, but the beginning and ending >points invariably "reach out" into the next ring because the line is too >fat. I suppose one solution to be simply to choose a narrower line, say >10-20 pixels wide and accept that some overlap onto the next ring is >going to happen and that the errors that result are minimal. >Any thoughts on this would be welcome. >Thanks. >-- >Pat Pringle > A GrowthRingsMacro I wrote in '96 attempted to make the best use of the available data. This is probably more complex than you want. It involved: Radial analysis of the maximum available sector or full 360 degree data using a first pass radial analysis with a narrow profilePlot line (n=6<>8pixels) to generate a (more or less) linearised 2D profile map where one dimension was distance from core and other dimension was angle around sector. This preliminary profile along this first pass radial was then used to trace (usually 3 well spaced) of these approximately linearised rings using either density sliceing and wand or manually using a segemented line selection. These were then in turn used to morph (or interpolate) their shape over the whole profile so that the whole sector data was linearised using the radially integrated data. The linearised profile was then plotprofiled to give accurate integrated peak spacing and densities. (peaks can be automatically found by derivative passing through zero). The morphing data was inverted to remap the determined rings back over the original image for easy verification. A lot depends on the nature of the project, your images, patience etc :-) Greg Joss, School of Biological Sciences, Phone:(61)(2) 9850 8212 Fax: 9850 8174 Macquarie University, Email gjoss@rna.bio.mq.edu.au North Ryde, (Sydney,) NSW 2109, Australia ------------------------------ Date: Tue, 5 Jan 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Message-Id: <199901051005.FAA15920@io.ece.drexel.edu> NIH-image Mailing List Help nih-image@biomed.drexel.edu - Sends mail to the list nih-image-request@biomed.drexel.edu - Administation for List nih-image-d-request@biomed.drexel.edu - Aministration for Digest Subscribe --------- To subscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: subscribe Subscribe to Digest ------------------- To subscribe to a digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "Subscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: subscribe Unsubscribe ----------- To unsubscribe to the list, send E-mail to nih-image-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-request@biomed.drexel.edu Subject: unsubscribe Unsubscribe to Digest -------------------- To unsubscribe to digested version of the list, send E-mail to nih-image-d-request@biomed.drexel.edu. The Subject of the message should contain "unsubscribe". As in: To: nih-image-d-request@biomed.drexel.edu Subject: unsubscribe Archive ------- Every submission sent to this list is archived. Following are the commands used to access the archive. Send Email to nih-image-request@biomed.drexel.edu with the command in the Subject line or in the body of the message. get filename ... ls directory ... egrep case_insensitive_regular_expression filename ... maxfiles nnn version quit Aliases for 'get': send, sendme, getme, gimme, retrieve, mail Aliases for 'ls': dir, directory, list, show Aliases for 'egrep': search, grep, fgrep, find Aliases for 'quit': exit If you append a non-standard signature, you should use the quit command to prevent the archive server from interpreting the signature. Examples: ls latest get latest/12 egrep some.word latest/* -- ------------------------------ Date: Tue, 5 Jan 1999 08:23:28 -0600 (CST) From: Malinda Fitzgerald To: nih-image@io.ece.drexel.edu cc: nih-image-d-request@io.ece.drexel.edu Subject: Re: Image in 99?? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I just surfaced from the chaos of the holidays and speaking as a one that spends way too much time working on my computer I wish I was snorkling!!Sounds like a good idea. How about an image retreat? We could all bring our laptops and discuss how to analyze coral reefs! Malinda -------------------------------- End of nih-image-d Digest V99 Issue #1 ************************************** From nih-image-request@io.ece.drexel.edu Tue Jan 5 12:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08171; Tue, 5 Jan 1999 12:49:08 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 12:49:08 -0500 (EST) Date: Tue, 5 Jan 1999 12:21:16 -0500 (EST) From: RICHARD RHIEW Sender: rbr16@columbia.edu To: nih-image@io.ece.drexel.edu Subject: pixel to meter conversion??? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"7C32v1.0.RO1.Xeaas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/754 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 80 is there a conversion to go from 1 pixel to meters/micrometers/inches,etc??? From nih-image-request@io.ece.drexel.edu Tue Jan 5 15:00 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA21357; Tue, 5 Jan 1999 14:59:37 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 14:59:37 -0500 (EST) Date: Tue, 5 Jan 1999 20:34:12 +0100 (MET) Message-Id: <199901051934.UAA10225@isidoro.unileon.es> X-Sender: dbcmjv@isidoro.unileon.es X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Maria Dolores Julian Subject: in situ hybridization Resent-Message-ID: <"ZNo1G1.0.tX4.rdcas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/755 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2175 Dear colleagues: I am analyzing some in situ hybridization films from brain sections and would appreciate any clarification of my doubts as well as any further suggestions. The version of Image that I have available is 1.22. 1.- How do you get more reliable results?, using the gray scale or with the threshold?, or do you vary this depending on the region to be studied and/or the probe (oligoprobe or riboprobe). 2.- After selecting a region with the mouse, the program gives us two columns with two different values (area and mean). I have been told to use the mean value (ignoring the area) when using the gray scale, whereas, when using the threshold, the value to be used is the product obtained multiplying the area by the mean; is that correct? 3.- Does anyone subtract the background? Do you think it is important/necessary? (Some people believe it is especially important when using riboprobes because the labeling is more intense and uneven between sections). And, if so, when and how do you do it? In this regard I have been tested to measure the background of a similar region between the dentate gyrus and CA1 when analyzing the hippocampus (riboprobe labeled) using the threshold method. In these cases, the area for the value is zero or a very small number (0.001, etc.); however, the values for the mean column, although sometimes are also zero, are otherwise bigger than the area value as, for example, 0.2, etc. Consequently, subtracting the background for each section I would have a very different result if I consider the value of this background as the product of the area by the mean or if I only consider the value of its mean column. 4.- In my studies I am analyzing brains of different sizes (male/female, young/adult) and thus their different regions would be bigger or smaller depending on the sex/age. Does the Image program compensate these differences in anyway or, by the contrary, it would give a bigger value for a male brain region (because it has a bigger surface) than for a female that has a higher labeling from the probe (because its surface is smaller)? Thank you very much in advance for your replays (dbcmjv@unileon.es). From nih-image-request@io.ece.drexel.edu Tue Jan 5 15:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA26805; Tue, 5 Jan 1999 15:57:06 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 15:57:06 -0500 (EST) Date: Tue, 5 Jan 99 12:33:06 PST From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: in situ hybridization In-Reply-To: Your message of Tue, 5 Jan 1999 20:34:12 +0100 (MET) Message-ID: Resent-Message-ID: <"vWxnX.0.nt5.TSdas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/756 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1244 Correction: In item 4, where you wrote: >might be difficult for clinical courses that are taught by faculty from >various different departments. please change 1 word: clinical to interdisciplinary. It should read: might be difficult for interdisciplinary that are taught by faculty from different departments. I also suggest deleting "various", as "various" and "different" is redundant. Walter ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ====================================================================== From nih-image-request@io.ece.drexel.edu Tue Jan 5 16:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA27422; Tue, 5 Jan 1999 16:02:11 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 16:02:11 -0500 (EST) Date: Tue, 5 Jan 99 12:38:00 PST From: Walter Wolf To: nih-image@io.ece.drexel.edu Cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: in situ hybridization In-Reply-To: Your message of Tue, 5 Jan 1999 20:34:12 +0100 (MET) Message-ID: Resent-Message-ID: <"NH_5z3.0.916.uWdas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/757 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 951 Dear Colleagues: It appears that a reply to a different message went to this list-server. My appologies. ====================================================================== | Professor Walter Wolf, Ph.D. E-Mail: wwolfw@hsc.usc.edu | | Distinguished Professor of Pharmaceutical Sciences | | Director, Pharmacokinetic Imaging Program | | Department of Pharmaceutical Sciences, School of Pharmacy | | University of Southern California Telephone: 323-442-1405 | | 1985 Zonal Ave., Los Angeles, CA 90033 Fax: 323-442-9804 | | | |Center for Noninvasive Pharmacology, Los Angeles Oncologic Institute| | MRI at St. Vincent Medical Center Telephone: 213-484-7235 | | 2131 Third St., Los Angeles, CA 90057 Fax: 213-484-7447 | ======================================================================