From nih-image-request@io.ece.drexel.edu Tue Jan 5 16:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA29874; Tue, 5 Jan 1999 16:21:16 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 16:21:16 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <93d0be53.36927cd3@aol.com> Date: Tue, 5 Jan 1999 15:57:55 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Updates to Image Processing Tool Kit Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 84 Resent-Message-ID: <"5E_Zx2.0.Lc6.hqdas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/758 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 616 A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ This package is particularly aimed at users of Digital Darkroom, which is included on the Tool Kit CD. Plug-ins provide functions such as Gaussian filtering, unsharp masking, contrast adjustment and equalization, image rotation, color lookup tables, and color plane manipulation that are included in Photoshop but are not part of the basic Digital Darkroom program. The site also has several other updates, new plug-ins, bug fixes, and tutorials, all identical for both Mac and PC users. From nih-image-request@io.ece.drexel.edu Tue Jan 5 16:22 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA29935; Tue, 5 Jan 1999 16:21:45 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 16:21:45 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Tue, 5 Jan 1999 15:57:16 EST To: it-list@sparky.uthscsa.edu, nih-image@io.ece.drexel.edu, Microscopy@sparc5.microscopy.com Mime-Version: 1.0 Subject: Image Analysis Short Course Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 84 Resent-Message-ID: <"ux8pB.0.jd6.8rdas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/759 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1263 Workshop on Quantitative Image Analysis May 20-22 and May 24-26, 1999, North Carolina State University, Raleigh, North Carolina, USA June 14-16, 1999, Danish Technological Institute, Taastrup, Denmark This highly regarded hands-on course taught by Dr. John Russ and other expert faculty has been presented annually for more than 15 years. It deals with all phases of quantitative and computer-assisted imaging from acquisition and processing through measurement and stereological interpretation. Attendees receive The Image Processing Handbook plus a CD-ROM containing images, algorithms (Photoshop-compatible for Mac and Windows) and an extensive tutorial. The course is appropriate for professionals scientists, technicians and administrators using these techniques for research. Attendees typically come from materials science, geology, biological and medical sciences, pharmaceuticals, food science, industrial quality control, remote sensing, and other disciplines. For detailed information and registration contact Cindy Allen, Dept. of Continuing and Professional Education, N. C. State University, Raleigh, NC 27695-7401, 919-515-8171, fax 919-515-7614, email: cindy_allen@ncsu.edu On-line information is available at http://members.aol.com/IPCourse/ From nih-image-request@io.ece.drexel.edu Tue Jan 5 16:37 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA01951; Tue, 5 Jan 1999 16:37:03 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 16:37:03 -0500 (EST) Message-ID: <19990105211311.9055.rocketmail@web4.rocketmail.com> Date: Tue, 5 Jan 1999 13:13:11 -0800 (PST) From: Mark Vivino Subject: Re: pixel to meter conversion??? To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"QoGfa.0.k77.T4eas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/760 X-Loop: nih-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 ---RICHARD RHIEW wrote: > > is there a conversion to go from 1 pixel to > meters/micrometers/inches,etc??? Look in the manual under set scale. == 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 Jan 5 16:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA02340; Tue, 5 Jan 1999 16:40:31 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 16:40:31 -0500 (EST) Message-ID: <19990105210502.11965.rocketmail@web1.rocketmail.com> Date: Tue, 5 Jan 1999 13:05:02 -0800 (PST) From: Mark Vivino Subject: Re: Image in 99?? To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"3ach3.0.HF7.m7eas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/761 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 608 ---Malinda Fitzgerald wrote: > > How about an image retreat? We could > all bring our laptops and discuss how to analyze coral reefs! Well I'm down here in Miami for the time being and the FL Keys aren't too far away providing an excellent setting for this research. I'm sure NIH will fund our research into these coral reefs...Just fill out the 30 page grant application, no sweat. == 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 Jan 5 17:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA09493; Tue, 5 Jan 1999 17:44:01 -0500 (EST) Resent-Date: Tue, 5 Jan 1999 17:44:01 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Tue, 05 Jan 1999 16:41:08 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: Updates to Image Processing Tool Kit Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"b0MF13.0.ob1.s-eas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/762 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1096 Dr. Russ, I'd be very interested in your comments or questions on my analysis of dual-stained color images that I mentioned in earlier posts to NIH-Image, in item 98.001 on http://www-persona.umich.edu/~schuette/imaging I own two editions of your fine book, but did not find there a discussion of this particular problem or solution. Best regards, R. Wade Schuette University of Michigan Ann Arbor, MI schuette@umich.edu >>> 01/05 4:20 PM >>> A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ This package is particularly aimed at users of Digital Darkroom, which is included on the Tool Kit CD. Plug-ins provide functions such as Gaussian filtering, unsharp masking, contrast adjustment and equalization, image rotation, color lookup tables, and color plane manipulation that are included in Photoshop but are not part of the basic Digital Darkroom program. The site also has several other updates, new plug-ins, bug fixes, and tutorials, all identical for both Mac and PC users. From nih-image-d-request@io.ece.drexel.edu Wed Jan 6 06:30 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA06913; Wed, 6 Jan 1999 06:30:49 -0500 (EST) Date: Wed, 6 Jan 1999 06:30:49 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901061130.GAA06913@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #2 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/2 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: 12002 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 2 Today's Topics: pixel to meter conversion??? [ RICHARD RHIEW ] in situ hybridization [ Maria Dolores Julian ] Re: in situ hybridization [ Walter Wolf ] Updates to Image Processing Tool Kit [ DrJohnRuss@aol.com ] Image Analysis Short Course [ DrJohnRuss@aol.com ] Re: pixel to meter conversion??? [ Mark Vivino To: nih-image@io.ece.drexel.edu Subject: pixel to meter conversion??? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII is there a conversion to go from 1 pixel to meters/micrometers/inches,etc??? ------------------------------ Date: Tue, 5 Jan 1999 20:34:12 +0100 (MET) From: Maria Dolores Julian To: nih-image@io.ece.drexel.edu Subject: in situ hybridization Message-Id: <199901051934.UAA10225@isidoro.unileon.es> Content-Type: text/plain; charset="us-ascii" 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). ------------------------------ 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 Message-ID: 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 | ====================================================================== ------------------------------ 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 Message-ID: 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 | ====================================================================== ------------------------------ Date: Tue, 5 Jan 1999 15:57:55 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Updates to Image Processing Tool Kit Message-ID: <93d0be53.36927cd3@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ This package is particularly aimed at users of Digital Darkroom, which is included on the Tool Kit CD. Plug-ins provide functions such as Gaussian filtering, unsharp masking, contrast adjustment and equalization, image rotation, color lookup tables, and color plane manipulation that are included in Photoshop but are not part of the basic Digital Darkroom program. The site also has several other updates, new plug-ins, bug fixes, and tutorials, all identical for both Mac and PC users. ------------------------------ Date: Tue, 5 Jan 1999 15:57:16 EST From: DrJohnRuss@aol.com To: it-list@sparky.uthscsa.edu, nih-image@io.ece.drexel.edu, Microscopy@sparc5.microscopy.com Subject: Image Analysis Short Course Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Workshop on Quantitative Image Analysis May 20-22 and May 24-26, 1999, North Carolina State University, Raleigh, North Carolina, USA June 14-16, 1999, Danish Technological Institute, Taastrup, Denmark This highly regarded hands-on course taught by Dr. John Russ and other expert faculty has been presented annually for more than 15 years. It deals with all phases of quantitative and computer-assisted imaging from acquisition and processing through measurement and stereological interpretation. Attendees receive The Image Processing Handbook plus a CD-ROM containing images, algorithms (Photoshop-compatible for Mac and Windows) and an extensive tutorial. The course is appropriate for professionals scientists, technicians and administrators using these techniques for research. Attendees typically come from materials science, geology, biological and medical sciences, pharmaceuticals, food science, industrial quality control, remote sensing, and other disciplines. For detailed information and registration contact Cindy Allen, Dept. of Continuing and Professional Education, N. C. State University, Raleigh, NC 27695-7401, 919-515-8171, fax 919-515-7614, email: cindy_allen@ncsu.edu On-line information is available at http://members.aol.com/IPCourse/ ------------------------------ Date: Tue, 5 Jan 1999 13:13:11 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: pixel to meter conversion??? Message-ID: <19990105211311.9055.rocketmail@web4.rocketmail.com> Content-Type: text/plain; charset=us-ascii ---RICHARD RHIEW wrote: > > is there a conversion to go from 1 pixel to > meters/micrometers/inches,etc??? Look in the manual under set scale. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 5 Jan 1999 13:05:02 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Image in 99?? Message-ID: <19990105210502.11965.rocketmail@web1.rocketmail.com> Content-Type: text/plain; charset=us-ascii ---Malinda Fitzgerald wrote: > > How about an image retreat? We could > all bring our laptops and discuss how to analyze coral reefs! Well I'm down here in Miami for the time being and the FL Keys aren't too far away providing an excellent setting for this research. I'm sure NIH will fund our research into these coral reefs...Just fill out the 30 page grant application, no sweat. == Mark Vivino mvivino@rocketmail.com Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Tue, 05 Jan 1999 16:41:08 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: Updates to Image Processing Tool Kit Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Dr. Russ, I'd be very interested in your comments or questions on my analysis of dual-stained color images that I mentioned in earlier posts to NIH-Image, in item 98.001 on http://www-persona.umich.edu/~schuette/imaging I own two editions of your fine book, but did not find there a discussion of this particular problem or solution. Best regards, R. Wade Schuette University of Michigan Ann Arbor, MI schuette@umich.edu >>> 01/05 4:20 PM >>> A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ This package is particularly aimed at users of Digital Darkroom, which is included on the Tool Kit CD. Plug-ins provide functions such as Gaussian filtering, unsharp masking, contrast adjustment and equalization, image rotation, color lookup tables, and color plane manipulation that are included in Photoshop but are not part of the basic Digital Darkroom program. The site also has several other updates, new plug-ins, bug fixes, and tutorials, all identical for both Mac and PC users. -------------------------------- End of nih-image-d Digest V99 Issue #2 ************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 6 09:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA28381; Wed, 6 Jan 1999 09:16:52 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 09:16:52 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Wed, 6 Jan 1999 08:44:41 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Re: Updates to Image Processing Tool Kit Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 84 Resent-Message-ID: <"C0Mh_1.0.us5.Fasas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/763 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 394 In a message dated 1/5/99 5:38:01 PM, you wrote: >Dr. Russ, I'd be very interested in your comments or questions on >my analysis of dual-stained color images that I mentioned in earlier >posts to NIH-Image, in item 98.001 on >http://www-persona.umich.edu/~schuette/imaging My browser can't find any site with such an ID, so I have no idea what you are talking about. Sorry. John Russ From nih-image-request@io.ece.drexel.edu Wed Jan 6 09:43 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA02068; Wed, 6 Jan 1999 09:43:00 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 09:43:00 -0500 (EST) Reply-To: From: "Ned Horning" To: "NIH-Image List" Subject: Enhancement with break points Date: Wed, 6 Jan 1999 17:19:39 +0300 Message-ID: <000e01be397f$983ac210$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 Resent-Message-ID: <"U-LwV2.0.N47.-4tas"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/764 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: 337 Greetings, I would like to know if someone has written a macro or made source code changes that would allow one to interactively enhance an image using break-points. The Map window allows one to enhance the image using a linear stretch but it would be nice to be able to define more than one inflection point. Thanks in advance, Ned From nih-image-request@io.ece.drexel.edu Wed Jan 6 10:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04628; Wed, 6 Jan 1999 10:01:11 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 10:01:11 -0500 (EST) X-Sender: p.h.johnston@pop.larc.nasa.gov Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Wed, 6 Jan 1999 09:39:31 -0500 To: nih-image@io.ece.drexel.edu From: "Patrick H. Johnston" Subject: Re: Re: Updates to Image Processing Tool Kit Resent-Message-ID: <"Yz2Ua1.0.xJ.3Ltas"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/765 X-Loop: nih-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 >>http://www-persona.umich.edu/~schuette/imaging > >My browser can't find any site with such an ID, so I have no idea what you are >talking about. Sorry. try deleting the "-persona" From nih-image-request@io.ece.drexel.edu Wed Jan 6 19:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA01495; Wed, 6 Jan 1999 19:53:56 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 19:53:56 -0500 (EST) Date: Wed, 6 Jan 1999 19:29:06 -0500 (EST) From: Pravin Patil X-Sender: pro@galaxian.rs.itd.umich.edu To: nih-image@io.ece.drexel.edu Subject: Description of Gel Plotting Macro In-Reply-To: <199901061130.GAA06791@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Hnj0B.0.K37.a__as"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/766 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 231 Does anyone have references of how people describe the use of the gel plotting macros in Image to do densitomeric analysis? Journal references would be great! I used them and was wondering how to describe it in a paper. Thanks From nih-image-request@io.ece.drexel.edu Wed Jan 6 20:33 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA06033; Wed, 6 Jan 1999 20:33:03 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 20:33:03 -0500 (EST) Message-Id: <3.0.1.32.19990106180212.0073f14c@spot.colorado.edu> X-Sender: tracybl@spot.colorado.edu X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Wed, 06 Jan 1999 18:02:12 -0700 To: nih-image@io.ece.drexel.edu From: "Brian L. Tracy" Subject: order of files opened using "open all" in import menu Mime-Version: 1.0 Resent-Message-ID: <"XVOgD.0.hw.Vf0bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/767 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1186 Hi folks, I desire to import and open multiple files from one directory all at once, and I know I can do this using the "open all" option in the import menu. I want to put the opened images, which are sequential axial MRI slices, into a stack, and I know how to do that. The "import" finder window displays the files in order according to their filename, which leads you to believe that they will opened in that order. The problem is, NIH Image opens the files in order of date, not of filename, resulting in a stack , when you do "windows to stack" that is not in order according to the filenames (e.g., XXXXX01, XXXX02, etc.). Obviously, I don't want to import the images one at a time. Can I get NIH Image to import and open these images in order of filename, the way they are displayed in the directory? Thanks in advance for your help , Brian L. Tracy Brian L. Tracy, Ph.D. Research Associate Neural Control of Movement Laboratory Department of Kinesiology and Applied Physiology University of Colorado Campus Box 354 Boulder, CO. 80309-0354 (303) 492-4965 lab (303) 492-5422 lab (303) 492-6778 fax tracybl@spot.colorado.edu http://spot.colorado.edu/~tracybl/Home.html From nih-image-request@io.ece.drexel.edu Wed Jan 6 21:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA12297; Wed, 6 Jan 1999 21:27:33 -0500 (EST) Resent-Date: Wed, 6 Jan 1999 21:27:33 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: pro@umich.edu, nih-image@io.ece.drexel.edu Date: Thu, 7 Jan 1999 13:08:21 GMT+1100 Subject: Re: Description of Gel Plotting Macro Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6E618927FC1@rna.bio.mq.edu.au> Resent-Message-ID: <"dbezF.0.8N2.6P1bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/768 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2062 >Received: from SpoolDir by RNA (Mercury 1.43); 7 Jan 99 11:50:28 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.43) with ESMTP; > 7 Jan 99 11:50:21 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id TAA00826; > Wed, 6 Jan 1999 19:47:30 -0500 (EST) >Resent-Date: Wed, 6 Jan 1999 19:47:30 -0500 (EST) >Date: Wed, 6 Jan 1999 19:29:06 -0500 (EST) >From: Pravin Patil >X-Sender: pro@galaxian.rs.itd.umich.edu >To: nih-image@io.ece.drexel.edu >Subject: Description of Gel Plotting Macro >In-Reply-To: <199901061130.GAA06791@io.ece.drexel.edu> >Message-ID: >MIME-Version: 1.0 >Content-Type: TEXT/PLAIN; charset=US-ASCII >Resent-Message-ID: <"Hnj0B.0.K37.a__as"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/766 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Does anyone have references of how people describe the use of the gel >plotting macros in Image to do densitomeric analysis? Journal references >would be great! I used them and was wondering how to describe it in a >paper. > >Thanks > from: http://rsb.info.nih.gov/nih-image/manual/faq.html#cite or NIH Image Manual FREQUENTLY ASKED QUESTIONS How should I cite NIH Image Published research assisted by NIH Image should use a statement similar to the following in the materials and methods section "... analysis performed on a Macintosh computer using the public domain NIH Image program (developed at the U.S. National Institutes of Health and available on the Internet at http://rsb.info.nih.gov/nih-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-request@io.ece.drexel.edu Thu Jan 7 00:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA29030; Thu, 7 Jan 1999 00:08:49 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 00:08:49 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: Brian.Tracy@Colorado.EDU, nih-image@io.ece.drexel.edu Date: Thu, 7 Jan 1999 15:39:54 GMT+1100 Subject: Re: order of files opened using "open all" in import menu Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6E89F3045CC@rna.bio.mq.edu.au> Resent-Message-ID: <"BXw_Q3.0.TD6.Id3bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/769 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 5531 >Date: Wed, 06 Jan 1999 18:02:12 -0700 >To: nih-image@io.ece.drexel.edu >From: "Brian L. Tracy" >Subject: order of files opened using "open all" in import menu > >Hi folks, > >I desire to import and open multiple files from one directory all at once, >and I know I can do this using the "open all" option in the import menu. I >want to put the opened images, which are sequential axial MRI slices, into >a stack, and I know how to do that. The "import" finder window displays >the files in order according to their filename, which leads you to believe >that they will opened in that order. The problem is, NIH Image opens the >files in order of date, not of filename, resulting in a stack , when you do >"windows to stack" that is not in order according to the filenames (e.g., >XXXXX01, XXXX02, etc.). Obviously, I don't want to import the images one >at a time. Can I get NIH Image to import and open these images in order of >filename, the way they are displayed in the directory? > >Thanks in advance for your help , > >Brian L. Tracy >Brian L. Tracy, Ph.D. >Research Associate >Neural Control of Movement Laboratory >Department of Kinesiology and Applied Physiology >University of Colorado >Campus Box 354 >Boulder, CO. 80309-0354 >(303) 492-4965 lab >(303) 492-5422 lab >(303) 492-6778 fax >tracybl@spot.colorado.edu >http://spot.colorado.edu/~tracybl/Home.html > A number of others and myself have responded to similar and related topics a number of times before. While I am inclined to contest some aspects of your problem statement (see copied email below); the macro batchNumberedFilesMacro included below will simply open files in incremented numeric order for a variety of numeric suffix formats. "___________________________________ >From GJOSS@rna.bio.mq.edu.au Thu Oct 16 18:39:03 CDT 1997 To: kwb@bserv.com, nih-image@Soils.Umn.EDU Date: Fri, 17 Oct 1997 9:44:50 GMT+1000 Subject: Re: Ordering of CSLM images for stacks >Date: Thu, 16 Oct 1997 18:16:56 -0500 (CDT) > >I would like to open a series of converted Biorad confocal *.tif images >(img001.tif, img002.tif, img003.tif......), convert the images to a stack >and retain the original image sequence within the stack. For whatever >reason the images stack out of sequence. Is there some naming convention or >stack re-ordering capability that I might use to get my images stacked in >the right order? > Ken, If you use Windows-to-Stack, images stack in order in list in Windows menu ie order in which they were opened. If you open in finder by clicking then you will open in click order. If you open in finder by draging a selection then you will open in veiw order ie date modified or name etc. If you open by "open all" then you will open in name order. If you use makeNewStack, then you can control stack order by order of select(Pic/Window) in addSlice;selectPic/Window(xxxx);selectAll;copy;paste; ____________________" {_____________________________________________________________________} { batchNumberedFilesMacro: NIH-Image macro for batch processing of numerically suffixed files After invoking macro, point open dialogue at first file in directory to be processed. respond to prompted 'Enter last image:' 'increment' macro will parse fileName for prefix and numeric suffix of forms: 1,2,3,4; xx 1,xx 2,xx 3,xx 4; xx01,xx02,xx03,xx04; xx1,xx2,xx3,xx4 etc Without modification of procedure processImage; macro will simply open files in incremented numeric order. Written by Greg Joss, 1997-12-14 last mod:1999-1-7 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 } procedure getImage;var FullPath, FileType:string; p,d,FileSize:integer; begin if directory='' then showMessage('open first image') else begin image:=image+inc; showMessage(directory,'\[',prefix,']\',image:digits);end; open(prefix,image:digits); if directory='' then begin directory:=GetPath('window'); p:=0;prefix:=windowTitle; while (ord(prefix)<48) or (ord(prefix)>57) do begin delete(prefix,1,1);p:=p+1;end; digits:=length(prefix); image:=StringToNum(prefix); prefix:=windowTitle; delete(prefix,p+1,99); lastimage:=image; showMessage(directory,'\[',prefix,']\',lastimage,'\',windowTitle); inc:=getnumber('increment',1); repeat begin lastimage:=lastimage+inc; FullPath:=''; for d:=length(concat(lastimage:0))+1 to digits do FullPath:=concat( FullPath,'0'); {this is because open zero fills but concat doesn't} FullPath:=concat(directory,prefix,FullPath,lastimage:0); showMessage(FullPath,'\',prefix,'\',lastimage); GetFileInfo(FullPath, FileType, FileSize);end; until FileSize<0; showMessage(FullPath,'\',prefix,'\',lastimage-inc); lastimage:=GetNumber(concat('start ',image:digits ,'; Enter last image:'),lastimage-inc); end; end; procedure processImage(n);begin end macro '/1 process images'; var image,lastimage,digits,inc:integer; directory,prefix:string; n:integer; begin directory:=''; repeat begin n:=n+1; getImage; processImage(n); end until image>=lastimage; 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 Jan 7 00:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01332; Thu, 7 Jan 1999 00:25:32 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 00:25:32 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Thu, 7 Jan 1999 16:06:25 GMT+1100 Subject: Mail list Archives since changeover 98/7/6? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6E9101550D6@rna.bio.mq.edu.au> Resent-Message-ID: <"dB-gR2.0.7z6.q14bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/770 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1521 I have previously lamented the loss of ability to effectively search the archives as available for mail list prior to switchover "__________________ From: Self To: nih-image@io.ece.drexel.edu Subject: Mail list Archives since changeover 98/7/6? Date: Mon, 21 Sep 1998 11:56:43 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? __________________" gopher://gopher.soils.umn.edu allowed "complex" logical conditions for searching of archived postings. The service via nih-image-request@biomed.drexel.edu help egrep case_insensitive_regular_expression filename ... doesn't appear to offer anything like a comparable facility and it appears to me that the quality of the maillist has suffered as a result. or Am I missing something? In Unix (and even DOS) one could pipe grep results to obtain successively refined searches. Is there some way of doing the same or corresponding thing via nih-image-request@biomed.drexel.edu? Is there any future hope for a combined archive post 98/7/6? or has pre 98/7/6 been assigned to ancient history? 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 Jan 7 00:30 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01925; Thu, 7 Jan 1999 00:30:06 -0500 (EST) Date: Thu, 7 Jan 1999 00:30:06 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901070530.AAA01925@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #3 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/3 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: 25660 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 3 Today's Topics: Re: Re: Updates to Image Processing [ DrJohnRuss@aol.com ] Enhancement with break points [ "Ned Horning" ] Re: Re: Updates to Image Processing [ "Patrick H. Johnston" ] Description of Gel Plotting Macro [ Pravin Patil ] order of files opened using "open al [ "Brian L. Tracy" Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/5/99 5:38:01 PM, you wrote: >Dr. Russ, I'd be very interested in your comments or questions on >my analysis of dual-stained color images that I mentioned in earlier >posts to NIH-Image, in item 98.001 on >http://www-persona.umich.edu/~schuette/imaging My browser can't find any site with such an ID, so I have no idea what you are talking about. Sorry. John Russ ------------------------------ Date: Wed, 6 Jan 1999 17:19:39 +0300 From: "Ned Horning" To: "NIH-Image List" Subject: Enhancement with break points Message-ID: <000e01be397f$983ac210$495499d0@nedh> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Greetings, I would like to know if someone has written a macro or made source code changes that would allow one to interactively enhance an image using break-points. The Map window allows one to enhance the image using a linear stretch but it would be nice to be able to define more than one inflection point. Thanks in advance, Ned ------------------------------ Date: Wed, 6 Jan 1999 09:39:31 -0500 From: "Patrick H. Johnston" To: nih-image@io.ece.drexel.edu Subject: Re: Re: Updates to Image Processing Tool Kit Message-Id: Content-Type: text/plain; charset="us-ascii" >>http://www-persona.umich.edu/~schuette/imaging > >My browser can't find any site with such an ID, so I have no idea what you are >talking about. Sorry. try deleting the "-persona" ------------------------------ Date: Wed, 06 Jan 1999 10:04:52 -0600 (CST) From: David Morilak To: dbcmjv@unileon.es Cc: nih-image-d@io.ece.drexel.edu Subject: Re: in situ hybridization Message-id: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT To the NIH list: After composing this, I see that it is quite lengthy, so if you are not interested in this subject, please delete or scroll down now! Maria: We perform exactly this sort of analysis, and I may have some helpful suggestions for you. I'll try to keep this reply as relevant to the general list as possible, but please feel free to contact me directly if you would like more clarification or detail, or just want to discuss the procedures further. First, I might suggest getting a more recent version of NIH-Image. Calibration is going to be an important function for you, and I'm not sure what the state of calibration was in v. 1.22. I use 1.56 (I've been too lazy to download anything more recent), which works very well for these functions. The second generic issue is your hardware. I have found the Northern Lights BL2 light box from Imaging Research to be indispensable for these analyses. It allows you to adjust the light source to optimize your signal. Then you don't have to artificially adjust by either changing the gain on your camera (bad - don't do it) or by software enhancement, which makes quantification less meaningful. Make the best films you can, then capture them as cleanly as you can. In addition to the Northern Lights lightbox, we use a SONY XC-77 CCD camera fitted with a Nikon 65 mm Nikkor Macro lens, and mounted on a Kaiser enlarger stand over the light box. We have a Scion LG3 in a PowerMac 7100 with a 19" Trinitron monitor, all the RAM it can handle, and an MO drive for storage. For analyzing film autoradiograms, we don't threshold. In fact, we only ever threshold in a few very rare instances where just a small proportion of scattered cells within a large region may express a high amount of signal and it is impossible to get a meaningfull density measure for the region as a whole. In these cases, we threshold, but very leniently, and then ONLY measure the area covered by the exposed silver grains. A change in area should then represent a change in signal (ie a change in the number of silver grains exposed), but I don't like this for a lot of reasons. It is NOT my preferred measure... So we measure density, and understand from the start that this is a relative measure. It is valid, appropriate and reliable for comparisons, ie looking for differences or changes in mRNA expression. It does not give an indication of absolute mRNA level, but in situ hybridization itself doesn't do that. Given this, it is very important to always process brains from different groups (control vs experimental, etc) together to avoid systematic errors that may influence your results. Test your exposure times so that the signal is within a moderate gray range - you don't want it to be so dark that it is saturated, otherwise a change in message expression will no longer be reflected by a proportional change in signal intensity. You may have to perform two different exposures if you have very dark and very light regions that need to be analyzed in the same sections. For quantitation, it is also very important to calibrate against some kind of standard. This is the ONLY thing that allows you to make comparisons across films, and even across different hybridizations with appropriate normalization. We use riboprobes labeled with 35S-UTP, so we use C14 standards from American Radiolabeled Chemicals (catalog # ARC 146A). These come mounted on a microscope slide so they can be placed on the film right along with the labeled sections. C14 has an energy profile very similar to S35, and has a half life that makes them useful for a very long period of time. All the standards we use (one on each film) come from the same lot, so the energy is the same. Other people use brain paste infiltrated with 35S. This is fine, but must be made fresh for every experiment, which is a pain. I also don't like contaminating my cryostat with radioactivity. An optical density wedge (Kodak) is also acceptable, but I prefer the C14 standards because of the similarity in signal to the 35S and the fact that the calibration curve is exposed right along with the signal, rather than being a constant scale as with a wedge. The important thing is to calibrate. We USUALLY do not subtract background because this particular standard has a zero sample included. So when we calibrate, the zero point accomplishes the same thing as subtracting background. Note however, that this is only true of FILM background. If your tissue background is particularly high, you may have to subtract background to get meaningful results. A better alternative would be to re-titrate your stringency or change your probe to reduce the background. Your results will be only as clean as your data, so the best strategy is always to start with the cleanest data. To subtract background AFTER capturing your calibrated images, go to an area of the tissue that you KNOW does not have signal in it. Of course if you don't know ahead of time where all the signal should be, maybe it isn't background but diffuse labeling, which is a problem. You can get around this by using sense control sections to measure tissue background, but it is also true that the background using sense probes can sometimes be very different from background using antisense, depending on G-C etc. So my best advice is to work very hard to get a clean signal and calibrate using a zero standard. When we measure density, we use what I call integrated density (it may not be the most accurate term, but it's useful...). We measure BOTH area and mean density (now expressed in calibrated units of nCi/mg - don't worry about whether the units make sense, they are standard!). We enter these values into a spreadsheet for convenience, then multiply them to get integrated density for each section. We measure 6-8 sections in EACH brain. We then add up all the integrated density values, add up all the area values (in pixels), then divide the total integrated density by the total area to get mean integrated density. This generates ONE value for each brain (important for valid ANOVA or other statistical analyses), and it also provides a weighted measure which takes into account the area of a section when producing the mean. To illustrate, we analyze locus coeruleus. In coronal section at it's mid-point, it is a relatively large peanut-shaped structure (area approximately 1800-2000 sq pixels at the magnification we use to capture). It is very easy to outline and has a strong, rather uniform signal for mRNA such as tyrosine hydroxylase, the NE transporter, etc. At it's most rostral end, it is a small spherical structure, with sometimes very intense labeling but with an area of only about 250-350 sq pixels. If we analyze 8 sections through the whole structure, our analysis means that the values from the large mid-region will contribute relatively more to the overall mean than will the values from the smaller rostral regions, proportional to the area of each section. This also allows you to compare brains with different sizes as you mention in your question. However, if they are different ages I would caution you to consider something else, and that is cell density. Embryonic or neonatal brains have a very different cell density than do adult brains, so comparisons may be impossible as this would confound ISHH signal density measures independent of any difference in mRNA expression. You may want to consider this in your male-female comparisons if the regions you are studying are structurally dimorphic. If you have to subtract background, don't measure the area, just the density of what you define as a background region. Than for your sections, subtract that background value from each density measure BEFORE you multiply by the area to get the integrated density. The next consideration: For large experiments (with many groups or many subjects) it can be difficult or impossible to process all the sections from all the brains for each probe together in one hybridization, which is the ideal procedure. If you can do this, you can just compare all the values, in calibrated standard units of mean integrated density, using whatever statistical analysis is appropriate. But, if the sections must be processed in more than one hybridization run, it is necessary to normalize the data to allow comparisons across runs. So, first we make sure that we have brains from each group represented in each hybridization. We don't use any cold UTP in our transcriptions, so our probes are generally of similar specific activity (I know - technically they are therefore identical in specific activity, but the concentration of probe makes the cpm/ml different - so we try to make this as close as possible). Hybridize with identical conditions (cpm/ml probe, hybridization time, stringency washes, etc) and also expose the films for a similar time to generate hopefully a signal that falls within about the same gray scale range. Try to adjust your light source when you capture your images to get a background level and calibration curve that are as similar as possible, which should not be difficult if your signal is clean and your probe is a good one that you know well. Measure as above and calculate the mean integrated density for each individual brain. Then in the spreadsheet we add one more calculation. For the films from any single hybridization, we divide the mean integrated density for every brain by the mean value calculated for all the "control" brains in that hybridization. You, of course, have to define what the "control" is, and I would recommend having no fewer than 3 control brains in each hybridization. So every value is now expressed as a percent of control within a hybridization, and as long as your processing has been consistent between hybridizations, this allows you to analyze all of your results together from different hybridizations in the same experiment. The values that are analyzed statistically are the "mean integrated density, percent of control", and again, each animal contributes only 1 value for valid statistical analysis. This is the only way we can process an experiment involving 4-8 groups of 8-10 animals (and often 8-12 probes per brain) without having an army of technicians working in an ISHH factory! Again, please feel free to contact me directly for more info. I've probably used up a months allowance of bandwidth for the list as a whole! Good luck! 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: Wed, 6 Jan 1999 19:29:06 -0500 (EST) From: Pravin Patil To: nih-image@io.ece.drexel.edu Subject: Description of Gel Plotting Macro Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have references of how people describe the use of the gel plotting macros in Image to do densitomeric analysis? Journal references would be great! I used them and was wondering how to describe it in a paper. Thanks ------------------------------ Date: Wed, 06 Jan 1999 18:02:12 -0700 From: "Brian L. Tracy" To: nih-image@io.ece.drexel.edu Subject: order of files opened using "open all" in import menu Message-Id: <3.0.1.32.19990106180212.0073f14c@spot.colorado.edu> Content-Type: text/plain; charset="us-ascii" Hi folks, I desire to import and open multiple files from one directory all at once, and I know I can do this using the "open all" option in the import menu. I want to put the opened images, which are sequential axial MRI slices, into a stack, and I know how to do that. The "import" finder window displays the files in order according to their filename, which leads you to believe that they will opened in that order. The problem is, NIH Image opens the files in order of date, not of filename, resulting in a stack , when you do "windows to stack" that is not in order according to the filenames (e.g., XXXXX01, XXXX02, etc.). Obviously, I don't want to import the images one at a time. Can I get NIH Image to import and open these images in order of filename, the way they are displayed in the directory? Thanks in advance for your help , Brian L. Tracy Brian L. Tracy, Ph.D. Research Associate Neural Control of Movement Laboratory Department of Kinesiology and Applied Physiology University of Colorado Campus Box 354 Boulder, CO. 80309-0354 (303) 492-4965 lab (303) 492-5422 lab (303) 492-6778 fax tracybl@spot.colorado.edu http://spot.colorado.edu/~tracybl/Home.html ------------------------------ Date: Thu, 7 Jan 1999 13:08:21 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: pro@umich.edu, nih-image@io.ece.drexel.edu Subject: Re: Description of Gel Plotting Macro Message-ID: <6E618927FC1@rna.bio.mq.edu.au> >Received: from SpoolDir by RNA (Mercury 1.43); 7 Jan 99 11:50:28 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.43) with ESMTP; > 7 Jan 99 11:50:21 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id TAA00826; > Wed, 6 Jan 1999 19:47:30 -0500 (EST) >Resent-Date: Wed, 6 Jan 1999 19:47:30 -0500 (EST) >Date: Wed, 6 Jan 1999 19:29:06 -0500 (EST) >From: Pravin Patil >X-Sender: pro@galaxian.rs.itd.umich.edu >To: nih-image@io.ece.drexel.edu >Subject: Description of Gel Plotting Macro >In-Reply-To: <199901061130.GAA06791@io.ece.drexel.edu> >Message-ID: >MIME-Version: 1.0 >Content-Type: TEXT/PLAIN; charset=US-ASCII >Resent-Message-ID: <"Hnj0B.0.K37.a__as"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/766 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Does anyone have references of how people describe the use of the gel >plotting macros in Image to do densitomeric analysis? Journal references >would be great! I used them and was wondering how to describe it in a >paper. > >Thanks > from: http://rsb.info.nih.gov/nih-image/manual/faq.html#cite or NIH Image Manual FREQUENTLY ASKED QUESTIONS How should I cite NIH Image Published research assisted by NIH Image should use a statement similar to the following in the materials and methods section "... analysis performed on a Macintosh computer using the public domain NIH Image program (developed at the U.S. National Institutes of Health and available on the Internet at http://rsb.info.nih.gov/nih-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 ------------------------------ Date: Thu, 7 Jan 1999 15:39:54 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: Brian.Tracy@Colorado.EDU, nih-image@io.ece.drexel.edu Subject: Re: order of files opened using "open all" in import menu Message-ID: <6E89F3045CC@rna.bio.mq.edu.au> >Date: Wed, 06 Jan 1999 18:02:12 -0700 >To: nih-image@io.ece.drexel.edu >From: "Brian L. Tracy" >Subject: order of files opened using "open all" in import menu > >Hi folks, > >I desire to import and open multiple files from one directory all at once, >and I know I can do this using the "open all" option in the import menu. I >want to put the opened images, which are sequential axial MRI slices, into >a stack, and I know how to do that. The "import" finder window displays >the files in order according to their filename, which leads you to believe >that they will opened in that order. The problem is, NIH Image opens the >files in order of date, not of filename, resulting in a stack , when you do >"windows to stack" that is not in order according to the filenames (e.g., >XXXXX01, XXXX02, etc.). Obviously, I don't want to import the images one >at a time. Can I get NIH Image to import and open these images in order of >filename, the way they are displayed in the directory? > >Thanks in advance for your help , > >Brian L. Tracy >Brian L. Tracy, Ph.D. >Research Associate >Neural Control of Movement Laboratory >Department of Kinesiology and Applied Physiology >University of Colorado >Campus Box 354 >Boulder, CO. 80309-0354 >(303) 492-4965 lab >(303) 492-5422 lab >(303) 492-6778 fax >tracybl@spot.colorado.edu >http://spot.colorado.edu/~tracybl/Home.html > A number of others and myself have responded to similar and related topics a number of times before. While I am inclined to contest some aspects of your problem statement (see copied email below); the macro batchNumberedFilesMacro included below will simply open files in incremented numeric order for a variety of numeric suffix formats. "___________________________________ >From GJOSS@rna.bio.mq.edu.au Thu Oct 16 18:39:03 CDT 1997 To: kwb@bserv.com, nih-image@Soils.Umn.EDU Date: Fri, 17 Oct 1997 9:44:50 GMT+1000 Subject: Re: Ordering of CSLM images for stacks >Date: Thu, 16 Oct 1997 18:16:56 -0500 (CDT) > >I would like to open a series of converted Biorad confocal *.tif images >(img001.tif, img002.tif, img003.tif......), convert the images to a stack >and retain the original image sequence within the stack. For whatever >reason the images stack out of sequence. Is there some naming convention or >stack re-ordering capability that I might use to get my images stacked in >the right order? > Ken, If you use Windows-to-Stack, images stack in order in list in Windows menu ie order in which they were opened. If you open in finder by clicking then you will open in click order. If you open in finder by draging a selection then you will open in veiw order ie date modified or name etc. If you open by "open all" then you will open in name order. If you use makeNewStack, then you can control stack order by order of select(Pic/Window) in addSlice;selectPic/Window(xxxx);selectAll;copy;paste; ____________________" {_____________________________________________________________________} { batchNumberedFilesMacro: NIH-Image macro for batch processing of numerically suffixed files After invoking macro, point open dialogue at first file in directory to be processed. respond to prompted 'Enter last image:' 'increment' macro will parse fileName for prefix and numeric suffix of forms: 1,2,3,4; xx 1,xx 2,xx 3,xx 4; xx01,xx02,xx03,xx04; xx1,xx2,xx3,xx4 etc Without modification of procedure processImage; macro will simply open files in incremented numeric order. Written by Greg Joss, 1997-12-14 last mod:1999-1-7 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 } procedure getImage;var FullPath, FileType:string; p,d,FileSize:integer; begin if directory='' then showMessage('open first image') else begin image:=image+inc; showMessage(directory,'\[',prefix,']\',image:digits);end; open(prefix,image:digits); if directory='' then begin directory:=GetPath('window'); p:=0;prefix:=windowTitle; while (ord(prefix)<48) or (ord(prefix)>57) do begin delete(prefix,1,1);p:=p+1;end; digits:=length(prefix); image:=StringToNum(prefix); prefix:=windowTitle; delete(prefix,p+1,99); lastimage:=image; showMessage(directory,'\[',prefix,']\',lastimage,'\',windowTitle); inc:=getnumber('increment',1); repeat begin lastimage:=lastimage+inc; FullPath:=''; for d:=length(concat(lastimage:0))+1 to digits do FullPath:=concat( FullPath,'0'); {this is because open zero fills but concat doesn't} FullPath:=concat(directory,prefix,FullPath,lastimage:0); showMessage(FullPath,'\',prefix,'\',lastimage); GetFileInfo(FullPath, FileType, FileSize);end; until FileSize<0; showMessage(FullPath,'\',prefix,'\',lastimage-inc); lastimage:=GetNumber(concat('start ',image:digits ,'; Enter last image:'),lastimage-inc); end; end; procedure processImage(n);begin end macro '/1 process images'; var image,lastimage,digits,inc:integer; directory,prefix:string; n:integer; begin directory:=''; repeat begin n:=n+1; getImage; processImage(n); end until image>=lastimage; 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, 7 Jan 1999 16:06:25 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu Subject: Mail list Archives since changeover 98/7/6? Message-ID: <6E9101550D6@rna.bio.mq.edu.au> I have previously lamented the loss of ability to effectively search the archives as available for mail list prior to switchover "__________________ From: Self To: nih-image@io.ece.drexel.edu Subject: Mail list Archives since changeover 98/7/6? Date: Mon, 21 Sep 1998 11:56:43 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? __________________" gopher://gopher.soils.umn.edu allowed "complex" logical conditions for searching of archived postings. The service via nih-image-request@biomed.drexel.edu help egrep case_insensitive_regular_expression filename ... doesn't appear to offer anything like a comparable facility and it appears to me that the quality of the maillist has suffered as a result. or Am I missing something? In Unix (and even DOS) one could pipe grep results to obtain successively refined searches. Is there some way of doing the same or corresponding thing via nih-image-request@biomed.drexel.edu? Is there any future hope for a combined archive post 98/7/6? or has pre 98/7/6 been assigned to ancient history? 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 V99 Issue #3 ************************************** From nih-image-request@io.ece.drexel.edu Thu Jan 7 06:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09928; Thu, 7 Jan 1999 06:17:50 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 06:17:50 -0500 (EST) Message-ID: <36948C52.AAD55A06@oo.upc.es> Date: Thu, 07 Jan 1999 11:28:35 +0100 From: morato Organization: Universitat =?iso-8859-1?Q?Polit=E8cnica?= de Catalunya X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Opening stacks files (tiff) with NIH-image Content-Transfer-Encoding: 8bit Resent-Message-ID: <"Ul_6R1.0.1i1.M99bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/771 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: 1038 Hello, I'm a new user of Confocal Microscopy, a new user of NIH-image and a new user of this list. Sorry if this is a basic, silly and stupid question, but I have a problem when I try to open some stacks files. I worked with a Leica confocal microscope (with TCS NT and Windows NT computer), and I save with the usual Tiff format different 8-bit images series using two or three channels (green and red, or green, red and blue). When I try to open or import using NIH-image (with Macintosh) or Scion Image with Windows NT, the result is allways the same: I can view the images corresponding to the first channel in their color (green), but not with the images with the second channel. In this case, the images are displayed with green and black and with a white background. It is not possible to work with two or three different luts at the same time? Thanks and my best wishes for 1999. Jordi Morató Water Technology Group Universitat Politècnica de Catalunya EUOOT C/Violinista Vellsola, 37 Terrassa-08222 BARCELONA (SPAIN) From nih-image-request@io.ece.drexel.edu Thu Jan 7 07:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA15212; Thu, 7 Jan 1999 07:04:08 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 07:04:08 -0500 (EST) Date: Thu, 07 Jan 1999 11:52:56 +0000 (GMT) From: Stamatis Pagakis Subject: Re: Opening stacks files (tiff) with NIH-image In-reply-to: <36948C52.AAD55A06@oo.upc.es> To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"nlV7M1.0.PA3.2v9bs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/772 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1864 On Thu, 7 Jan 1999, morato wrote: > Hello, > > I'm a new user of Confocal Microscopy, a new user of NIH-image and a new > user of this list. Sorry if this is a basic, silly and stupid question, > but I have a problem when I try to open some stacks files. I worked with > a Leica confocal microscope (with TCS NT and Windows NT computer), and > I save with the usual Tiff format different 8-bit images series using > two or three channels (green and red, or green, red and blue). When I > try to open or import using NIH-image (with Macintosh) or Scion Image > with Windows NT, the result is allways the same: I can view the images > corresponding to the first channel in their color (green), but not with > the images with the second channel. In this case, the images are > displayed with green and black and with a white background. > Yes, all the images have the LUT of the first channel which is the green. The only way to see the other channels with their own color, is to create a new stack for each channel. To see the overlay of course, you need to use a program that uses 24-bit color, like photoshop. But of course photoshop does not understand stacks... To solve the problem with the white bakcground, besides inverting which has already been suggested, you can choose the fix colors command. Hope it helps *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < > Mobile: 0370 654288 < From nih-image-request@io.ece.drexel.edu Thu Jan 7 11:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA17185; Thu, 7 Jan 1999 11:55:00 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 11:55:00 -0500 (EST) From: SolamereTG@aol.com Message-ID: <69ae1a9.3694dbd4@aol.com> Date: Thu, 7 Jan 1999 11:07:48 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Opening stacks files (tiff) with NIH-image Content-transfer-encoding: 7bit X-Mailer: AOL 4.0 for Windows 95 sub 226 Resent-Message-ID: <"F7zt_.0.Kx2.8mDbs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/773 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 135 You could also use CG-7 Scion board that is made for RGB color input. George A. Peeters Solamere Technology Group Salt Lake City UT From nih-image-request@io.ece.drexel.edu Thu Jan 7 21:48 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA21872; Thu, 7 Jan 1999 21:46:57 -0500 (EST) Resent-Date: Thu, 7 Jan 1999 21:46:57 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: morato@oo.upc.es, nih-image@io.ece.drexel.edu Date: Fri, 8 Jan 1999 13:28:26 GMT+1100 Subject: Re: Opening stacks files (tiff) with NIH-image Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <6FE6FE3338A@rna.bio.mq.edu.au> Resent-Message-ID: <"djjsw2.0.Sb4.9oMbs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/774 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2919 >Date: Thu, 07 Jan 1999 11:28:35 +0100 >From: morato >To: nih-image@io.ece.drexel.edu >Subject: Opening stacks files (tiff) with NIH-image > >I'm a new user of Confocal Microscopy, a new user of NIH-image and a new >user of this list. Sorry if this is a basic, silly and stupid question, >but I have a problem when I try to open some stacks files. I worked with >a Leica confocal microscope (with TCS NT and Windows NT computer), and >I save with the usual Tiff format different 8-bit images series using >two or three channels (green and red, or green, red and blue). When I >try to open or import using NIH-image (with Macintosh) or Scion Image >with Windows NT, the result is allways the same: I can view the images >corresponding to the first channel in their color (green), but not with >the images with the second channel. In this case, the images are >displayed with green and black and with a white background. > >It is not possible to work with two or three different luts at the same >time? > >Thanks and my best wishes for 1999. > >Jordi Morat=F3 >Water Technology Group >Universitat Polit=E8cnica de Catalunya > Working with colour images can be straight forward in those cases where your images are in a standard format and suit the software that you are attempting to use. As soon as you get off the beaten track and wish to do things considered non-standard by the software you are using, colour can be more problematic. In doing measurement/segmentation and much other analysis of color images, it is usual to work with individual channel images or defined mathematical combinations of a pair. NIH-Image is quite competant to support such color image analysis and operation but its LUTs are limited to 8bits ie 256 colours for display. NIH-Image expects its TIF color image stacks to be RGB and in that order. You can make any 3 slice stack and treat it as RGB color. eg you can use "RGB to 8bit color" in stacks menu to convert a 3 slice (RGB) stack to 8bit color. NIH-Image will construct a suitable custom LUT to apply to the indexed image. This image is usually only useful for operator presentation/perception. Image analysis is normally done on the individual channels (or combinations eg via imageMath). In your case, you can load your 2 channel stack and use the 2 slices to make a 3 slice stack (in the order RGB) by duplicating one channel or filling with black or calculating the 3rd channel as a combination of the other 2. Your 3 slice RGB stack can then be converted/viewed as 8 bit color or saved as an NIH-Image RGB TIF stack which will then be recognised by Photoshop or ImageJ as a 24 bit color image...if you want to play with color presentaion aspects. 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 Jan 7 21:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA22424; Thu, 7 Jan 1999 21:50:29 -0500 (EST) Date: Thu, 7 Jan 1999 21:50:29 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901080250.VAA22424@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #4 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/4 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: 8512 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 4 Today's Topics: Myelinated Nerve Fibre Analysis [ Chris Lynch ] Re: Opening stacks files (tiff) with [ Stamatis Pagakis To: Subject: Myelinated Nerve Fibre Analysis Message-Id: Content-Type: text/plain; charset="us-ascii" I have a question regarding- Myelinated Nerve Fibre Analysis Can anyone tell me whether they have had any success with NIH-Image compatible software or Macros to semi automate analysis of nerve morphology under light microscopy so that data (eg fibre diameter, myelin thickness and area, circularity, histograms etc) can be generated? Dr Chris Lynch Neurology Research Fellow Department of Medicine Dr Chris Lynch Neurology Research Fellow Department of Medicine ------------------------------ Date: Thu, 07 Jan 1999 11:28:35 +0100 From: morato To: nih-image@io.ece.drexel.edu Subject: Opening stacks files (tiff) with NIH-image Message-ID: <36948C52.AAD55A06@oo.upc.es> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, I'm a new user of Confocal Microscopy, a new user of NIH-image and a new user of this list. Sorry if this is a basic, silly and stupid question, but I have a problem when I try to open some stacks files. I worked with a Leica confocal microscope (with TCS NT and Windows NT computer), and I save with the usual Tiff format different 8-bit images series using two or three channels (green and red, or green, red and blue). When I try to open or import using NIH-image (with Macintosh) or Scion Image with Windows NT, the result is allways the same: I can view the images corresponding to the first channel in their color (green), but not with the images with the second channel. In this case, the images are displayed with green and black and with a white background. It is not possible to work with two or three different luts at the same time? Thanks and my best wishes for 1999. Jordi Morató Water Technology Group Universitat Politècnica de Catalunya EUOOT C/Violinista Vellsola, 37 Terrassa-08222 BARCELONA (SPAIN) ------------------------------ Date: Thu, 07 Jan 1999 11:52:56 +0000 (GMT) From: Stamatis Pagakis To: nih-image@io.ece.drexel.edu Subject: Re: Opening stacks files (tiff) with NIH-image Message-id: Content-type: TEXT/PLAIN; charset=US-ASCII On Thu, 7 Jan 1999, morato wrote: > Hello, > > I'm a new user of Confocal Microscopy, a new user of NIH-image and a new > user of this list. Sorry if this is a basic, silly and stupid question, > but I have a problem when I try to open some stacks files. I worked with > a Leica confocal microscope (with TCS NT and Windows NT computer), and > I save with the usual Tiff format different 8-bit images series using > two or three channels (green and red, or green, red and blue). When I > try to open or import using NIH-image (with Macintosh) or Scion Image > with Windows NT, the result is allways the same: I can view the images > corresponding to the first channel in their color (green), but not with > the images with the second channel. In this case, the images are > displayed with green and black and with a white background. > Yes, all the images have the LUT of the first channel which is the green. The only way to see the other channels with their own color, is to create a new stack for each channel. To see the overlay of course, you need to use a program that uses 24-bit color, like photoshop. But of course photoshop does not understand stacks... To solve the problem with the white bakcground, besides inverting which has already been suggested, you can choose the fix colors command. Hope it helps *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < > Mobile: 0370 654288 < ------------------------------ Date: Thu, 7 Jan 1999 11:07:48 EST From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Opening stacks files (tiff) with NIH-image Message-ID: <69ae1a9.3694dbd4@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit You could also use CG-7 Scion board that is made for RGB color input. George A. Peeters Solamere Technology Group Salt Lake City UT ------------------------------ Date: Fri, 8 Jan 1999 13:28:26 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: morato@oo.upc.es, nih-image@io.ece.drexel.edu Subject: Re: Opening stacks files (tiff) with NIH-image Message-ID: <6FE6FE3338A@rna.bio.mq.edu.au> >Date: Thu, 07 Jan 1999 11:28:35 +0100 >From: morato >To: nih-image@io.ece.drexel.edu >Subject: Opening stacks files (tiff) with NIH-image > >I'm a new user of Confocal Microscopy, a new user of NIH-image and a new >user of this list. Sorry if this is a basic, silly and stupid question, >but I have a problem when I try to open some stacks files. I worked with >a Leica confocal microscope (with TCS NT and Windows NT computer), and >I save with the usual Tiff format different 8-bit images series using >two or three channels (green and red, or green, red and blue). When I >try to open or import using NIH-image (with Macintosh) or Scion Image >with Windows NT, the result is allways the same: I can view the images >corresponding to the first channel in their color (green), but not with >the images with the second channel. In this case, the images are >displayed with green and black and with a white background. > >It is not possible to work with two or three different luts at the same >time? > >Thanks and my best wishes for 1999. > >Jordi Morat=F3 >Water Technology Group >Universitat Polit=E8cnica de Catalunya > Working with colour images can be straight forward in those cases where your images are in a standard format and suit the software that you are attempting to use. As soon as you get off the beaten track and wish to do things considered non-standard by the software you are using, colour can be more problematic. In doing measurement/segmentation and much other analysis of color images, it is usual to work with individual channel images or defined mathematical combinations of a pair. NIH-Image is quite competant to support such color image analysis and operation but its LUTs are limited to 8bits ie 256 colours for display. NIH-Image expects its TIF color image stacks to be RGB and in that order. You can make any 3 slice stack and treat it as RGB color. eg you can use "RGB to 8bit color" in stacks menu to convert a 3 slice (RGB) stack to 8bit color. NIH-Image will construct a suitable custom LUT to apply to the indexed image. This image is usually only useful for operator presentation/perception. Image analysis is normally done on the individual channels (or combinations eg via imageMath). In your case, you can load your 2 channel stack and use the 2 slices to make a 3 slice stack (in the order RGB) by duplicating one channel or filling with black or calculating the 3rd channel as a combination of the other 2. Your 3 slice RGB stack can then be converted/viewed as 8 bit color or saved as an NIH-Image RGB TIF stack which will then be recognised by Photoshop or ImageJ as a 24 bit color image...if you want to play with color presentaion aspects. 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 V99 Issue #4 ************************************** From nih-image-d-request@io.ece.drexel.edu Sat Jan 9 06:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA15610; Sat, 9 Jan 1999 06:08:50 -0500 (EST) Date: Sat, 9 Jan 1999 06:08:50 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901091108.GAA15610@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #5 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/5 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: 924 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 5 Today's Topics: No Subject [ OneWeaver@aol.com ] ------------------------------ Date: Fri, 8 Jan 1999 08:32:14 EST From: OneWeaver@aol.com To: nih-image-d@io.ece.drexel.edu Subject: No Subject Message-ID: <31e94dee.369608de@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit I am a paleoanthropolgy student working on a dissertation which involves using Image for cranial volumetric measurements of ape and human MRIs (as well as fossil human CT scans). I have access to ape MRIs made on a Phillips scanner, but need to know how to get these into a format appropriate for Image. Can anyone help me with this? Many thanks in advance, Anne Weaver -------------------------------- End of nih-image-d Digest V99 Issue #5 ************************************** From nih-image-request@io.ece.drexel.edu Sat Jan 9 12:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06593; Sat, 9 Jan 1999 12:24:51 -0500 (EST) Resent-Date: Sat, 9 Jan 1999 12:24:51 -0500 (EST) Message-ID: <36978DA6.3210AF93@sdsc.edu> Date: Sat, 09 Jan 1999 09:12:20 -0800 From: "Harvey J. Karten" Reply-To: hjkarten@UCSD.EDU Organization: UCSD/Yesh Tech X-Mailer: Mozilla 4.04 (Macintosh; U; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Comments on Image/J re confocal References: <199901091106.GAA15262@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"mjwnv2.0.K51.3tubs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/775 X-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: 1444 One of the big drawbacks of NIH-Image is that it was restricted to 8 bit images. With the shift to 12/16 bit images in all the major confocal instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away from the otherwise powerful capabilities of NIH-Image. In order to use NIH-Image the confocal microscopist had to discard the much greater flexibility of 12 bits of data in each of the channels (i.e. 12 bits in red, 12 bits in green, 12 bits in blue, plus a potential additional 12 bits of alpha). Though clearly still a work in progress, Image/J shows the continuing creativity of Wayne Rasband. The latest version supports 16 bit stacks - though at present it only allows you to open, animate, and minimally manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit stacks - but hopefully that will happen. Hopefully, a forthcoming version of Image/J will support a multi-channel 16 bit/channel capability. This will emerge as a requisite technology with further development of multi-channel imaging of living cells, fMRI, etc. regards, Harvey -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California @ San Diego La Jolla, CA 92093-0608 WCBR EMail: WCBR@ucsd.edu Other EMail: hjkarten@ucsd.edu Phone (Lab): 619-534-4938 FAX (Lab): 619-534-6602 Home Phone: 619-755-8573 Retina Information System: http://www-cajal.ucsd.edu See WCBR WebPage (Note CHANGE OF ADDRESS) http://www.wcbrBrain.org/ From nih-image-d-request@io.ece.drexel.edu Sun Jan 10 06:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA20789; Sun, 10 Jan 1999 06:16:54 -0500 (EST) Date: Sun, 10 Jan 1999 06:16:54 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901101116.GAA20789@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #6 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/6 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: 2105 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 6 Today's Topics: Comments on Image/J re confocal [ "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: Comments on Image/J re confocal Message-ID: <36978DA6.3210AF93@sdsc.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit One of the big drawbacks of NIH-Image is that it was restricted to 8 bit images. With the shift to 12/16 bit images in all the major confocal instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away from the otherwise powerful capabilities of NIH-Image. In order to use NIH-Image the confocal microscopist had to discard the much greater flexibility of 12 bits of data in each of the channels (i.e. 12 bits in red, 12 bits in green, 12 bits in blue, plus a potential additional 12 bits of alpha). Though clearly still a work in progress, Image/J shows the continuing creativity of Wayne Rasband. The latest version supports 16 bit stacks - though at present it only allows you to open, animate, and minimally manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit stacks - but hopefully that will happen. Hopefully, a forthcoming version of Image/J will support a multi-channel 16 bit/channel capability. This will emerge as a requisite technology with further development of multi-channel imaging of living cells, fMRI, etc. regards, Harvey -- Harvey J. Karten, M.D. Dept. of Neurosciences University of California @ San Diego La Jolla, CA 92093-0608 WCBR EMail: WCBR@ucsd.edu Other EMail: hjkarten@ucsd.edu Phone (Lab): 619-534-4938 FAX (Lab): 619-534-6602 Home Phone: 619-755-8573 Retina Information System: http://www-cajal.ucsd.edu See WCBR WebPage (Note CHANGE OF ADDRESS) http://www.wcbrBrain.org/ -------------------------------- End of nih-image-d Digest V99 Issue #6 ************************************** From nih-image-request@io.ece.drexel.edu Sun Jan 10 21:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA05556; Sun, 10 Jan 1999 21:59:02 -0500 (EST) Resent-Date: Sun, 10 Jan 1999 21:59:02 -0500 (EST) Date: Sun, 10 Jan 1999 21:34:01 -0500 (EST) From: R Wade Schuette X-Sender: schuette@pacman.rs.itd.umich.edu To: NIH Image List cc: schuette@umich.edu Subject: Slide thickness from image histogram Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"UJyo41.0.la.aCMcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/776 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 839 I've put a working paper on my web site describing a theoretical method that might be used to derive the thickness of a pathology slide specimen from the image histogram. The paper describes a simulation of a 3-D specimen with embedded spheres and shows, in that ideal case, empirically, that the virtual slide "thickness" can be derived from the image grey-scale histogram, with some caveats. Feedback/discussion is welcome, especially with anyone who has a set of slides of known thicknesses with images available to try this out on. The Paper is posted in Acrobat PDF format as http://www-personal.umich.edu/~schuette/imaging/slides.pdf Wade --------------------------------------------- R.Wade Schuette University of Michigan Medical Center Information Technology University of Michican Ann Arbor, MI 48105 schuette@umich.edu From nih-image-request@io.ece.drexel.edu Mon Jan 11 10:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA06484; Mon, 11 Jan 1999 10:52:06 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 10:52:06 -0500 (EST) Date: Mon, 11 Jan 1999 10:24:36 -0500 (EST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Re: Mail list Archives since changeover 98/7/6? Resent-Message-ID: <"3bDNe.0.tk.4SXcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/777 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2426 I second the lament. The ability to easily search the archives before the transition was a big plus. I didn't use it often, but in addition to getting a specific answer, it also gave 'legs' to many of the carefully written responses, it noted queries that no one could (or would) answer, and it gave the searcher an overview of the area being queried. I haven't tried searching since July. I know it's a hassle to set up a new archive, but one like the old one would be much appreciated (and could include all the backfiles now at 'soils' or whatever that address. Best, Harry >I have previously lamented the loss of ability to effectively search the >archives >as available for mail list prior to switchover > >"__________________ >From: Self >To: nih-image@io.ece.drexel.edu >Subject: Mail list Archives since changeover 98/7/6? >Date: Mon, 21 Sep 1998 11:56:43 > >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? >__________________" > >gopher://gopher.soils.umn.edu allowed "complex" logical conditions for >searching >of archived postings. > >The service via nih-image-request@biomed.drexel.edu help > >egrep case_insensitive_regular_expression filename ... > >doesn't appear to offer anything like a comparable facility >and it appears to me that the quality of the maillist has suffered as a result. >or >Am I missing something? > >In Unix (and even DOS) one could pipe grep results to obtain successively >refined >searches. >Is there some way of doing the same or corresponding thing via >nih-image-request@biomed.drexel.edu? > >Is there any future hope for a combined archive post 98/7/6? >or has pre 98/7/6 been assigned to ancient history? > > > >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 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-request@io.ece.drexel.edu Mon Jan 11 12:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA14888; Mon, 11 Jan 1999 12:12:56 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 12:12:56 -0500 (EST) Mime-Version: 1.0 X-Sender: rwadkins@ctrc7.ucc.saci.org Message-Id: In-Reply-To: <199901101100.GAA18584@io.ece.drexel.edu> Date: Mon, 11 Jan 1999 10:45:47 -0600 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: IPLab question Resent-Message-ID: <"zqm9g1.0.Ns2.UeYcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/778 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3124 We're in the same boat as Dr. Karten. We need to operate on 16-bit images, not 8 bit. Image/J may work in the future, but so far it's still in progress. We have IPLab, which we collect images with. The dongle thing is too annoying to deal with most of the time, so we have been processing everything with NIH Image (for example, it's nice to be able to process old images on one computer while new ones are being acquired on another). Plus, Image's scripting is much, much better. However, we're at a point now where we absolutely need 16-bit data, and therefore are back to using IPLab. Does anyone know if there's a mailing list or web page for IPLab users? Specifically, I'm trying to write a plug-in that will let me make non-standard measurements on the segments of an image, and return a table of the values. Thanks. I hope this isn't too off-topic. --Randy >------------------------------ >Date: Sat, 09 Jan 1999 09:12:20 -0800 >From: "Harvey J. Karten" >To: nih-image@io.ece.drexel.edu >Subject: Comments on Image/J re confocal >Message-ID: <36978DA6.3210AF93@sdsc.edu> >Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >x-mac-creator="4D4F5353" >Content-Transfer-Encoding: 7bit > >One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >images. With the shift to 12/16 bit images in all the major confocal >instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >from the otherwise powerful capabilities of NIH-Image. In order to use >NIH-Image the confocal microscopist had to discard the much greater >flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >bits of alpha). > >Though clearly still a work in progress, Image/J shows the continuing >creativity of Wayne Rasband. The latest version supports 16 bit stacks >- though at present it only allows you to open, animate, and minimally >manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >stacks - but hopefully that will happen. > >Hopefully, a forthcoming version of Image/J will support a multi-channel >16 bit/channel capability. This will emerge as a requisite technology >with further development of multi-channel imaging of living cells, fMRI, >etc. > >regards, Harvey > >-- >Harvey J. Karten, M.D. >Dept. of Neurosciences >University of California @ San Diego >La Jolla, CA 92093-0608 >WCBR EMail: WCBR@ucsd.edu >Other EMail: hjkarten@ucsd.edu >Phone (Lab): 619-534-4938 >FAX (Lab): 619-534-6602 >Home Phone: 619-755-8573 >Retina Information System: http://www-cajal.ucsd.edu > >See WCBR WebPage (Note CHANGE OF ADDRESS) >http://www.wcbrBrain.org/ > >-------------------------------- ****************************************************************** Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-request@io.ece.drexel.edu Mon Jan 11 15:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA00293; Mon, 11 Jan 1999 15:09:06 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 15:09:06 -0500 (EST) Date: Mon, 11 Jan 1999 14:43:58 -0500 (EST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: hmthomas@med.cornell.edu (Henry M. Thomas) Subject: Re: IPLab question Resent-Message-ID: <"pqByX.0.lY6.8Fbcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/779 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3900 Query: What biological data is measured with such accuracy that 8 bits is insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, one can do better on weight or length, but can you really do better on images of a biologically relevant variable such as calcium concentration (fluorescence)? That is, how much information are you discarding when NIH Image rounds each pixel from 16 bits to 8? Best, Harry >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, >not 8 bit. Image/J may work in the future, but so far it's still in >progress. We have IPLab, which we collect images with. The dongle thing >is too annoying to deal with most of the time, so we have been processing >everything with NIH Image (for example, it's nice to be able to process old >images on one computer while new ones are being acquired on another). >Plus, Image's scripting is much, much better. > >However, we're at a point now where we absolutely need 16-bit data, and >therefore are back to using IPLab. Does anyone know if there's a mailing >list or web page for IPLab users? Specifically, I'm trying to write a >plug-in that will let me make non-standard measurements on the segments of >an image, and return a table of the values. > >Thanks. I hope this isn't too off-topic. >--Randy > >>------------------------------ >>Date: Sat, 09 Jan 1999 09:12:20 -0800 >>From: "Harvey J. Karten" >>To: nih-image@io.ece.drexel.edu >>Subject: Comments on Image/J re confocal >>Message-ID: <36978DA6.3210AF93@sdsc.edu> >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >>x-mac-creator="4D4F5353" >>Content-Transfer-Encoding: 7bit >> >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >>images. With the shift to 12/16 bit images in all the major confocal >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >>from the otherwise powerful capabilities of NIH-Image. In order to use >>NIH-Image the confocal microscopist had to discard the much greater >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >>bits of alpha). >> >>Though clearly still a work in progress, Image/J shows the continuing >>creativity of Wayne Rasband. The latest version supports 16 bit stacks >>- though at present it only allows you to open, animate, and minimally >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >>stacks - but hopefully that will happen. >> >>Hopefully, a forthcoming version of Image/J will support a multi-channel >>16 bit/channel capability. This will emerge as a requisite technology >>with further development of multi-channel imaging of living cells, fMRI, >>etc. >> >>regards, Harvey >> >>-- >>Harvey J. Karten, M.D. >>Dept. of Neurosciences >>University of California @ San Diego >>La Jolla, CA 92093-0608 >>WCBR EMail: WCBR@ucsd.edu >>Other EMail: hjkarten@ucsd.edu >>Phone (Lab): 619-534-4938 >>FAX (Lab): 619-534-6602 >>Home Phone: 619-755-8573 >>Retina Information System: http://www-cajal.ucsd.edu >> >>See WCBR WebPage (Note CHANGE OF ADDRESS) >>http://www.wcbrBrain.org/ >> >>-------------------------------- > >****************************************************************** >Randy M. Wadkins, Ph.D. >Cancer Therapy & Research Center >Institute for Drug Development >14960 Omicron Drive >San Antonio, TX 78245 >phone: (210)-677-3835 >fax: (210)-677-0058 >E-mail: rwadkins@saci.org >CTRC Homepage: http://www.ccc.saci.org >****************************************************************** 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 Mon Jan 11 15:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA01462; Mon, 11 Jan 1999 15:14:44 -0500 (EST) Date: Mon, 11 Jan 1999 15:14:44 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901112014.PAA01462@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #7 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/7 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: 12063 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 7 Today's Topics: Slide thickness from image histogram [ R Wade Schuette To: NIH Image List cc: schuette@umich.edu Subject: Slide thickness from image histogram Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I've put a working paper on my web site describing a theoretical method that might be used to derive the thickness of a pathology slide specimen from the image histogram. The paper describes a simulation of a 3-D specimen with embedded spheres and shows, in that ideal case, empirically, that the virtual slide "thickness" can be derived from the image grey-scale histogram, with some caveats. Feedback/discussion is welcome, especially with anyone who has a set of slides of known thicknesses with images available to try this out on. The Paper is posted in Acrobat PDF format as http://www-personal.umich.edu/~schuette/imaging/slides.pdf Wade --------------------------------------------- R.Wade Schuette University of Michigan Medical Center Information Technology University of Michican Ann Arbor, MI 48105 schuette@umich.edu ------------------------------ Date: Mon, 11 Jan 1999 10:24:36 -0500 (EST) From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu Subject: Re: Mail list Archives since changeover 98/7/6? Message-Id: Content-Type: text/plain; charset="us-ascii" I second the lament. The ability to easily search the archives before the transition was a big plus. I didn't use it often, but in addition to getting a specific answer, it also gave 'legs' to many of the carefully written responses, it noted queries that no one could (or would) answer, and it gave the searcher an overview of the area being queried. I haven't tried searching since July. I know it's a hassle to set up a new archive, but one like the old one would be much appreciated (and could include all the backfiles now at 'soils' or whatever that address. Best, Harry >I have previously lamented the loss of ability to effectively search the >archives >as available for mail list prior to switchover > >"__________________ >From: Self >To: nih-image@io.ece.drexel.edu >Subject: Mail list Archives since changeover 98/7/6? >Date: Mon, 21 Sep 1998 11:56:43 > >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? >__________________" > >gopher://gopher.soils.umn.edu allowed "complex" logical conditions for >searching >of archived postings. > >The service via nih-image-request@biomed.drexel.edu help > >egrep case_insensitive_regular_expression filename ... > >doesn't appear to offer anything like a comparable facility >and it appears to me that the quality of the maillist has suffered as a result. >or >Am I missing something? > >In Unix (and even DOS) one could pipe grep results to obtain successively >refined >searches. >Is there some way of doing the same or corresponding thing via >nih-image-request@biomed.drexel.edu? > >Is there any future hope for a combined archive post 98/7/6? >or has pre 98/7/6 been assigned to ancient history? > > > >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 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 ------------------------------ Date: Mon, 11 Jan 1999 10:45:47 -0600 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: IPLab question Message-Id: Content-Type: text/plain; charset="us-ascii" We're in the same boat as Dr. Karten. We need to operate on 16-bit images, not 8 bit. Image/J may work in the future, but so far it's still in progress. We have IPLab, which we collect images with. The dongle thing is too annoying to deal with most of the time, so we have been processing everything with NIH Image (for example, it's nice to be able to process old images on one computer while new ones are being acquired on another). Plus, Image's scripting is much, much better. However, we're at a point now where we absolutely need 16-bit data, and therefore are back to using IPLab. Does anyone know if there's a mailing list or web page for IPLab users? Specifically, I'm trying to write a plug-in that will let me make non-standard measurements on the segments of an image, and return a table of the values. Thanks. I hope this isn't too off-topic. --Randy >------------------------------ >Date: Sat, 09 Jan 1999 09:12:20 -0800 >From: "Harvey J. Karten" >To: nih-image@io.ece.drexel.edu >Subject: Comments on Image/J re confocal >Message-ID: <36978DA6.3210AF93@sdsc.edu> >Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >x-mac-creator="4D4F5353" >Content-Transfer-Encoding: 7bit > >One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >images. With the shift to 12/16 bit images in all the major confocal >instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >from the otherwise powerful capabilities of NIH-Image. In order to use >NIH-Image the confocal microscopist had to discard the much greater >flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >bits of alpha). > >Though clearly still a work in progress, Image/J shows the continuing >creativity of Wayne Rasband. The latest version supports 16 bit stacks >- though at present it only allows you to open, animate, and minimally >manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >stacks - but hopefully that will happen. > >Hopefully, a forthcoming version of Image/J will support a multi-channel >16 bit/channel capability. This will emerge as a requisite technology >with further development of multi-channel imaging of living cells, fMRI, >etc. > >regards, Harvey > >-- >Harvey J. Karten, M.D. >Dept. of Neurosciences >University of California @ San Diego >La Jolla, CA 92093-0608 >WCBR EMail: WCBR@ucsd.edu >Other EMail: hjkarten@ucsd.edu >Phone (Lab): 619-534-4938 >FAX (Lab): 619-534-6602 >Home Phone: 619-755-8573 >Retina Information System: http://www-cajal.ucsd.edu > >See WCBR WebPage (Note CHANGE OF ADDRESS) >http://www.wcbrBrain.org/ > >-------------------------------- ****************************************************************** Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** ------------------------------ Date: Mon, 11 Jan 1999 14:43:58 -0500 (EST) From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu Subject: Re: IPLab question Message-Id: Content-Type: text/plain; charset="us-ascii" Query: What biological data is measured with such accuracy that 8 bits is insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, one can do better on weight or length, but can you really do better on images of a biologically relevant variable such as calcium concentration (fluorescence)? That is, how much information are you discarding when NIH Image rounds each pixel from 16 bits to 8? Best, Harry >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, >not 8 bit. Image/J may work in the future, but so far it's still in >progress. We have IPLab, which we collect images with. The dongle thing >is too annoying to deal with most of the time, so we have been processing >everything with NIH Image (for example, it's nice to be able to process old >images on one computer while new ones are being acquired on another). >Plus, Image's scripting is much, much better. > >However, we're at a point now where we absolutely need 16-bit data, and >therefore are back to using IPLab. Does anyone know if there's a mailing >list or web page for IPLab users? Specifically, I'm trying to write a >plug-in that will let me make non-standard measurements on the segments of >an image, and return a table of the values. > >Thanks. I hope this isn't too off-topic. >--Randy > >>------------------------------ >>Date: Sat, 09 Jan 1999 09:12:20 -0800 >>From: "Harvey J. Karten" >>To: nih-image@io.ece.drexel.edu >>Subject: Comments on Image/J re confocal >>Message-ID: <36978DA6.3210AF93@sdsc.edu> >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >>x-mac-creator="4D4F5353" >>Content-Transfer-Encoding: 7bit >> >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >>images. With the shift to 12/16 bit images in all the major confocal >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >>from the otherwise powerful capabilities of NIH-Image. In order to use >>NIH-Image the confocal microscopist had to discard the much greater >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >>bits of alpha). >> >>Though clearly still a work in progress, Image/J shows the continuing >>creativity of Wayne Rasband. The latest version supports 16 bit stacks >>- though at present it only allows you to open, animate, and minimally >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >>stacks - but hopefully that will happen. >> >>Hopefully, a forthcoming version of Image/J will support a multi-channel >>16 bit/channel capability. This will emerge as a requisite technology >>with further development of multi-channel imaging of living cells, fMRI, >>etc. >> >>regards, Harvey >> >>-- >>Harvey J. Karten, M.D. >>Dept. of Neurosciences >>University of California @ San Diego >>La Jolla, CA 92093-0608 >>WCBR EMail: WCBR@ucsd.edu >>Other EMail: hjkarten@ucsd.edu >>Phone (Lab): 619-534-4938 >>FAX (Lab): 619-534-6602 >>Home Phone: 619-755-8573 >>Retina Information System: http://www-cajal.ucsd.edu >> >>See WCBR WebPage (Note CHANGE OF ADDRESS) >>http://www.wcbrBrain.org/ >> >>-------------------------------- > >****************************************************************** >Randy M. Wadkins, Ph.D. >Cancer Therapy & Research Center >Institute for Drug Development >14960 Omicron Drive >San Antonio, TX 78245 >phone: (210)-677-3835 >fax: (210)-677-0058 >E-mail: rwadkins@saci.org >CTRC Homepage: http://www.ccc.saci.org >****************************************************************** 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 V99 Issue #7 ************************************** From nih-image-request@io.ece.drexel.edu Mon Jan 11 17:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA14919; Mon, 11 Jan 1999 17:20:51 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 17:20:51 -0500 (EST) Message-Id: <199901112148.QAA00619@kanga.INS.CWRU.Edu> Date: Mon, 11 Jan 1999 16:48:41 -0500 (EST) From: nbd@po.cwru.edu (Nagendu B. Dev) To: nih-image@io.ece.drexel.edu Subject: help Reply-To: nih-image@io.ece.drexel.edu Resent-Message-ID: <"7Qf3R.0.Ct2.07dcs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/780 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 301 Hi: I am new to NIH image. How does NIH measure command calculate area? I have sets of circular, oval and triangular structure. I need the integrated area for each particular structure. Can NIH image do that? Is there any help in the NIH manual. I would appreciate your reply.many thanks ---Dev. ### From nih-image-request@io.ece.drexel.edu Mon Jan 11 17:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA19040; Mon, 11 Jan 1999 17:54:12 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 17:54:12 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nbd@po.cwru.edu, nih-image@io.ece.drexel.edu Date: Tue, 12 Jan 1999 9:33:07 GMT+1100 Subject: Re: help Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <5709B45A08@rna.bio.mq.edu.au> Resent-Message-ID: <"d9J8k.0._v3.fjdcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/781 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3401 >Received: from SpoolDir by RNA (Mercury 1.44); 12 Jan 99 09:14:20 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.44) with ESMTP; > 12 Jan 99 09:14:15 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id RAA13911; > Mon, 11 Jan 1999 17:11:56 -0500 (EST) >Resent-Date: Mon, 11 Jan 1999 17:11:56 -0500 (EST) >Message-Id: <199901112148.QAA00619@kanga.INS.CWRU.Edu> >Date: Mon, 11 Jan 1999 16:48:41 -0500 (EST) >From: nbd@po.CWRU.Edu (Nagendu B. Dev) >To: nih-image@io.ece.drexel.edu >Subject: help >Reply-To: nih-image@io.ece.drexel.edu >Resent-Message-ID: <"7Qf3R.0.Ct2.07dcs"@io> >Resent-From: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/780 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 33554560 0 > >Hi: >I am new to NIH image. How does NIH measure command calculate area? I have >sets of circular, oval and triangular structure. I need the integrated area >for each particular structure. Can NIH image do that? Is there any help in >the NIH manual. I would appreciate your reply.many thanks ---Dev. >### > Is there any help in the NIH manual??? page 7: "__________________________ Making Measurements To make a manual area measurement, first outline a region of interest using the rectangular, oval, polygonal, or freehand selection tool. Then select the Measure command, which will compute the area, mean gray value, and the minimum and maximum gray value. Other measurements, such as perimeter, can be enabled using the Options command in the Analysis menu. Measure distances by making a straight, freehand or segmented line selection, and then using the measure command. (Note that the line selection tool uses a pop-up menu for selecting different line types.) Use the angle tool to measure angles. The cross hair tool counts objects, marks them, and records their X-Y coordinates. The wand tools automatically outlines structures isolated using thresholding. Results from the most recent measurement are displayed in the Info window. Use Show Results to display a table of results since the last time the Reset command was used. The Analyze Particles command automatically counts and measures features of interest. This requires thresholding to discriminate objects of interest from surrounding background based on their gray values. Image has two thresholding methods. In thresholding mode (Threshold is checked in the Options menu), all pixels equal to or greater than a single threshold level are displayed in black, and all other pixels (the background) are displayed in white. In Density Slicing mode (Density Slice is checked), all pixels between a lower and upper threshold are highlighted in red. For both modes, you adjust threshold levels by dragging the LUT tool (the one with the double-headed arrow) in the LUT window. For successful thresholding, it may be necessary to use the Subtract Background command to remove the effects of uneven illumination. _________________________" Is there something deeper in your question ? 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 Jan 11 18:05 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA20446; Mon, 11 Jan 1999 18:05:34 -0500 (EST) Resent-Date: Mon, 11 Jan 1999 18:05:34 -0500 (EST) Date: Mon, 11 Jan 1999 14:37:10 -0800 (PST) From: David Ehrhardt To: "Henry M. Thomas" cc: nih-image@io.ece.drexel.edu Subject: Re: IPLab question In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"DpwvK3.0.4J4.gvdcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/782 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 5021 While it is true that for many biological applications 256 bits of resolution is plenty, there are significant advantages in greater bit depths. For my applications, the primary advantage is greater dynamic range. It is not uncommon to need to quantify differences in the dimmer regions of an image, which oftens means letting the brightest regions get clipped in an 8 bit image. With greater bit depth, it is possible to quantify intensity in both the brightest and dimmest parts of a greater range of images. A second advantage is that image processing routines have more information to work with. I have been told that this is a particular advantage for photon-reassignment routines (deconvolution). -David On Mon, 11 Jan 1999, Henry M. Thomas wrote: > Query: What biological data is measured with such accuracy that 8 bits is > insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, > one can do better on weight or length, but can you really do better on > images of a biologically relevant variable such as calcium concentration > (fluorescence)? That is, how much information are you discarding when NIH > Image rounds each pixel from 16 bits to 8? > Best, Harry > > >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, > >not 8 bit. Image/J may work in the future, but so far it's still in > >progress. We have IPLab, which we collect images with. The dongle thing > >is too annoying to deal with most of the time, so we have been processing > >everything with NIH Image (for example, it's nice to be able to process old > >images on one computer while new ones are being acquired on another). > >Plus, Image's scripting is much, much better. > > > >However, we're at a point now where we absolutely need 16-bit data, and > >therefore are back to using IPLab. Does anyone know if there's a mailing > >list or web page for IPLab users? Specifically, I'm trying to write a > >plug-in that will let me make non-standard measurements on the segments of > >an image, and return a table of the values. > > > >Thanks. I hope this isn't too off-topic. > >--Randy > > > >>------------------------------ > >>Date: Sat, 09 Jan 1999 09:12:20 -0800 > >>From: "Harvey J. Karten" > >>To: nih-image@io.ece.drexel.edu > >>Subject: Comments on Image/J re confocal > >>Message-ID: <36978DA6.3210AF93@sdsc.edu> > >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; > >>x-mac-creator="4D4F5353" > >>Content-Transfer-Encoding: 7bit > >> > >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit > >>images. With the shift to 12/16 bit images in all the major confocal > >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away > >>from the otherwise powerful capabilities of NIH-Image. In order to use > >>NIH-Image the confocal microscopist had to discard the much greater > >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in > >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 > >>bits of alpha). > >> > >>Though clearly still a work in progress, Image/J shows the continuing > >>creativity of Wayne Rasband. The latest version supports 16 bit stacks > >>- though at present it only allows you to open, animate, and minimally > >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit > >>stacks - but hopefully that will happen. > >> > >>Hopefully, a forthcoming version of Image/J will support a multi-channel > >>16 bit/channel capability. This will emerge as a requisite technology > >>with further development of multi-channel imaging of living cells, fMRI, > >>etc. > >> > >>regards, Harvey > >> > >>-- > >>Harvey J. Karten, M.D. > >>Dept. of Neurosciences > >>University of California @ San Diego > >>La Jolla, CA 92093-0608 > >>WCBR EMail: WCBR@ucsd.edu > >>Other EMail: hjkarten@ucsd.edu > >>Phone (Lab): 619-534-4938 > >>FAX (Lab): 619-534-6602 > >>Home Phone: 619-755-8573 > >>Retina Information System: http://www-cajal.ucsd.edu > >> > >>See WCBR WebPage (Note CHANGE OF ADDRESS) > >>http://www.wcbrBrain.org/ > >> > >>-------------------------------- > > > >****************************************************************** > >Randy M. Wadkins, Ph.D. > >Cancer Therapy & Research Center > >Institute for Drug Development > >14960 Omicron Drive > >San Antonio, TX 78245 > >phone: (210)-677-3835 > >fax: (210)-677-0058 > >E-mail: rwadkins@saci.org > >CTRC Homepage: http://www.ccc.saci.org > >****************************************************************** > > 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 > > > 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 Tue Jan 12 03:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA03147; Tue, 12 Jan 1999 03:40:27 -0500 (EST) Resent-Date: Tue, 12 Jan 1999 03:40:27 -0500 (EST) Message-ID: <369B018A.9C6987BD@sdsc.edu> Date: Tue, 12 Jan 1999 00:02:19 -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: IPL Question and 12/16 bits of data References: <199901112007.PAA29943@io.ece.drexel.edu> Resent-Message-ID: <"XXBE02.0.vv6.w9mcs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/783 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="------------5811E6FCA45369D3E6A6CEF2" Content-Length: 9404 --------------5811E6FCA45369D3E6A6CEF2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr Thomas reasonably raised the question of the importance of 12/16 bits of graphical data rather than the more common 8 bits. "Query: What biological data is measured with such accuracy that 8 bits is insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, one can do better on weight or length, but can you really do better on images of a biologically relevant variable such as calcium concentration (fluorescence)? That is, how much information are you discarding when NIH Image rounds each pixel from 16 bits to 8? Best, Harry" If you consider the range of brightness values that you will find in a single fluorescent intracellular filled neuron, this exceeds the 8 bit value range. The soma is intensely labeled while small peripheral dendrites are very faint. If you try to capture such a cell with 8 bit and compare the results that are obtained with a 12 bit system, you will find that the 12 bit system provides a much greater range of values (0-4095). This reduces the problem of either flooding the image with the soma in order to display the fine faintly stained dendrites, or by reducing the bright staining of the soma, you will lose the dendrites completely. With good software, it is possible to then sample selected portions of the range of values. Remapping a portion of a 12 bit image to the 8 bit display will also provide a more data-rich image, as shown by the number of points represented in the histogram. The common argument that is also advanced when criticizing 12 or more bits of graphical data is that the human eye cannot detect more than X gray levels - a number that varies with the author, but often between 16 and 64. This fails to take into account the dynamic remapping that occurs so rapidly in human vision. Consider the range of values that you encounter when examining a rich textured region in the bright sun, then turn to a shaded area and again you will see a wide range of brightness values. We stitch this range together so rapidly and so well, that we fail to realize that we are covering many log units of brightness - much more than merely 8 bits worth. You might also consider the marked difference between the appearance to your eye of complex histological field in fluorescence, and the 8 bit digital image of the same field. The 8 bit image is lacking in much of the finesse. It may not even show many of the fine processes, or subtle detail in the midst of an intensely labeled cell. Another way to think of this is that we cannot "see" all the information that is of importance - this is apparent if reference is made to e.g. infra-red, UV, etc. It is also true in radiographs and Electron Microscope images. You might also consider that more and more of the desktop scanners are providing 12 - 16 bits/per channel. This is not merely for advertizing purposes. There is a significant and noticeable difference in the images obtained from these scanners, compared to images previously obtained from scanners with 8 bits/channel. You are generally correct when discussing calcium imaging, but that reflects the sensitivity of the dyes used, and the ability to reliably discriminate various brightness levels in those particular conditions. Many modern confocal microscopes now routinely provide 12 bits/channel, with marked improvement in the quality of the resulting images. This is an issue that deserves much additional discussion. But 12/16 bit images in biology and medicine are rapidly proving their worth. The lack of availability of suitable software has retarded progress in this field. The few programs that do provide some 12/16 bit functions, are often very expensive, and extremely limited in their operations. When we then have to deal with multiple channels shown in different colors, each in 12/16 bits, then the selection of available software diminishes very rapidly. This constitutes the 64 bit software (16 bits/channel, with 4 channels - RGB-Alpha). The lack of tools has slowed progress in this area. IPLab does not adequately deal with such data. 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 --------------5811E6FCA45369D3E6A6CEF2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dr Thomas reasonably raised the question of the importance of 12/16 bits of graphical data rather than the more common 8 bits.
"Query: What biological data is measured with such accuracy that 8 bits is
insufficient?  That's 1 in 256 (well, 1 in 254) which is 0.4%.  Granted,
one can do better on weight or length, but can you really do better on
images of a biologically relevant variable such as calcium concentration
(fluorescence)?  That is, how much information are you discarding when NIH
Image rounds each pixel from 16 bits to 8?
Best,  Harry"

If you consider the range of brightness values that you will find in a single fluorescent intracellular filled neuron, this exceeds the 8 bit value range. The soma is intensely labeled while small peripheral dendrites are very faint. If you try to capture such a cell with 8 bit and compare the results that are obtained with a 12 bit system, you will find that the 12 bit system provides a much greater range of values (0-4095). This reduces the problem of either flooding the image with the soma in order to display the fine faintly stained dendrites, or by reducing the bright staining of the soma, you will lose the dendrites completely. With good software, it is possible to then sample selected portions of the range of values. Remapping a portion of a 12 bit image to the 8 bit display will also provide a more data-rich image, as shown by the number of points represented in the histogram.

The common argument that is also advanced when criticizing 12 or more bits of graphical data is that the human eye cannot detect more than X gray levels - a number that varies with the author, but often between 16 and 64. This fails to take into account the dynamic remapping that occurs so rapidly in human vision. Consider the range of values that you encounter when examining a rich textured region in the bright sun, then turn  to a shaded area and again you will see a wide range of brightness values. We stitch this range together so rapidly and so well, that we fail to realize that we are covering many log units of brightness - much more than merely 8 bits worth. You might also consider the marked difference between the appearance to your eye of complex histological field in fluorescence, and the 8 bit digital image of the same field. The 8 bit image is lacking in much of the finesse. It may not even show many of the fine processes, or subtle detail in the midst of an intensely labeled cell.

Another way to think of this is that we cannot "see" all the information that is of importance - this is apparent if reference is made to e.g. infra-red, UV, etc. It is also true in radiographs and Electron Microscope images. You might also consider that more and more of the desktop scanners are providing 12 - 16 bits/per channel. This is not merely for advertizing purposes. There is a significant and noticeable difference in the images obtained from these scanners, compared to images previously obtained from scanners with 8 bits/channel.

You are generally correct when discussing calcium imaging, but that reflects the sensitivity of the dyes used, and the ability to reliably discriminate various brightness levels in those particular conditions. Many modern confocal microscopes now routinely provide 12 bits/channel, with marked improvement in the quality of the resulting images.

This is an issue that deserves much additional discussion. But 12/16 bit images in biology and medicine are rapidly proving their worth. The lack of availability of suitable software has retarded progress in this field. The few programs that do provide some 12/16 bit functions, are often very expensive, and extremely limited in their operations. When we then have to deal with multiple channels shown in different colors, each in 12/16 bits, then the selection of available software diminishes very rapidly. This constitutes the 64 bit software (16 bits/channel, with 4 channels - RGB-Alpha). The lack of tools has slowed progress in this area. IPLab does not adequately deal with such data.

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
  --------------5811E6FCA45369D3E6A6CEF2-- From nih-image-request@io.ece.drexel.edu Tue Jan 12 05:36 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA18538; Tue, 12 Jan 1999 05:36:25 -0500 (EST) Resent-Date: Tue, 12 Jan 1999 05:36:25 -0500 (EST) Message-ID: <369B91DC.2233@bme.ym.edu.tw> Date: Tue, 12 Jan 1999 14:20:49 +0000 From: Woeichyn Chu Reply-To: wchu@bme.ym.edu.tw Organization: National Yang Ming University X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: IPL Question and 12/16 bits of data References: <199901112007.PAA29943@io.ece.drexel.edu> <369B018A.9C6987BD@sdsc.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"6C5p1.0.Un3.52ocs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/784 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=big5 Content-Length: 926 > This is an issue that deserves much additional discussion. But 12/16 > bit images in biology and medicine are rapidly proving their worth. > The lack of availability of suitable software has retarded progress in > this field. The few programs that do provide some 12/16 bit functions, > are often very expensive, and extremely limited in their operations. > When we then have to deal with multiple channels shown in different > colors, each in 12/16 bits, then the selection of available software > diminishes very rapidly. This constitutes the 64 bit software (16 > bits/channel, with 4 channels - RGB-Alpha). The lack of tools has > slowed progress in this area. IPLab does not adequately deal with such > data. It definitely depends on how much extra bulks one needs to pay for those added bits. Could someone give me an idea just how expensive, in terms of 8 vs. 12 vs. 16 bits, we are talking about here? Woeichyn From nih-image-request@io.ece.drexel.edu Tue Jan 12 09:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA21277; Tue, 12 Jan 1999 09:44:53 -0500 (EST) Resent-Date: Tue, 12 Jan 1999 09:44:53 -0500 (EST) Date: Tue, 12 Jan 1999 09:25:42 -0500 (EST) X-Authentication-Warning: pop.uky.edu: [128.163.85.61] didn't use HELO protocol Message-Id: <2.2.16.19990112092541.32bf5cbe@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 From: "Bill Clerici, Ph.D." Subject: Re: IPLab question Resent-Message-ID: <"r-uTa.0.6T4.tjrcs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/785 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 5655 David, Thanks for the information. Bill At 02:37 PM 1/11/99 -0800, you wrote: >While it is true that for many biological applications 256 bits of >resolution is plenty, there are significant advantages in greater bit >depths. For my applications, the primary advantage is greater dynamic >range. It is not uncommon to need to quantify differences in >the dimmer regions of an image, which oftens means letting the brightest >regions get clipped in an 8 bit image. With greater bit depth, it is >possible to quantify intensity in both the brightest and dimmest parts of >a greater range of images. > >A second advantage is that image processing routines have more information >to work with. I have been told that this is a particular advantage for >photon-reassignment routines (deconvolution). > >-David > >On Mon, 11 Jan 1999, Henry M. Thomas wrote: > >> Query: What biological data is measured with such accuracy that 8 bits is >> insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, >> one can do better on weight or length, but can you really do better on >> images of a biologically relevant variable such as calcium concentration >> (fluorescence)? That is, how much information are you discarding when NIH >> Image rounds each pixel from 16 bits to 8? >> Best, Harry >> >> >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, >> >not 8 bit. Image/J may work in the future, but so far it's still in >> >progress. We have IPLab, which we collect images with. The dongle thing >> >is too annoying to deal with most of the time, so we have been processing >> >everything with NIH Image (for example, it's nice to be able to process old >> >images on one computer while new ones are being acquired on another). >> >Plus, Image's scripting is much, much better. >> > >> >However, we're at a point now where we absolutely need 16-bit data, and >> >therefore are back to using IPLab. Does anyone know if there's a mailing >> >list or web page for IPLab users? Specifically, I'm trying to write a >> >plug-in that will let me make non-standard measurements on the segments of >> >an image, and return a table of the values. >> > >> >Thanks. I hope this isn't too off-topic. >> >--Randy >> > >> >>------------------------------ >> >>Date: Sat, 09 Jan 1999 09:12:20 -0800 >> >>From: "Harvey J. Karten" >> >>To: nih-image@io.ece.drexel.edu >> >>Subject: Comments on Image/J re confocal >> >>Message-ID: <36978DA6.3210AF93@sdsc.edu> >> >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >> >>x-mac-creator="4D4F5353" >> >>Content-Transfer-Encoding: 7bit >> >> >> >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >> >>images. With the shift to 12/16 bit images in all the major confocal >> >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >> >>from the otherwise powerful capabilities of NIH-Image. In order to use >> >>NIH-Image the confocal microscopist had to discard the much greater >> >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >> >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >> >>bits of alpha). >> >> >> >>Though clearly still a work in progress, Image/J shows the continuing >> >>creativity of Wayne Rasband. The latest version supports 16 bit stacks >> >>- though at present it only allows you to open, animate, and minimally >> >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >> >>stacks - but hopefully that will happen. >> >> >> >>Hopefully, a forthcoming version of Image/J will support a multi-channel >> >>16 bit/channel capability. This will emerge as a requisite technology >> >>with further development of multi-channel imaging of living cells, fMRI, >> >>etc. >> >> >> >>regards, Harvey >> >> >> >>-- >> >>Harvey J. Karten, M.D. >> >>Dept. of Neurosciences >> >>University of California @ San Diego >> >>La Jolla, CA 92093-0608 >> >>WCBR EMail: WCBR@ucsd.edu >> >>Other EMail: hjkarten@ucsd.edu >> >>Phone (Lab): 619-534-4938 >> >>FAX (Lab): 619-534-6602 >> >>Home Phone: 619-755-8573 >> >>Retina Information System: http://www-cajal.ucsd.edu >> >> >> >>See WCBR WebPage (Note CHANGE OF ADDRESS) >> >>http://www.wcbrBrain.org/ >> >> >> >>-------------------------------- >> > >> >****************************************************************** >> >Randy M. Wadkins, Ph.D. >> >Cancer Therapy & Research Center >> >Institute for Drug Development >> >14960 Omicron Drive >> >San Antonio, TX 78245 >> >phone: (210)-677-3835 >> >fax: (210)-677-0058 >> >E-mail: rwadkins@saci.org >> >CTRC Homepage: http://www.ccc.saci.org >> >****************************************************************** >> >> 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 >> >> >> > >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 > > > -------------------------------------------- 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-d-request@io.ece.drexel.edu Tue Jan 12 09:53 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA22538; Tue, 12 Jan 1999 09:53:49 -0500 (EST) Date: Tue, 12 Jan 1999 09:53:49 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901121453.JAA22538@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #8 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/8 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: 27111 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 8 Today's Topics: help [ nbd@po.CWRU.Edu (Nagendu B. Dev) ] Re: help [ GJOSS@rna.bio.mq.edu.au ] Re: IPLab question [ David Ehrhardt ] Re: IPLab question [ "Bill Clerici, Ph.D." Hi: I am new to NIH image. How does NIH measure command calculate area? I have sets of circular, oval and triangular structure. I need the integrated area for each particular structure. Can NIH image do that? Is there any help in the NIH manual. I would appreciate your reply.many thanks ---Dev. ### ------------------------------ Date: Tue, 12 Jan 1999 9:33:07 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: nbd@po.CWRU.Edu, nih-image@io.ece.drexel.edu Subject: Re: help Message-ID: <5709B45A08@rna.bio.mq.edu.au> >Received: from SpoolDir by RNA (Mercury 1.44); 12 Jan 99 09:14:20 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.44) with ESMTP; > 12 Jan 99 09:14:15 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id RAA13911; > Mon, 11 Jan 1999 17:11:56 -0500 (EST) >Resent-Date: Mon, 11 Jan 1999 17:11:56 -0500 (EST) >Message-Id: <199901112148.QAA00619@kanga.INS.CWRU.Edu> >Date: Mon, 11 Jan 1999 16:48:41 -0500 (EST) >From: nbd@po.CWRU.Edu (Nagendu B. Dev) >To: nih-image@io.ece.drexel.edu >Subject: help >Reply-To: nih-image@io.ece.drexel.edu >Resent-Message-ID: <"7Qf3R.0.Ct2.07dcs"@io> >Resent-From: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/780 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 33554560 0 > >Hi: >I am new to NIH image. How does NIH measure command calculate area? I have >sets of circular, oval and triangular structure. I need the integrated area >for each particular structure. Can NIH image do that? Is there any help in >the NIH manual. I would appreciate your reply.many thanks ---Dev. >### > Is there any help in the NIH manual??? page 7: "__________________________ Making Measurements To make a manual area measurement, first outline a region of interest using the rectangular, oval, polygonal, or freehand selection tool. Then select the Measure command, which will compute the area, mean gray value, and the minimum and maximum gray value. Other measurements, such as perimeter, can be enabled using the Options command in the Analysis menu. Measure distances by making a straight, freehand or segmented line selection, and then using the measure command. (Note that the line selection tool uses a pop-up menu for selecting different line types.) Use the angle tool to measure angles. The cross hair tool counts objects, marks them, and records their X-Y coordinates. The wand tools automatically outlines structures isolated using thresholding. Results from the most recent measurement are displayed in the Info window. Use Show Results to display a table of results since the last time the Reset command was used. The Analyze Particles command automatically counts and measures features of interest. This requires thresholding to discriminate objects of interest from surrounding background based on their gray values. Image has two thresholding methods. In thresholding mode (Threshold is checked in the Options menu), all pixels equal to or greater than a single threshold level are displayed in black, and all other pixels (the background) are displayed in white. In Density Slicing mode (Density Slice is checked), all pixels between a lower and upper threshold are highlighted in red. For both modes, you adjust threshold levels by dragging the LUT tool (the one with the double-headed arrow) in the LUT window. For successful thresholding, it may be necessary to use the Subtract Background command to remove the effects of uneven illumination. _________________________" Is there something deeper in your question ? 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, 11 Jan 1999 14:37:10 -0800 (PST) From: David Ehrhardt To: "Henry M. Thomas" cc: nih-image@io.ece.drexel.edu Subject: Re: IPLab question Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII While it is true that for many biological applications 256 bits of resolution is plenty, there are significant advantages in greater bit depths. For my applications, the primary advantage is greater dynamic range. It is not uncommon to need to quantify differences in the dimmer regions of an image, which oftens means letting the brightest regions get clipped in an 8 bit image. With greater bit depth, it is possible to quantify intensity in both the brightest and dimmest parts of a greater range of images. A second advantage is that image processing routines have more information to work with. I have been told that this is a particular advantage for photon-reassignment routines (deconvolution). -David On Mon, 11 Jan 1999, Henry M. Thomas wrote: > Query: What biological data is measured with such accuracy that 8 bits is > insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, > one can do better on weight or length, but can you really do better on > images of a biologically relevant variable such as calcium concentration > (fluorescence)? That is, how much information are you discarding when NIH > Image rounds each pixel from 16 bits to 8? > Best, Harry > > >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, > >not 8 bit. Image/J may work in the future, but so far it's still in > >progress. We have IPLab, which we collect images with. The dongle thing > >is too annoying to deal with most of the time, so we have been processing > >everything with NIH Image (for example, it's nice to be able to process old > >images on one computer while new ones are being acquired on another). > >Plus, Image's scripting is much, much better. > > > >However, we're at a point now where we absolutely need 16-bit data, and > >therefore are back to using IPLab. Does anyone know if there's a mailing > >list or web page for IPLab users? Specifically, I'm trying to write a > >plug-in that will let me make non-standard measurements on the segments of > >an image, and return a table of the values. > > > >Thanks. I hope this isn't too off-topic. > >--Randy > > > >>------------------------------ > >>Date: Sat, 09 Jan 1999 09:12:20 -0800 > >>From: "Harvey J. Karten" > >>To: nih-image@io.ece.drexel.edu > >>Subject: Comments on Image/J re confocal > >>Message-ID: <36978DA6.3210AF93@sdsc.edu> > >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; > >>x-mac-creator="4D4F5353" > >>Content-Transfer-Encoding: 7bit > >> > >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit > >>images. With the shift to 12/16 bit images in all the major confocal > >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away > >>from the otherwise powerful capabilities of NIH-Image. In order to use > >>NIH-Image the confocal microscopist had to discard the much greater > >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in > >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 > >>bits of alpha). > >> > >>Though clearly still a work in progress, Image/J shows the continuing > >>creativity of Wayne Rasband. The latest version supports 16 bit stacks > >>- though at present it only allows you to open, animate, and minimally > >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit > >>stacks - but hopefully that will happen. > >> > >>Hopefully, a forthcoming version of Image/J will support a multi-channel > >>16 bit/channel capability. This will emerge as a requisite technology > >>with further development of multi-channel imaging of living cells, fMRI, > >>etc. > >> > >>regards, Harvey > >> > >>-- > >>Harvey J. Karten, M.D. > >>Dept. of Neurosciences > >>University of California @ San Diego > >>La Jolla, CA 92093-0608 > >>WCBR EMail: WCBR@ucsd.edu > >>Other EMail: hjkarten@ucsd.edu > >>Phone (Lab): 619-534-4938 > >>FAX (Lab): 619-534-6602 > >>Home Phone: 619-755-8573 > >>Retina Information System: http://www-cajal.ucsd.edu > >> > >>See WCBR WebPage (Note CHANGE OF ADDRESS) > >>http://www.wcbrBrain.org/ > >> > >>-------------------------------- > > > >****************************************************************** > >Randy M. Wadkins, Ph.D. > >Cancer Therapy & Research Center > >Institute for Drug Development > >14960 Omicron Drive > >San Antonio, TX 78245 > >phone: (210)-677-3835 > >fax: (210)-677-0058 > >E-mail: rwadkins@saci.org > >CTRC Homepage: http://www.ccc.saci.org > >****************************************************************** > > 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 > > > 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: Tue, 12 Jan 1999 00:02:19 -0800 From: "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: IPL Question and 12/16 bits of data Message-ID: <369B018A.9C6987BD@sdsc.edu> Content-Type: multipart/alternative; boundary="------------5811E6FCA45369D3E6A6CEF2" --------------5811E6FCA45369D3E6A6CEF2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr Thomas reasonably raised the question of the importance of 12/16 bits of graphical data rather than the more common 8 bits. "Query: What biological data is measured with such accuracy that 8 bits is insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, one can do better on weight or length, but can you really do better on images of a biologically relevant variable such as calcium concentration (fluorescence)? That is, how much information are you discarding when NIH Image rounds each pixel from 16 bits to 8? Best, Harry" If you consider the range of brightness values that you will find in a single fluorescent intracellular filled neuron, this exceeds the 8 bit value range. The soma is intensely labeled while small peripheral dendrites are very faint. If you try to capture such a cell with 8 bit and compare the results that are obtained with a 12 bit system, you will find that the 12 bit system provides a much greater range of values (0-4095). This reduces the problem of either flooding the image with the soma in order to display the fine faintly stained dendrites, or by reducing the bright staining of the soma, you will lose the dendrites completely. With good software, it is possible to then sample selected portions of the range of values. Remapping a portion of a 12 bit image to the 8 bit display will also provide a more data-rich image, as shown by the number of points represented in the histogram. The common argument that is also advanced when criticizing 12 or more bits of graphical data is that the human eye cannot detect more than X gray levels - a number that varies with the author, but often between 16 and 64. This fails to take into account the dynamic remapping that occurs so rapidly in human vision. Consider the range of values that you encounter when examining a rich textured region in the bright sun, then turn to a shaded area and again you will see a wide range of brightness values. We stitch this range together so rapidly and so well, that we fail to realize that we are covering many log units of brightness - much more than merely 8 bits worth. You might also consider the marked difference between the appearance to your eye of complex histological field in fluorescence, and the 8 bit digital image of the same field. The 8 bit image is lacking in much of the finesse. It may not even show many of the fine processes, or subtle detail in the midst of an intensely labeled cell. Another way to think of this is that we cannot "see" all the information that is of importance - this is apparent if reference is made to e.g. infra-red, UV, etc. It is also true in radiographs and Electron Microscope images. You might also consider that more and more of the desktop scanners are providing 12 - 16 bits/per channel. This is not merely for advertizing purposes. There is a significant and noticeable difference in the images obtained from these scanners, compared to images previously obtained from scanners with 8 bits/channel. You are generally correct when discussing calcium imaging, but that reflects the sensitivity of the dyes used, and the ability to reliably discriminate various brightness levels in those particular conditions. Many modern confocal microscopes now routinely provide 12 bits/channel, with marked improvement in the quality of the resulting images. This is an issue that deserves much additional discussion. But 12/16 bit images in biology and medicine are rapidly proving their worth. The lack of availability of suitable software has retarded progress in this field. The few programs that do provide some 12/16 bit functions, are often very expensive, and extremely limited in their operations. When we then have to deal with multiple channels shown in different colors, each in 12/16 bits, then the selection of available software diminishes very rapidly. This constitutes the 64 bit software (16 bits/channel, with 4 channels - RGB-Alpha). The lack of tools has slowed progress in this area. IPLab does not adequately deal with such data. 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 --------------5811E6FCA45369D3E6A6CEF2 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dr Thomas reasonably raised the question of the importance of 12/16 bits of graphical data rather than the more common 8 bits.
"Query: What biological data is measured with such accuracy that 8 bits is
insufficient?  That's 1 in 256 (well, 1 in 254) which is 0.4%.  Granted,
one can do better on weight or length, but can you really do better on
images of a biologically relevant variable such as calcium concentration
(fluorescence)?  That is, how much information are you discarding when NIH
Image rounds each pixel from 16 bits to 8?
Best,  Harry"

If you consider the range of brightness values that you will find in a single fluorescent intracellular filled neuron, this exceeds the 8 bit value range. The soma is intensely labeled while small peripheral dendrites are very faint. If you try to capture such a cell with 8 bit and compare the results that are obtained with a 12 bit system, you will find that the 12 bit system provides a much greater range of values (0-4095). This reduces the problem of either flooding the image with the soma in order to display the fine faintly stained dendrites, or by reducing the bright staining of the soma, you will lose the dendrites completely. With good software, it is possible to then sample selected portions of the range of values. Remapping a portion of a 12 bit image to the 8 bit display will also provide a more data-rich image, as shown by the number of points represented in the histogram.

The common argument that is also advanced when criticizing 12 or more bits of graphical data is that the human eye cannot detect more than X gray levels - a number that varies with the author, but often between 16 and 64. This fails to take into account the dynamic remapping that occurs so rapidly in human vision. Consider the range of values that you encounter when examining a rich textured region in the bright sun, then turn  to a shaded area and again you will see a wide range of brightness values. We stitch this range together so rapidly and so well, that we fail to realize that we are covering many log units of brightness - much more than merely 8 bits worth. You might also consider the marked difference between the appearance to your eye of complex histological field in fluorescence, and the 8 bit digital image of the same field. The 8 bit image is lacking in much of the finesse. It may not even show many of the fine processes, or subtle detail in the midst of an intensely labeled cell.

Another way to think of this is that we cannot "see" all the information that is of importance - this is apparent if reference is made to e.g. infra-red, UV, etc. It is also true in radiographs and Electron Microscope images. You might also consider that more and more of the desktop scanners are providing 12 - 16 bits/per channel. This is not merely for advertizing purposes. There is a significant and noticeable difference in the images obtained from these scanners, compared to images previously obtained from scanners with 8 bits/channel.

You are generally correct when discussing calcium imaging, but that reflects the sensitivity of the dyes used, and the ability to reliably discriminate various brightness levels in those particular conditions. Many modern confocal microscopes now routinely provide 12 bits/channel, with marked improvement in the quality of the resulting images.

This is an issue that deserves much additional discussion. But 12/16 bit images in biology and medicine are rapidly proving their worth. The lack of availability of suitable software has retarded progress in this field. The few programs that do provide some 12/16 bit functions, are often very expensive, and extremely limited in their operations. When we then have to deal with multiple channels shown in different colors, each in 12/16 bits, then the selection of available software diminishes very rapidly. This constitutes the 64 bit software (16 bits/channel, with 4 channels - RGB-Alpha). The lack of tools has slowed progress in this area. IPLab does not adequately deal with such data.

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
  --------------5811E6FCA45369D3E6A6CEF2-- ------------------------------ Date: Tue, 12 Jan 1999 14:20:49 +0000 From: Woeichyn Chu To: nih-image@io.ece.drexel.edu Subject: Re: IPL Question and 12/16 bits of data Message-ID: <369B91DC.2233@bme.ym.edu.tw> Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit > This is an issue that deserves much additional discussion. But 12/16 > bit images in biology and medicine are rapidly proving their worth. > The lack of availability of suitable software has retarded progress in > this field. The few programs that do provide some 12/16 bit functions, > are often very expensive, and extremely limited in their operations. > When we then have to deal with multiple channels shown in different > colors, each in 12/16 bits, then the selection of available software > diminishes very rapidly. This constitutes the 64 bit software (16 > bits/channel, with 4 channels - RGB-Alpha). The lack of tools has > slowed progress in this area. IPLab does not adequately deal with such > data. It definitely depends on how much extra bulks one needs to pay for those added bits. Could someone give me an idea just how expensive, in terms of 8 vs. 12 vs. 16 bits, we are talking about here? Woeichyn ------------------------------ Date: Tue, 12 Jan 1999 09:25:42 -0500 (EST) From: "Bill Clerici, Ph.D." To: nih-image@io.ece.drexel.edu Subject: Re: IPLab question Message-Id: <2.2.16.19990112092541.32bf5cbe@pop.uky.edu> Content-Type: text/plain; charset="us-ascii" David, Thanks for the information. Bill At 02:37 PM 1/11/99 -0800, you wrote: >While it is true that for many biological applications 256 bits of >resolution is plenty, there are significant advantages in greater bit >depths. For my applications, the primary advantage is greater dynamic >range. It is not uncommon to need to quantify differences in >the dimmer regions of an image, which oftens means letting the brightest >regions get clipped in an 8 bit image. With greater bit depth, it is >possible to quantify intensity in both the brightest and dimmest parts of >a greater range of images. > >A second advantage is that image processing routines have more information >to work with. I have been told that this is a particular advantage for >photon-reassignment routines (deconvolution). > >-David > >On Mon, 11 Jan 1999, Henry M. Thomas wrote: > >> Query: What biological data is measured with such accuracy that 8 bits is >> insufficient? That's 1 in 256 (well, 1 in 254) which is 0.4%. Granted, >> one can do better on weight or length, but can you really do better on >> images of a biologically relevant variable such as calcium concentration >> (fluorescence)? That is, how much information are you discarding when NIH >> Image rounds each pixel from 16 bits to 8? >> Best, Harry >> >> >We're in the same boat as Dr. Karten. We need to operate on 16-bit images, >> >not 8 bit. Image/J may work in the future, but so far it's still in >> >progress. We have IPLab, which we collect images with. The dongle thing >> >is too annoying to deal with most of the time, so we have been processing >> >everything with NIH Image (for example, it's nice to be able to process old >> >images on one computer while new ones are being acquired on another). >> >Plus, Image's scripting is much, much better. >> > >> >However, we're at a point now where we absolutely need 16-bit data, and >> >therefore are back to using IPLab. Does anyone know if there's a mailing >> >list or web page for IPLab users? Specifically, I'm trying to write a >> >plug-in that will let me make non-standard measurements on the segments of >> >an image, and return a table of the values. >> > >> >Thanks. I hope this isn't too off-topic. >> >--Randy >> > >> >>------------------------------ >> >>Date: Sat, 09 Jan 1999 09:12:20 -0800 >> >>From: "Harvey J. Karten" >> >>To: nih-image@io.ece.drexel.edu >> >>Subject: Comments on Image/J re confocal >> >>Message-ID: <36978DA6.3210AF93@sdsc.edu> >> >>Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; >> >>x-mac-creator="4D4F5353" >> >>Content-Transfer-Encoding: 7bit >> >> >> >>One of the big drawbacks of NIH-Image is that it was restricted to 8 bit >> >>images. With the shift to 12/16 bit images in all the major confocal >> >>instruments (Zeiss, Olympus, BioRAD), this has resulted in a shift away >> >>from the otherwise powerful capabilities of NIH-Image. In order to use >> >>NIH-Image the confocal microscopist had to discard the much greater >> >>flexibility of 12 bits of data in each of the channels (i.e. 12 bits in >> >>red, 12 bits in green, 12 bits in blue, plus a potential additional 12 >> >>bits of alpha). >> >> >> >>Though clearly still a work in progress, Image/J shows the continuing >> >>creativity of Wayne Rasband. The latest version supports 16 bit stacks >> >>- though at present it only allows you to open, animate, and minimally >> >>manipulate the LUT. (Filters, copy, crop, etc. doesn't work on 16 bit >> >>stacks - but hopefully that will happen. >> >> >> >>Hopefully, a forthcoming version of Image/J will support a multi-channel >> >>16 bit/channel capability. This will emerge as a requisite technology >> >>with further development of multi-channel imaging of living cells, fMRI, >> >>etc. >> >> >> >>regards, Harvey >> >> >> >>-- >> >>Harvey J. Karten, M.D. >> >>Dept. of Neurosciences >> >>University of California @ San Diego >> >>La Jolla, CA 92093-0608 >> >>WCBR EMail: WCBR@ucsd.edu >> >>Other EMail: hjkarten@ucsd.edu >> >>Phone (Lab): 619-534-4938 >> >>FAX (Lab): 619-534-6602 >> >>Home Phone: 619-755-8573 >> >>Retina Information System: http://www-cajal.ucsd.edu >> >> >> >>See WCBR WebPage (Note CHANGE OF ADDRESS) >> >>http://www.wcbrBrain.org/ >> >> >> >>-------------------------------- >> > >> >****************************************************************** >> >Randy M. Wadkins, Ph.D. >> >Cancer Therapy & Research Center >> >Institute for Drug Development >> >14960 Omicron Drive >> >San Antonio, TX 78245 >> >phone: (210)-677-3835 >> >fax: (210)-677-0058 >> >E-mail: rwadkins@saci.org >> >CTRC Homepage: http://www.ccc.saci.org >> >****************************************************************** >> >> 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 >> >> >> > >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 > > > -------------------------------------------- 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 -------------------------------------------- -------------------------------- End of nih-image-d Digest V99 Issue #8 ************************************** From nih-image-request@io.ece.drexel.edu Tue Jan 12 10:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA29060; Tue, 12 Jan 1999 10:44:53 -0500 (EST) Resent-Date: Tue, 12 Jan 1999 10:44:53 -0500 (EST) Date: Tue, 12 Jan 1999 15:24:10 +0000 (GMT) From: James Alexander Ainge X-Sender: jaa7@st-andrews.ac.uk To: nih-image@io.ece.drexel.edu Subject: Help Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"nRo1e2.0.mO6.Wascs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/786 X-Loop: nih-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 I'm new to NIH image and I'm trying to qauntify slides of brain sections stained for vesicular acetylcholine transporter. Essentially I'd like to compare levels of staining in different structures. Can I do this and if so how? Any help would be very much appreciated. James A. Ainge School of Psychology, St Andrews. (01334) 462077 From nih-image-request@io.ece.drexel.edu Tue Jan 12 22:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA05858; Tue, 12 Jan 1999 22:54:06 -0500 (EST) Resent-Date: Tue, 12 Jan 1999 22:54:06 -0500 (EST) Message-ID: From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: 8 bits, 16 bits and etc Date: Wed, 13 Jan 1999 14:26:17 +1100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"3cyRj1.0.WT.hB1ds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/787 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 3332 Hi, I am in agreement that 16 bits is better than 8, however, I would wonder if these extra bits are actually meaningful. Having spent some years looking at digital image data, I offer the following suggestion. First, if you are only looking at data as pictures then 100 grey levels is more than you can see. So even if you have 16 bit data which has a dynamic range of 16 bits, to visually present this the brightness range will have to be drastically compressed to allow the human eye to see this data over its whole range. If on the other hand you wish to measure differences between pixels then the more bits the better if you can actually show what you are measuring is real. Produce a series of images of a static test object, using the conditions of illumination and imaging that your real objects will have. Compare these images by for instance subtraction. Expand the density range and if you see no difference at all then good. As in all data gathering exercises the distinction between precision and accuracy must be made. It may well be the case that it is difficult to accurately digitise a video image at better than 8 bits, but having done it at say 8 bits then computations might be done at 32 bits or even more, to prevent loss of precision by rounding errors. But the final answers should then be reduced to 8 bits. So if you have a camera which can produce stable, repeatable 16 bit deep images, then of course you might like to start discriminating between grey level 32,000 and 32,009, but be aware that in the case of a 16 bit deep image each grey level is only one part in 65536, or in rounded terms 1 part in 100,000. This is a really precise measurement. I would like to see some validation of this precision. And then we can talk about accuracy. This is, "what does a grey level mea", in real world terms, that is the brightness of a star, the amount of dye fluorescing, the density of a film in a certain area, the actual reflectivity of a surface and so-on. To make these numbers meaningful requires calibration. And once again, repeated calibrations should give the same answers. Another reason for liking cameras which can produce more than 8 bits is that these are frequently cooled CCD cameras with chips whose individuals cells are physically large. eg 24 microns square. Such a large cell potentially contains many more electrons than a small 6 micron square cell. (number is proportional to area). When these cells are read out using good modern electronics the ability to tell how many elecrons are in the cell is a function of the difference between a full and an empty cell. It is clear that this is much greater with a large cell and so the signal to noise is better for the bigger one. So we can tell the diffference between intensities over a larger range with a bigger cell. This means we can image objects which contain a large brightness range, such as stars in a black sky. And of course if we are carful with calibrations then the intensities collected can truly be made to reflect the actual incident intensities, but I believe it is not easy to do precisely. The cooling helps in the case of low intensities by reducing the thermal signal. And thus for longer exposures should help in the repeatability area. I hope this is not too confused. Best regards Noel Goldsmith From nih-image-d-request@io.ece.drexel.edu Wed Jan 13 06:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12411; Wed, 13 Jan 1999 06:18:26 -0500 (EST) Date: Wed, 13 Jan 1999 06:18:26 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901131118.GAA12411@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #9 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/9 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: 4662 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 9 Today's Topics: Help [ James Alexander Ainge To: nih-image@io.ece.drexel.edu Subject: Help Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I'm new to NIH image and I'm trying to qauntify slides of brain sections stained for vesicular acetylcholine transporter. Essentially I'd like to compare levels of staining in different structures. Can I do this and if so how? Any help would be very much appreciated. James A. Ainge School of Psychology, St Andrews. (01334) 462077 ------------------------------ Date: Wed, 13 Jan 1999 14:26:17 +1100 From: "Goldsmith, Noel" To: "'Image Mailing List'" Subject: 8 bits, 16 bits and etc Message-ID: Content-Type: text/plain Hi, I am in agreement that 16 bits is better than 8, however, I would wonder if these extra bits are actually meaningful. Having spent some years looking at digital image data, I offer the following suggestion. First, if you are only looking at data as pictures then 100 grey levels is more than you can see. So even if you have 16 bit data which has a dynamic range of 16 bits, to visually present this the brightness range will have to be drastically compressed to allow the human eye to see this data over its whole range. If on the other hand you wish to measure differences between pixels then the more bits the better if you can actually show what you are measuring is real. Produce a series of images of a static test object, using the conditions of illumination and imaging that your real objects will have. Compare these images by for instance subtraction. Expand the density range and if you see no difference at all then good. As in all data gathering exercises the distinction between precision and accuracy must be made. It may well be the case that it is difficult to accurately digitise a video image at better than 8 bits, but having done it at say 8 bits then computations might be done at 32 bits or even more, to prevent loss of precision by rounding errors. But the final answers should then be reduced to 8 bits. So if you have a camera which can produce stable, repeatable 16 bit deep images, then of course you might like to start discriminating between grey level 32,000 and 32,009, but be aware that in the case of a 16 bit deep image each grey level is only one part in 65536, or in rounded terms 1 part in 100,000. This is a really precise measurement. I would like to see some validation of this precision. And then we can talk about accuracy. This is, "what does a grey level mea", in real world terms, that is the brightness of a star, the amount of dye fluorescing, the density of a film in a certain area, the actual reflectivity of a surface and so-on. To make these numbers meaningful requires calibration. And once again, repeated calibrations should give the same answers. Another reason for liking cameras which can produce more than 8 bits is that these are frequently cooled CCD cameras with chips whose individuals cells are physically large. eg 24 microns square. Such a large cell potentially contains many more electrons than a small 6 micron square cell. (number is proportional to area). When these cells are read out using good modern electronics the ability to tell how many elecrons are in the cell is a function of the difference between a full and an empty cell. It is clear that this is much greater with a large cell and so the signal to noise is better for the bigger one. So we can tell the diffference between intensities over a larger range with a bigger cell. This means we can image objects which contain a large brightness range, such as stars in a black sky. And of course if we are carful with calibrations then the intensities collected can truly be made to reflect the actual incident intensities, but I believe it is not easy to do precisely. The cooling helps in the case of low intensities by reducing the thermal signal. And thus for longer exposures should help in the repeatability area. I hope this is not too confused. Best regards Noel Goldsmith -------------------------------- End of nih-image-d Digest V99 Issue #9 ************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 13 06:51 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA17791 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 06:51:59 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 06:51:59 -0500 (EST) Message-Id: <3.0.5.32.19990113063559.00bec100@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: Wed, 13 Jan 1999 06:35:59 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: 8 bits, 16 bits and etc In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"WZNdS.0.Ml3.dL8ds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/788 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2334 At 02:26 PM 1/13/99 +1100, you wrote: >Hi, >I am in agreement that 16 bits is better than 8, however, I would wonder if >these extra bits are actually meaningful. I seem to recall that there are many cases in which the information content of increased depth (8 to 16 bit) is more or less equivalent to increasing spatial resolution by the same amount. (Certainly the reverse can be true, as with a grid of 16x16 black and white tiny pixels, one can represent 256 shades of one larger "pixel". ) So, aside from the capture-at-all issues that H. Kaplan described so well, a somewhat equivalent question is: "Why would anyone want a higher SPATIAL resolution image?" Or, backing up a generation, what's wrong with 24x80 IBM PC screens with 2mmx4mm 'pixels' for imaging? I think also it's not just semantics here, but a much deeper issue that nature in general and biology in particular is 'fractal' in nature, and there is information content at any new higher resolution one can obtain. A stronger assertion was made by I think Carl Sagan and Frank Drake in the area of astronomy some years back, on debating what the point was of using "infrared astronomy" -- I mean, what was the point, we had optical astronomy and radio-wavelength astronomy -- who needed another band of the spectrum? Their hypothesis, empirically supported, was that every time one opened a new window on the universe (a new spectral band, a new resolution in space or color), what was seen was not just more details of the same phenomena, but BRAND NEW PREVIOUSLY-UNSUSPECTED natural phenomena. Thus, we now have infrared, optical, radio, ultraviolet, gamma-ray, etc. astronomy, each adding new wonders to the zoo. (For non-astronomers, the first big finding of "radio-wavelength astronomy" in 1926 or so was finding this really, really bright spot in the sky, which turned out to be the center of our galaxy, which previously had been thought to have the earth near the center, since the optical sky did not reveal the center, due to increased dust in the plane of the galaxy.) So, no, it's not just another few percentage point accuracy one is after, ultimately, it's discovering brand new phenomena, seen for the first time with this new, better tool. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Wed Jan 13 08:38 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA03801 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 08:38:38 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 08:38:38 -0500 (EST) Message-ID: <369D1BF4.4A6@cris.enel.it> Date: Wed, 13 Jan 1999 14:19:32 -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: 8 bits, 16 bits and etc References: <199901131112.GAA11400@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"wF0cH.0.O6.-o9ds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/789 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 2439 Dear Noel and Dear Imagers, Concerning Noel's suggestions > Hi, > I am in agreement that 16 bits is better than 8, however, I would wonder if > these extra bits are actually meaningful. > > Having spent some years looking at digital image data, I offer the following > suggestion. > First, if you are only looking at data as pictures then 100 grey levels is > more than you can see. So even if you have 16 bit data which has a dynamic > range of 16 bits, to visually present this the brightness range will have to > be drastically compressed to allow the human eye to see this data over its > whole range. If on the other hand you wish to measure differences between > pixels then the more bits the better if you can actually show what you are > measuring is real. > ... I wish to add something about my personal experience: digitization of X-ray films for non-medical purposes (e.g. radiographs of weldings, of castings, etc.). These films have optical density up to 4; this means that they usually appear completely black if not viewed with a special lighting-box. In this case 8 bits are not enough to cover the whole optical density range with sufficient contrast. To digitize these films without information loss you do need a scanner with more than 8-bit analog to digital conversion, because the information contained in the film exceeds 8 bits/pixel. Such scanners exist on the market today; a few years ago we developed a 12-bit digitizer. You get images with 4096 grey levels; 2 bits correspond to noise but the other 10 bits are really meaningful and make the difference between an 8-bit-device and a 12-bit-device. As Noel points out, the human eye cannot perceive more than about 100 grey levels on a computer monitor. Brightness and contrast provided by industrial lighting-boxes are far superior. Anyway, we developed a visualisation software that allows real-time adjustment of brightness and contrast, similar to LUT adjustment in NIH-Image. You can dinamically choose the grey-level-window to show in the 4096 levels range. Human inspectors accustomed to ordinary lighting-boxes admitted that by looking at the digital image they could get all the information contained in the radiography. 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 From nih-image-request@io.ece.drexel.edu Wed Jan 13 09:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA14130 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 09:45:45 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 09:45:45 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Wed, 13 Jan 1999 16:21:34 +0200 To: nih-image From: Matti Haveri Subject: Importing DICOM with fixed windows Cc: Wayne Rasband Resent-Message-ID: <"iPglj2.0.2W2.olAds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/790 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1541 Let's say I want to open multiple DICOM CT-slices to 1029-1099 densities (i.e. Hounsfield units W/L 70/40) to get a standard viewing window and finer plots for a given density range in a 12-bit image data. I can, with much work, DICOM import all the slices with Shift down (fixed 16-bit to 8-bit scaling for all images), then brightness/contrast one image with the mouse, choose Options/Propagate/LUT and Rescale each image separately. However, the problem with NIH Image is that it is impossible to adjust an image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via the mouse. Furthermore, after Rescaling the HU-correction is lost and the scale begings from 0 instead of -1024. The ability to adjust brightness/contrast numerically would be nice but also this approach would be clumsy. I guess the best solution would be to add the possibility to DICOM-import a selected density range just like it is possible via Custom import/Fixed Scale. Why don't I then just use the existing Custom import? Well, the problem with DICOM files is that the Offset may be different for each CT slice. I can calculate the Offset provided I know the matrix (Offset = file size - (x * y * 2)) but this isn't practical if there are many images. Custom import also doesn't automatically calibrate densities to Hounfield units like DICOM import does (although now this HU-info gets lost when Rescaling). What do you think (or am I just missing another solution)? -- Matti Haveri From nih-image-request@io.ece.drexel.edu Wed Jan 13 10:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19186 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 10:21:50 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 10:21:50 -0500 (EST) Mime-Version: 1.0 X-Sender: rwadkins@ctrc7.ucc.saci.org Message-Id: In-Reply-To: <199901121427.JAA18518@io.ece.drexel.edu> Date: Wed, 13 Jan 1999 09:03:49 -0600 To: nih-image@io.ece.drexel.edu From: "Randy M. Wadkins" Subject: 12/16 bit software Resent-Message-ID: <"iEvmZ3.0.9-3.qKBds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/791 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 876 > The lack of tools has slowed progress in this area. IPLab does not >adequately deal with such data. > >regards, Harvey I agree that IPLab is not the greatest for 12/16-bit images. The best image processing software for these images that I've worked with is ISee from Inovision (www.inovis.com). Unfortunately, it runs under Unix on SGI or Sun machines. I understand there's a port to Linux in the works, so it may be possible to eventually run it on a Mac or PC by booting into Linux. --Randy ****************************************************************** Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 13 15:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA29635 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 15:14:14 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 15:14:14 -0500 (EST) Mime-Version: 1.0 X-Sender: (Unverified) Message-Id: In-Reply-To: References: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> Date: Wed, 13 Jan 1999 14:51:42 -0500 To: nih-image@io.ece.drexel.edu From: Alex Abate Subject: AppleScript Support Resent-Message-ID: <"T52332.0.lN6.XbFds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/792 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> Content-Length: 451 Is there any chance that Applescript will be supported in the future? It would be great if we could have more flexibility automating the behaviour of Image and its interaction with other apps. Thanks, Alessandro Abate alex@roffs.com ROFFS * Roffer's Ocean Fishing Forecasting Service, Inc. 2871 Southwest 69th Court * Miami, Florida 33155-2829 Tel: 800 677-7633/305 262-8336 * Fax: 305 265-9077 Internet: www.roffs.com * Email: fish@roffs.com From nih-image-request@io.ece.drexel.edu Wed Jan 13 15:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA29848 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 15:15:32 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 15:15:32 -0500 (EST) Message-ID: <369D08EA.4FC1@lehigh.edu> Date: Wed, 13 Jan 1999 15:58:40 -0500 From: Jennifer Swann Organization: Lehigh University X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: stereology Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Resent-Message-ID: <"CJhjh2.0.Pe6.JiFds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/793 X-Loop: nih-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 Greetings! I am new to this news group and I need some help - is anyone familiar with a package system for sterology that uses a mac based program? I am presently considering buying a system from microbrightfield but as a mac user I am concerned about bringing an IBM into my lab! Jennifer Swann From nih-image-request@io.ece.drexel.edu Wed Jan 13 17:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA16491 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 17:10:31 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 17:10:31 -0500 (EST) X-Sender: kwb@bserv.com (Unverified) Message-Id: In-Reply-To: <369D08EA.4FC1@lehigh.edu> Mime-Version: 1.0 Date: Wed, 13 Jan 1999 16:36:47 -0500 To: nih-image@io.ece.drexel.edu From: kwb Subject: Re: stereology Resent-Message-ID: <"wwknJ.0.Q13.-CHds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/794 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 633 >Greetings! I am new to this news group and I need some help - is anyone >familiar with a package system for sterology that uses a mac based >program? I am presently considering buying a system from >microbrightfield but as a mac user I am concerned about bringing an IBM >into my lab! >Jennifer Swann You might check out the MacStereology demo at: ftp://zippy.nimh.nih.gov/pub/nih-image/demos/ Regards, Ken Ken Baker RR 2, Acton (4943, 4th Line, Erin Twnshp) Ontario, Canada L7J-2L8 KWB@bserv.com 519-853-4787 From nih-image-request@io.ece.drexel.edu Wed Jan 13 17:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA17541 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 17:18:03 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 17:18:03 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Wed, 13 Jan 1999 16:50:56 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: stereology Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 84 Resent-Message-ID: <"Qz4Wt2.0.1U3.VOHds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/795 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1214 In a message dated 1/13/99 3:09:51 PM, you wrote: >Greetings! I am new to this news group and I need some help - is anyone >familiar with a package system for sterology that uses a mac based >program? I am presently considering buying a system from >microbrightfield but as a mac user I am concerned about bringing an IBM >into my lab! There are several sets of macros that provide good basic stereological tools within Image, including one of mine, that can be downloaded from the zippy site. Also (not free, but not too expensive either) the Image Processing Tool Kit has an extensive set of stereological aids, grids, etc. for both manual and automatic application (and a lengthy tutorial on their use). These plug- ins will work in any Photoshop-compatible program (Mac or Win), including NIH- Image. The Image implementation of Photoshop plug-in support is minimal but adequate as long as you are working with grey scale images. It does not support native PPC code in the Tool Kit plugins, but this is a minor gripe only. And the Tool Kit CD does include Digital Darkroom, which runs the plug- ins well and provides other Photoshop-like aids. Check out the info at http://members.aol.com/ImageProcTK/ From nih-image-request@io.ece.drexel.edu Wed Jan 13 17:48 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA22158 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 17:48:46 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 17:48:46 -0500 (EST) Date: Wed, 13 Jan 1999 14:25:30 -0800 From: David Linker To: "'Image Mailing List'" Subject: Frame grabber for new G3 towers? Message-ID: <112973.3125226330@huginn.medicine.washington.edu> Originator-Info: login-id=dtlinker; server=dtlinker.deskmail.washington.edu X-Mailer: Mulberry (MacOS) [1.4.0, s/n U-300938] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline Resent-Message-ID: <"SfiS53.0.KY4.nrHds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/796 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1141 We need to digitize black and white S-VHS (NTSC) video from video tape. We currently use a 7100AV, with the digitizer set to 8 bit gray scale images, at 640x480, using NIHImage. This is perfectly adequate for our work, but the 7100 is slow, and we applied for funding for a G3 tower (333MHz). We received the funding, but Apple has apparently discontinued the line, and the video capture cards. The new G3's look great in terms of performance, but I am told that there is no video frame grabber from Apple for them. I looked in the catalogs I get of Apple hardware, which used to have several options for video capture, but see none now. I would appreciate any pointers to companies/hardware that would meet this need. Also, any experiences using the hardware. Our application depends on measuring distances on the screen, not on absolute image densities. We have a significant number of macros that we use, so we would prefer to continue using NIHImage. I would like to get one of the fastest new G3's, but then will not have a very large budget for a frame grabber. We do not need to grab continuous video. Thank you, David Linker From nih-image-request@io.ece.drexel.edu Wed Jan 13 17:53 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA23035 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 17:53:55 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 17:53:55 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: mhaveri@walli.uwasa.fi, nih-image@io.ece.drexel.edu Date: Thu, 14 Jan 1999 9:35:03 GMT+1100 Subject: Re: Importing DICOM with fixed windows Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <8715C7554E@rna.bio.mq.edu.au> Resent-Message-ID: <"sNVU43.0.Oo4.gxHds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/797 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 5215 >Date: Wed, 13 Jan 1999 16:21:34 +0200 >To: nih-image >From: Matti Haveri >Subject: Importing DICOM with fixed windows > >Let's say I want to open multiple DICOM CT-slices to 1029-1099 densities >(i.e. Hounsfield units W/L 70/40) to get a standard viewing window and >finer plots for a given density range in a 12-bit image data. > >I can, with much work, DICOM import all the slices with Shift down (fixed >16-bit to 8-bit scaling for all images), then brightness/contrast one image >with the mouse, choose Options/Propagate/LUT and Rescale each image >separately. > >However, the problem with NIH Image is that it is impossible to adjust an >image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via the >mouse. Furthermore, after Rescaling the HU-correction is lost and the scale >begings from 0 instead of -1024. The ability to adjust brightness/contrast >numerically would be nice but also this approach would be clumsy. > >I guess the best solution would be to add the possibility to DICOM-import a >selected density range just like it is possible via Custom import/Fixed >Scale. > >Why don't I then just use the existing Custom import? Well, the problem >with DICOM files is that the Offset may be different for each CT slice. I >can calculate the Offset provided I know the matrix (Offset = file size - >(x * y * 2)) but this isn't practical if there are many images. Custom >import also doesn't automatically calibrate densities to Hounfield units >like DICOM import does (although now this HU-info gets lost when Rescaling). > >What do you think (or am I just missing another solution)? > >-- >Matti Haveri > > I dont know about DICOM, but it seems to me that, as long as frames are uncommpressed, you should be able to import most formats using image macros. I used the following macros to sample large stacks. With the additional use of SetImportMinMax(min,max); you should be able to achieve what you want. Note the use of SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); to dynamically calculate each frame offset. Also "[F3]Header" illustrates that you can read any part of the file for header info or to follow chains etc. { NIH-Image macro ImportStackSlices Import selected stack slices from 256graylevel NonCompressed Tif or QuickTime Written by Greg Joss, last mod:1999-1-14 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 to set PicSize, use prototype as current image ( use NEW N or load a sample image or terminate full load with . to get palette etc) [F1] will allow file selection 256 gray level No compression Quicktime has 8 byte header Tiff 768 allows access to a sequence in middle of stack or sampling of a sequence } var width,height,offset,slices,fromSlice,n,m,i,stack,type:integer; name,nullChr,typeText:string; qt,t:boolean; procedure ImportIt;begin {SetImport('Custom');} SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); Import(name); end; procedure fileType(i:integer); begin if i=0 then begin offset:=0; typeText:='tiff'; end else if i=1 then begin offset:=768; typeText:='tiff';end else if i=2 then begin offset:=8; typeText:='qtmoov';end; end; procedure matchLine(m:string,i:integer); begin t:=true; while (length(m)>0) AND t do begin if ord(m)<>LineBuffer[i] then if (ord(m)<>ord(nullChr)) OR (LineBuffer[i]<>0) then t:=false; i:=i+1; delete(m,1,1); end; end; macro'[F1]Import 256graylevel NonCompressed Tif or QT'; begin if type=0 then begin qt:=GetNumber('QuickTime?0/1',0); if qt<>0 then type:=2 else type:=1; end; fileType(type); fromSlice:=GetNumber('fromSlice',1); slices:=GetNumber('slices',1000); GetPicSize(width,height); ImportIt; end; macro'[F2]SampleStack'; begin qt:=GetNumber('QuickTime?0/1',0); if qt then offset:=8 else offset:=768; {QuickTime/Tiff} fromSlice:=GetNumber('fromSlice',1); n:=GetNumber('every n th slice',2); m:=GetNumber('slices',1000/n); slices:=1; GetPicSize(width,height); if qt then name:='QuickTimeStack' else name:='TimeLapseMovie1'; name:=GetString('name',name); MakeNewStack(name);stack:=pidNumber; for i:=1 to m do begin ImportIt;SelectAll;Copy;Dispose; ChoosePic(stack); if i<>1 then addSlice; paste; fromSlice:=fromSlice+n; end; end; macro '[F3]Header'; var w,h:integer; begin {getPicSize(w,h);} saveState; width:=256; height:=8; offset:=0; fromSlice:=1;slices:=1; ImportIt; GetRow(0,0,8); nullChr:='.'; matchLine('MM.*',0); if t then type:=1 else begin matchLine('....mdat',0); if t then type:=2; end; fileType(type); SetPicName(windowTitle,' header.',typeText); {SetNewSize(w,h);} restoreState; 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 Wed Jan 13 18:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA24872 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 18:07:18 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 18:07:18 -0500 (EST) Message-ID: <009c01bdf704$4dc18560$0e145392@ciencias.uchile.cl> From: "Miguel Ferrada" To: Subject: Color quantification Date: Tue, 13 Oct 1998 19:50:48 -0400 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.0518.4 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0518.4 Resent-Message-ID: <"3dXwU2.0.iJ5.29Ids"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/798 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: 425 Hi! exist a macro which can quantify the colors of an image?. Example: if a flower's yellow with small circles of red. And the red circles vary in a lot of flowers in area and dispersion. Exist a macro which quantify the color of the circles in relation to total color of flower?. ex: the flower has a% of yellow with tone=b+/- a range respectly. The total numbers of pixels is the 100%. Thanks and regards! Miguel Ferrada. From nih-image-request@io.ece.drexel.edu Wed Jan 13 18:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA25500 for cshtest@io.ece.drexel.edu; Wed, 13 Jan 1999 18:10:23 -0500 (EST) Resent-Date: Wed, 13 Jan 1999 18:10:23 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Thu, 14 Jan 1999 9:56:40 GMT+1100 Subject: 8/12 bits Ca fluorescence laser scanning confocal Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <8771915C2A@rna.bio.mq.edu.au> Resent-Message-ID: <"za8l53.0.6c5.YFIds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/799 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1215 In the context of the recent 8/12 bit discussion, I would like to ask for information sources regarding imaging aspects of Ca fluorescence using a laser scanning confocal microscope. I have been working with Ca fluorescence images for some months (captured by another lab). I have gathered the impression that the intensity distribution of the fluorescence is a reflection of the actual number of fluorophores per pixel that have been exited by the laser as it scans. ie the intensity distribution is a blurred integral probability distribution of fluorophores excited. The fluorophore count per pixel would appear to be relatively small, ie of the order of 50, so that if blurring didnt occur, the histogram of pixel intensities would be a distribution of excited fluorophore counts from 0 to 50 ie a well contrasted image has a histogram with second order peaks 254/50 ie 5 pixel values apart. Could someone please give me a reference to any material which discusses this aspect of the imaging physics/technology. 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 Jan 14 03:47 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA16883 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 03:47:28 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 03:47:28 -0500 (EST) X-Sender: elk@129.233.21.18 Message-Id: In-Reply-To: <112973.3125226330@huginn.medicine.washington.edu> Mime-Version: 1.0 Date: Thu, 14 Jan 1999 09:33:05 +0100 To: nih-image@io.ece.drexel.edu From: Ben Elkin Subject: Re: Frame grabber for new G3 towers? Resent-Message-ID: <"5QDe61.0.GQ3.oiQds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/800 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1329 David Linker wrote: >We need to digitize black and white S-VHS (NTSC) video from video tape. We >currently use a 7100AV, with the digitizer set to 8 bit gray scale images, >at 640x480, using NIHImage. This is perfectly adequate for our work, but >the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > >We received the funding, but Apple has apparently discontinued the line, >and the video capture cards. The new G3's look great in terms of >performance, but I am told that there is no video frame grabber from Apple >for them. > We have recently installed a Newer Technology ( http://www.newertech.com ) MAXpowr G3 processor upgrade card onto an old NuBus computer. A card with 1 MB backside cache and 240 MHz processor costs below 1000$ even in Germany. It made a pretty fast modern computer from an old one, and we can continue to use our NuBus framegrabber from Scion. The only problem you are going to have in this case: what to do with the rest of the funding :-) 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-d-request@io.ece.drexel.edu Thu Jan 14 03:55 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA18394; Thu, 14 Jan 1999 03:55:58 -0500 (EST) Date: Thu, 14 Jan 1999 03:55:58 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901140855.DAA18394@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #10 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/10 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: 25117 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 10 Today's Topics: Re: 8 bits, 16 bits and etc [ Wade & Cheryll Schuette ] stereology [ Jennifer Swann ] Re: stereology [ kwb ] Re: stereology [ DrJohnRuss@aol.com ] Frame grabber for new G3 towers? [ David Linker ] ------------------------------ Date: Wed, 13 Jan 1999 06:35:59 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: 8 bits, 16 bits and etc Message-Id: <3.0.5.32.19990113063559.00bec100@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" At 02:26 PM 1/13/99 +1100, you wrote: >Hi, >I am in agreement that 16 bits is better than 8, however, I would wonder if >these extra bits are actually meaningful. I seem to recall that there are many cases in which the information content of increased depth (8 to 16 bit) is more or less equivalent to increasing spatial resolution by the same amount. (Certainly the reverse can be true, as with a grid of 16x16 black and white tiny pixels, one can represent 256 shades of one larger "pixel". ) So, aside from the capture-at-all issues that H. Kaplan described so well, a somewhat equivalent question is: "Why would anyone want a higher SPATIAL resolution image?" Or, backing up a generation, what's wrong with 24x80 IBM PC screens with 2mmx4mm 'pixels' for imaging? I think also it's not just semantics here, but a much deeper issue that nature in general and biology in particular is 'fractal' in nature, and there is information content at any new higher resolution one can obtain. A stronger assertion was made by I think Carl Sagan and Frank Drake in the area of astronomy some years back, on debating what the point was of using "infrared astronomy" -- I mean, what was the point, we had optical astronomy and radio-wavelength astronomy -- who needed another band of the spectrum? Their hypothesis, empirically supported, was that every time one opened a new window on the universe (a new spectral band, a new resolution in space or color), what was seen was not just more details of the same phenomena, but BRAND NEW PREVIOUSLY-UNSUSPECTED natural phenomena. Thus, we now have infrared, optical, radio, ultraviolet, gamma-ray, etc. astronomy, each adding new wonders to the zoo. (For non-astronomers, the first big finding of "radio-wavelength astronomy" in 1926 or so was finding this really, really bright spot in the sky, which turned out to be the center of our galaxy, which previously had been thought to have the earth near the center, since the optical sky did not reveal the center, due to increased dust in the plane of the galaxy.) So, no, it's not just another few percentage point accuracy one is after, ultimately, it's discovering brand new phenomena, seen for the first time with this new, better tool. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Wed, 13 Jan 1999 14:19:32 -0800 From: "Zuccala David" To: nih-image@io.ece.drexel.edu Subject: Re: 8 bits, 16 bits and etc Message-ID: <369D1BF4.4A6@cris.enel.it> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Noel and Dear Imagers, Concerning Noel's suggestions > Hi, > I am in agreement that 16 bits is better than 8, however, I would wonder if > these extra bits are actually meaningful. > > Having spent some years looking at digital image data, I offer the following > suggestion. > First, if you are only looking at data as pictures then 100 grey levels is > more than you can see. So even if you have 16 bit data which has a dynamic > range of 16 bits, to visually present this the brightness range will have to > be drastically compressed to allow the human eye to see this data over its > whole range. If on the other hand you wish to measure differences between > pixels then the more bits the better if you can actually show what you are > measuring is real. > ... I wish to add something about my personal experience: digitization of X-ray films for non-medical purposes (e.g. radiographs of weldings, of castings, etc.). These films have optical density up to 4; this means that they usually appear completely black if not viewed with a special lighting-box. In this case 8 bits are not enough to cover the whole optical density range with sufficient contrast. To digitize these films without information loss you do need a scanner with more than 8-bit analog to digital conversion, because the information contained in the film exceeds 8 bits/pixel. Such scanners exist on the market today; a few years ago we developed a 12-bit digitizer. You get images with 4096 grey levels; 2 bits correspond to noise but the other 10 bits are really meaningful and make the difference between an 8-bit-device and a 12-bit-device. As Noel points out, the human eye cannot perceive more than about 100 grey levels on a computer monitor. Brightness and contrast provided by industrial lighting-boxes are far superior. Anyway, we developed a visualisation software that allows real-time adjustment of brightness and contrast, similar to LUT adjustment in NIH-Image. You can dinamically choose the grey-level-window to show in the 4096 levels range. Human inspectors accustomed to ordinary lighting-boxes admitted that by looking at the digital image they could get all the information contained in the radiography. 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 ------------------------------ Date: Wed, 13 Jan 1999 16:21:34 +0200 From: Matti Haveri To: nih-image Cc: Wayne Rasband Subject: Importing DICOM with fixed windows Message-Id: Content-Type: text/plain; charset="us-ascii" Let's say I want to open multiple DICOM CT-slices to 1029-1099 densities (i.e. Hounsfield units W/L 70/40) to get a standard viewing window and finer plots for a given density range in a 12-bit image data. I can, with much work, DICOM import all the slices with Shift down (fixed 16-bit to 8-bit scaling for all images), then brightness/contrast one image with the mouse, choose Options/Propagate/LUT and Rescale each image separately. However, the problem with NIH Image is that it is impossible to adjust an image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via the mouse. Furthermore, after Rescaling the HU-correction is lost and the scale begings from 0 instead of -1024. The ability to adjust brightness/contrast numerically would be nice but also this approach would be clumsy. I guess the best solution would be to add the possibility to DICOM-import a selected density range just like it is possible via Custom import/Fixed Scale. Why don't I then just use the existing Custom import? Well, the problem with DICOM files is that the Offset may be different for each CT slice. I can calculate the Offset provided I know the matrix (Offset = file size - (x * y * 2)) but this isn't practical if there are many images. Custom import also doesn't automatically calibrate densities to Hounfield units like DICOM import does (although now this HU-info gets lost when Rescaling). What do you think (or am I just missing another solution)? -- Matti Haveri ------------------------------ Date: Wed, 13 Jan 1999 15:25:25 +0100 From: "High Tech Systems" To: Subject: XWindow Message-ID: <01be3f00$8fe8c860$LocalHost@olivetti> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hello, I have to display images on a sun Workstation (Ultra 10). These images are 12 or 16 bits per pixel and I don't succed in using a Visual with a depth greater than 8. So these images are represented with only 256 colors ... I'd like to display these images with a depth of 16 but I don't have the solution to . Is there anyone who have encountered these problem and could send me some information about this ? Note : The application is developped using C Language and XWindow Library (XCreateImage, XPutImage ...). Thank you, Bye. Support Technique HTS Email : support@htsys.com ------------------------------ Date: Wed, 13 Jan 1999 09:03:49 -0600 From: "Randy M. Wadkins" To: nih-image@io.ece.drexel.edu Subject: 12/16 bit software Message-Id: Content-Type: text/plain; charset="us-ascii" > The lack of tools has slowed progress in this area. IPLab does not >adequately deal with such data. > >regards, Harvey I agree that IPLab is not the greatest for 12/16-bit images. The best image processing software for these images that I've worked with is ISee from Inovision (www.inovis.com). Unfortunately, it runs under Unix on SGI or Sun machines. I understand there's a port to Linux in the works, so it may be possible to eventually run it on a Mac or PC by booting into Linux. --Randy ****************************************************************** Randy M. Wadkins, Ph.D. Cancer Therapy & Research Center Institute for Drug Development 14960 Omicron Drive San Antonio, TX 78245 phone: (210)-677-3835 fax: (210)-677-0058 E-mail: rwadkins@saci.org CTRC Homepage: http://www.ccc.saci.org ****************************************************************** ------------------------------ Date: Wed, 13 Jan 1999 14:51:42 -0500 From: Alex Abate To: nih-image@io.ece.drexel.edu Subject: AppleScript Support Message-Id: Content-Type: text/plain; charset="us-ascii" Is there any chance that Applescript will be supported in the future? It would be great if we could have more flexibility automating the behaviour of Image and its interaction with other apps. Thanks, Alessandro Abate alex@roffs.com ROFFS * Roffer's Ocean Fishing Forecasting Service, Inc. 2871 Southwest 69th Court * Miami, Florida 33155-2829 Tel: 800 677-7633/305 262-8336 * Fax: 305 265-9077 Internet: www.roffs.com * Email: fish@roffs.com ------------------------------ Date: Wed, 13 Jan 1999 15:58:40 -0500 From: Jennifer Swann To: nih-image@io.ece.drexel.edu Subject: stereology Message-ID: <369D08EA.4FC1@lehigh.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Greetings! I am new to this news group and I need some help - is anyone familiar with a package system for sterology that uses a mac based program? I am presently considering buying a system from microbrightfield but as a mac user I am concerned about bringing an IBM into my lab! Jennifer Swann ------------------------------ Date: Wed, 13 Jan 1999 16:36:47 -0500 From: kwb To: nih-image@io.ece.drexel.edu Subject: Re: stereology Message-Id: Content-Type: text/plain; charset="us-ascii" >Greetings! I am new to this news group and I need some help - is anyone >familiar with a package system for sterology that uses a mac based >program? I am presently considering buying a system from >microbrightfield but as a mac user I am concerned about bringing an IBM >into my lab! >Jennifer Swann You might check out the MacStereology demo at: ftp://zippy.nimh.nih.gov/pub/nih-image/demos/ Regards, Ken Ken Baker RR 2, Acton (4943, 4th Line, Erin Twnshp) Ontario, Canada L7J-2L8 KWB@bserv.com 519-853-4787 ------------------------------ Date: Wed, 13 Jan 1999 16:50:56 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: stereology Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/13/99 3:09:51 PM, you wrote: >Greetings! I am new to this news group and I need some help - is anyone >familiar with a package system for sterology that uses a mac based >program? I am presently considering buying a system from >microbrightfield but as a mac user I am concerned about bringing an IBM >into my lab! There are several sets of macros that provide good basic stereological tools within Image, including one of mine, that can be downloaded from the zippy site. Also (not free, but not too expensive either) the Image Processing Tool Kit has an extensive set of stereological aids, grids, etc. for both manual and automatic application (and a lengthy tutorial on their use). These plug- ins will work in any Photoshop-compatible program (Mac or Win), including NIH- Image. The Image implementation of Photoshop plug-in support is minimal but adequate as long as you are working with grey scale images. It does not support native PPC code in the Tool Kit plugins, but this is a minor gripe only. And the Tool Kit CD does include Digital Darkroom, which runs the plug- ins well and provides other Photoshop-like aids. Check out the info at http://members.aol.com/ImageProcTK/ ------------------------------ Date: Wed, 13 Jan 1999 14:25:30 -0800 From: David Linker To: "'Image Mailing List'" Subject: Frame grabber for new G3 towers? Message-ID: <112973.3125226330@huginn.medicine.washington.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline We need to digitize black and white S-VHS (NTSC) video from video tape. We currently use a 7100AV, with the digitizer set to 8 bit gray scale images, at 640x480, using NIHImage. This is perfectly adequate for our work, but the 7100 is slow, and we applied for funding for a G3 tower (333MHz). We received the funding, but Apple has apparently discontinued the line, and the video capture cards. The new G3's look great in terms of performance, but I am told that there is no video frame grabber from Apple for them. I looked in the catalogs I get of Apple hardware, which used to have several options for video capture, but see none now. I would appreciate any pointers to companies/hardware that would meet this need. Also, any experiences using the hardware. Our application depends on measuring distances on the screen, not on absolute image densities. We have a significant number of macros that we use, so we would prefer to continue using NIHImage. I would like to get one of the fastest new G3's, but then will not have a very large budget for a frame grabber. We do not need to grab continuous video. Thank you, David Linker ------------------------------ Date: Thu, 14 Jan 1999 9:35:03 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: mhaveri@walli.uwasa.fi, nih-image@io.ece.drexel.edu Subject: Re: Importing DICOM with fixed windows Message-ID: <8715C7554E@rna.bio.mq.edu.au> >Date: Wed, 13 Jan 1999 16:21:34 +0200 >To: nih-image >From: Matti Haveri >Subject: Importing DICOM with fixed windows > >Let's say I want to open multiple DICOM CT-slices to 1029-1099 densities >(i.e. Hounsfield units W/L 70/40) to get a standard viewing window and >finer plots for a given density range in a 12-bit image data. > >I can, with much work, DICOM import all the slices with Shift down (fixed >16-bit to 8-bit scaling for all images), then brightness/contrast one image >with the mouse, choose Options/Propagate/LUT and Rescale each image >separately. > >However, the problem with NIH Image is that it is impossible to adjust an >image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via the >mouse. Furthermore, after Rescaling the HU-correction is lost and the scale >begings from 0 instead of -1024. The ability to adjust brightness/contrast >numerically would be nice but also this approach would be clumsy. > >I guess the best solution would be to add the possibility to DICOM-import a >selected density range just like it is possible via Custom import/Fixed >Scale. > >Why don't I then just use the existing Custom import? Well, the problem >with DICOM files is that the Offset may be different for each CT slice. I >can calculate the Offset provided I know the matrix (Offset = file size - >(x * y * 2)) but this isn't practical if there are many images. Custom >import also doesn't automatically calibrate densities to Hounfield units >like DICOM import does (although now this HU-info gets lost when Rescaling). > >What do you think (or am I just missing another solution)? > >-- >Matti Haveri > > I dont know about DICOM, but it seems to me that, as long as frames are uncommpressed, you should be able to import most formats using image macros. I used the following macros to sample large stacks. With the additional use of SetImportMinMax(min,max); you should be able to achieve what you want. Note the use of SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); to dynamically calculate each frame offset. Also "[F3]Header" illustrates that you can read any part of the file for header info or to follow chains etc. { NIH-Image macro ImportStackSlices Import selected stack slices from 256graylevel NonCompressed Tif or QuickTime Written by Greg Joss, last mod:1999-1-14 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 to set PicSize, use prototype as current image ( use NEW N or load a sample image or terminate full load with . to get palette etc) [F1] will allow file selection 256 gray level No compression Quicktime has 8 byte header Tiff 768 allows access to a sequence in middle of stack or sampling of a sequence } var width,height,offset,slices,fromSlice,n,m,i,stack,type:integer; name,nullChr,typeText:string; qt,t:boolean; procedure ImportIt;begin {SetImport('Custom');} SetCustom(width,height,offset+(fromSlice-1)*width*height,slices); Import(name); end; procedure fileType(i:integer); begin if i=0 then begin offset:=0; typeText:='tiff'; end else if i=1 then begin offset:=768; typeText:='tiff';end else if i=2 then begin offset:=8; typeText:='qtmoov';end; end; procedure matchLine(m:string,i:integer); begin t:=true; while (length(m)>0) AND t do begin if ord(m)<>LineBuffer[i] then if (ord(m)<>ord(nullChr)) OR (LineBuffer[i]<>0) then t:=false; i:=i+1; delete(m,1,1); end; end; macro'[F1]Import 256graylevel NonCompressed Tif or QT'; begin if type=0 then begin qt:=GetNumber('QuickTime?0/1',0); if qt<>0 then type:=2 else type:=1; end; fileType(type); fromSlice:=GetNumber('fromSlice',1); slices:=GetNumber('slices',1000); GetPicSize(width,height); ImportIt; end; macro'[F2]SampleStack'; begin qt:=GetNumber('QuickTime?0/1',0); if qt then offset:=8 else offset:=768; {QuickTime/Tiff} fromSlice:=GetNumber('fromSlice',1); n:=GetNumber('every n th slice',2); m:=GetNumber('slices',1000/n); slices:=1; GetPicSize(width,height); if qt then name:='QuickTimeStack' else name:='TimeLapseMovie1'; name:=GetString('name',name); MakeNewStack(name);stack:=pidNumber; for i:=1 to m do begin ImportIt;SelectAll;Copy;Dispose; ChoosePic(stack); if i<>1 then addSlice; paste; fromSlice:=fromSlice+n; end; end; macro '[F3]Header'; var w,h:integer; begin {getPicSize(w,h);} saveState; width:=256; height:=8; offset:=0; fromSlice:=1;slices:=1; ImportIt; GetRow(0,0,8); nullChr:='.'; matchLine('MM.*',0); if t then type:=1 else begin matchLine('....mdat',0); if t then type:=2; end; fileType(type); SetPicName(windowTitle,' header.',typeText); {SetNewSize(w,h);} restoreState; 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: Tue, 13 Oct 1998 19:50:48 -0400 From: "Miguel Ferrada" To: Subject: Color quantification Message-ID: <009c01bdf704$4dc18560$0e145392@ciencias.uchile.cl> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hi! exist a macro which can quantify the colors of an image?. Example: if a flower's yellow with small circles of red. And the red circles vary in a lot of flowers in area and dispersion. Exist a macro which quantify the color of the circles in relation to total color of flower?. ex: the flower has a% of yellow with tone=b+/- a range respectly. The total numbers of pixels is the 100%. Thanks and regards! Miguel Ferrada. ------------------------------ Date: Thu, 14 Jan 1999 9:56:40 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu Subject: 8/12 bits Ca fluorescence laser scanning confocal Message-ID: <8771915C2A@rna.bio.mq.edu.au> In the context of the recent 8/12 bit discussion, I would like to ask for information sources regarding imaging aspects of Ca fluorescence using a laser scanning confocal microscope. I have been working with Ca fluorescence images for some months (captured by another lab). I have gathered the impression that the intensity distribution of the fluorescence is a reflection of the actual number of fluorophores per pixel that have been exited by the laser as it scans. ie the intensity distribution is a blurred integral probability distribution of fluorophores excited. The fluorophore count per pixel would appear to be relatively small, ie of the order of 50, so that if blurring didnt occur, the histogram of pixel intensities would be a distribution of excited fluorophore counts from 0 to 50 ie a well contrasted image has a histogram with second order peaks 254/50 ie 5 pixel values apart. Could someone please give me a reference to any material which discusses this aspect of the imaging physics/technology. 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, 14 Jan 1999 09:33:05 +0100 From: Ben Elkin To: nih-image@io.ece.drexel.edu Subject: Re: Frame grabber for new G3 towers? Message-Id: Content-Type: text/plain; charset="us-ascii" David Linker wrote: >We need to digitize black and white S-VHS (NTSC) video from video tape. We >currently use a 7100AV, with the digitizer set to 8 bit gray scale images, >at 640x480, using NIHImage. This is perfectly adequate for our work, but >the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > >We received the funding, but Apple has apparently discontinued the line, >and the video capture cards. The new G3's look great in terms of >performance, but I am told that there is no video frame grabber from Apple >for them. > We have recently installed a Newer Technology ( http://www.newertech.com ) MAXpowr G3 processor upgrade card onto an old NuBus computer. A card with 1 MB backside cache and 240 MHz processor costs below 1000$ even in Germany. It made a pretty fast modern computer from an old one, and we can continue to use our NuBus framegrabber from Scion. The only problem you are going to have in this case: what to do with the rest of the funding :-) 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 -------------------------------- End of nih-image-d Digest V99 Issue #10 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jan 14 09:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA08839 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 09:39:57 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 09:39:57 -0500 (EST) Mime-Version: 1.0 X-Sender: pauln@maine.maine.edu Message-Id: Date: Thu, 14 Jan 1999 09:15:44 -0500 To: nih-image@io.ece.drexel.edu From: Paul Nakroshis Subject: Progressive Scan CCD and Board Resent-Message-ID: <"H2Alk3.0.hG1.PmVds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/801 X-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: 1522 Hello, I am in the process of setting up a granular physics lab and need to get a progressive scan ccd camera and a suitable board for the MAC. Currently, I am thinking about getting a Pulnix TM-9701 camera and am searching for a suitable capture board (not successfully yet)that will allow me to control operation of the camera from within my own C or C++ program. Jim Rowell from JKN Electronics told me to look for a PCI Bus Master frame grabber board and this board would likely come with C/C++ programming API's that I could use. 1) Does anyone have any experience with Pulnix cameras? Can you recommend them? 2) Any advice on frame grabber boards for a PowerMac 9600 that will allow me to digitize to disk directly and have complete control over the camera? 3) Would I be able to simultaneously take other data from a seperate I/O board, or will the camera take over the computer and prevent this? 4) should I give up hope finding a suitable MAC video board and get a windows machine (where these boards are easy to find) or is their a viable Linux alternative? Any wisdom is greatly appreciated! -paul ================================================================= Paul Nakroshis pauln@usm.maine.edu Department of Physics http://www.usm.maine.edu/~pauln/ Room 252 Science Building 207.780.4158 (OFFICE) University of Southern Maine 207.780.5607 (FAX) PO Box 9300 Portland, ME 04104-9300 ================================================================= From nih-image-request@io.ece.drexel.edu Thu Jan 14 09:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA11918 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 09:58:34 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 09:58:34 -0500 (EST) Message-ID: <369DBB70.6804E7E5@maine.rr.com> Date: Thu, 14 Jan 1999 09:40:06 +0000 From: Marcia Goldfarb X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) MIME-Version: 1.0 To: Nih-image Subject: digital camera Content-Transfer-Encoding: 7bit Resent-Message-ID: <"ElbBJ3.0.l42.K5Wds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/802 X-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: 740 I use Nih-Image to quantitate spots on 2-D gels. I have purchased a digital camera (Olympus D-620L) and now use this to input the gel image into computer. I can down load directly into Photoshop 3.0. Can someone who understands the differences in computer languages help me to optimize the steps. The downloaded camera image is JPEG. I do multiple steps in Photoshop with IPTK plugins to isolate areas of interest for transfer to Nih-Image. Is it best to leave the image in JPEG or save it in Photoshop 3.0 or go directly to tiff for this work. Final product is saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. Thank you for help Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 Email: anatekep@maine.rr.com From nih-image-request@io.ece.drexel.edu Thu Jan 14 10:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA13754 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 10:08:41 -0500 (EST) <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> Resent-Date: Thu, 14 Jan 1999 10:08:41 -0500 (EST) Message-Id: In-Reply-To: References: <3.0.1.32.19981105170548.007bc970@pop.service.ohio-state.edu> <3.0.1.32.19981105104220.007b0770@pop.service.ohio-state.ed u> Mime-Version: 1.0 Date: Thu, 14 Jan 1999 10:56:56 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: AppleScript Support Resent-Message-ID: <"Y9uG41.0.MY2.QGWds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/803 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 353 >Is there any chance that Applescript will be supported in the future? It >would be great if we could have more flexibility automating the behaviour >of Image and its interaction with other apps. I have no plans to add Applescript support to NIH Image. I spend most of my free time these days working on ImageJ (http://rsb.info.nih.gov/ij/). -wayne From nih-image-request@io.ece.drexel.edu Thu Jan 14 10:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA16262 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 10:23:14 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 10:23:14 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <365d90e5.369e052c@aol.com> Date: Thu, 14 Jan 1999 09:54:36 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: digital camera Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 84 Resent-Message-ID: <"ivX54.0.zr2.KNWds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/804 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1283 In a message dated 1/14/99 9:50:36 AM, you wrote: >I use Nih-Image to quantitate spots on 2-D gels. I have purchased a >digital camera (Olympus D-620L) and now use this to input the gel image >into computer. I can down load directly into Photoshop 3.0. Can someone >who understands the differences in computer languages help me to >optimize the steps. The downloaded camera image is JPEG. I do multiple >steps in Photoshop with IPTK plugins to isolate areas of interest for >transfer to Nih-Image. Is it best to leave the image in JPEG or save it >in Photoshop 3.0 or go directly to tiff for this work. Final product is >saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. It doesn't matter. But not for a good reason. Converting the image back to tif will not recover the lost data from the jpeg compression. jpeg changes pixel values, and you will find that the brightness and dimensions of features will be altered in the process. I realize you already have this camera and probably can't return it, but PLEASE folks, don't let anyone else make this kind of mistake. Get a camera that transmits or stores images without lossy compression. jpeg is fine for pictures of the kids, but not image analysis where the pixel values are used for anything. John Russ From nih-image-request@io.ece.drexel.edu Thu Jan 14 10:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19575 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 10:41:48 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 10:41:48 -0500 (EST) Message-ID: <369E19D0.10D3@lehigh.edu> Date: Thu, 14 Jan 1999 11:22:41 -0500 From: Jennifer Swann Organization: Lehigh University X-Mailer: Mozilla 3.01 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Frame grabber for new G3 towers? References: <112973.3125226330@huginn.medicine.washington.edu> Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Resent-Message-ID: <"B6XPw3.0.Hz3.UlWds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/807 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1422 I have heard that the Targas 2000 is the fram grabber that works well with apples - I do not know their copatability with the new series of G3s but you migh contac them - they have a web site! Jennifer Swann\ David Linker wrote: > > We need to digitize black and white S-VHS (NTSC) video from video tape. We > currently use a 7100AV, with the digitizer set to 8 bit gray scale images, > at 640x480, using NIHImage. This is perfectly adequate for our work, but > the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > > We received the funding, but Apple has apparently discontinued the line, > and the video capture cards. The new G3's look great in terms of > performance, but I am told that there is no video frame grabber from Apple > for them. > > I looked in the catalogs I get of Apple hardware, which used to have > several options for video capture, but see none now. > > I would appreciate any pointers to companies/hardware that would meet this > need. Also, any experiences using the hardware. Our application depends on > measuring distances on the screen, not on absolute image densities. We have > a significant number of macros that we use, so we would prefer to continue > using NIHImage. I would like to get one of the fastest new G3's, but then > will not have a very large budget for a frame grabber. We do not need to > grab continuous video. > > Thank you, > > David Linker From nih-image-request@io.ece.drexel.edu Thu Jan 14 10:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19617 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 10:41:56 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 10:41:56 -0500 (EST) Message-Id: <3.0.5.32.19990114102202.007edd10@mohawk.net> X-Sender: microbill@mohawk.net X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Thu, 14 Jan 1999 10:22:02 -0500 To: nih-image@io.ece.drexel.edu From: Bill Miller Subject: Re: digital camera In-Reply-To: <369DBB70.6804E7E5@maine.rr.com> Mime-Version: 1.0 Resent-Message-ID: <"c9PyD3.0.Bw3.ckWds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/806 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 919 Be VERY carful about quantifying JPEG images - it is NOT a lossless compression either spatially or intensity wise. At 09:40 AM 1/14/99 +0000, you wrote: >I use Nih-Image to quantitate spots on 2-D gels. I have purchased a >digital camera (Olympus D-620L) and now use this to input the gel image >into computer. I can down load directly into Photoshop 3.0. Can someone >who understands the differences in computer languages help me to >optimize the steps. The downloaded camera image is JPEG. I do multiple >steps in Photoshop with IPTK plugins to isolate areas of interest for >transfer to Nih-Image. Is it best to leave the image in JPEG or save it >in Photoshop 3.0 or go directly to tiff for this work. Final product is >saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. > >Thank you for help > >Marcia Goldfarb >Anatek-EP >17 Bishop St >Portland,ME 04103 > >Email: anatekep@maine.rr.com > > > From nih-image-request@io.ece.drexel.edu Thu Jan 14 10:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA19622 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 10:41:58 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 10:41:58 -0500 (EST) Message-ID: <369E09A1.F65AA474@sdcc12.ucsd.edu> Date: Thu, 14 Jan 1999 07:13:38 -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: Stereology on the Mac References: <199901140854.DAA17975@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"FzpJB2.0.ii3.BgWds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/805 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 803 The recent thread on Stereology on the Mac can be addressed directly by looking at NeuroZoom. This is a Freeware Program written by Warren Young his colleagues at Scripps Research Foundation. It was developed as part of the Human Brain Project, and is freely available. It is very sophisticated, with a very distinctly Mac type of interface. You will need a motorized stage (as with all such programs) to use it most efficiently. 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 Thu Jan 14 11:22 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA25429 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 11:22:04 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 11:22:04 -0500 (EST) Message-Id: From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Frame grabber for new G3 towers? Date: Thu, 14 Jan 1999 10:57:53 -0500 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Resent-Message-ID: <"Hil0H1.0.dO5.KGXds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/808 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 631 David/list It does appear that Apple is leaving the built-in digitizer business, at least according to a spot check of their web page. I can readily recommend the Scion LG-3 frame grabber for $900. It only supports 8-bit grayscale and 24-bit RGB color (they do have composite color framegrabbers, too), but does it very well and is nicely supported from NIH Image. supports 4 separate video lines, plus digital control line I/O. Also works very well in Windows machines with Scion Image, just not quite as elegantly.... No commercial interest, just an obviously satisfied customer! Bill Heeschen Microscopy Group Dow Chemical From nih-image-request@io.ece.drexel.edu Thu Jan 14 12:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA06538 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 12:44:55 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 12:44:55 -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: Mime-Version: 1.0 Date: Thu, 14 Jan 1999 18:24:55 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Object-Image and AppleScript Resent-Message-ID: <"yd8Zg2.0.bh.TSYds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/809 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1894 I respond to the question of Alessandro Abate with a modified subject title. I have started to implement AppleScript into Object-Image1.62n9. I'll put it onto my server within a month or two. However, it can be obtained right now on request by anyone who wants to try it out and give me some feedback. The examples mentioned below are already working. There are two different methods of interaction: A) an AppleScript tells Object-Image to execute an already loaded macro. In the example below, a script asks Object-Image to say "Hello AppleScript!" B) an AppleScript is embedded into an NIH macro text and is executed from within Object-Image. In the example below, Object-Image empties the trash. The today's version has the following limitations: - Only one AppleScript can be embedded; - Besides the clipboard, no parameters can be passed - The embedded script has no access yet to the macro variables - Error messages are not yet supported, so you better try a script out with a script editor before embedding it. - RunMacro always executes the first macro, ignoring the macro name - It works only on PowerMacs Macro text in Object-Image: =========================== macro 'Say Hello'; begin PutMessage('Hello AppleScript!'); end; macro 'Empty Trash' begin PutMessage('Now emptying the trash...'); BeginScript tell application "Finder" Empty Trash end tell EndScript; PutMessage('The trash is empty'); end; Script Text in Script Editor ============================ tell application "Object-Image" activate runmacro "Say Hello" end tell 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 Thu Jan 14 12:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08859 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 12:58:50 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 12:58:50 -0500 (EST) Message-ID: <369E38FC.79B4@wxs.nl> Date: Thu, 14 Jan 1999 18:35:43 +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: upgrading mac. 7100 AV. References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"-sNnf.0.AC1.IhYds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/810 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 640 Dear Imagers, (David) I use the 7100 AV powermac (Nubus mac)) for grabbing microscopical images. The AV card works very good for color images , (for B/W I use the LG3 card of Scion. Last summer I upgraded the 7100/AV with the SONNET CRESCENDO G3 PROCESSOR UPGRADE CARD.INCLUDED THE VIDEO ADAPTOR KIT FOR THE AV CARD. Since then I work with the 7100/AV like a modern G3 (214 MHz) with no problems at all. Look for Sonnet on the internet hhtp://www.sonnettech.com Like Bill I have no commercial interest, just an obviously satisfied customer! Best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 00703504466 From nih-image-request@io.ece.drexel.edu Thu Jan 14 13:12 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA11265 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 13:12:16 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 13:12:16 -0500 (EST) Message-ID: <369E2E2D.57E6C9AA@netmatters.co.uk> Date: Thu, 14 Jan 1999 17:50:06 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Frame grabber for new G3 towers? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"5Bj7G1.0.9j1.LtYds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/811 X-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: 1779 Ben Elkin wrote: > David Linker wrote: > >We need to digitize black and white S-VHS (NTSC) video from video tape. We > >currently use a 7100AV, with the digitizer set to 8 bit gray scale images, > >at 640x480, using NIHImage. This is perfectly adequate for our work, but > >the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > > > >We received the funding, but Apple has apparently discontinued the line, > >and the video capture cards. The new G3's look great in terms of > >performance, but I am told that there is no video frame grabber from Apple > >for them. > > > > We have recently installed a Newer Technology ( http://www.newertech.com ) > MAXpowr G3 processor upgrade card onto an old NuBus computer. A card with 1 > MB backside cache and 240 MHz processor costs below 1000$ even in Germany. > It made a pretty fast modern computer from an old one, and we can continue > to use our NuBus framegrabber from Scion. > > The only problem you are going to have in this case: what to do with the > rest of the funding :-) > > 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 There are two Firewire ports in the new G3 macs, but have yet to hear of a scientific camera that supports firewire. Anyone know a good reason for this? ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ From nih-image-request@io.ece.drexel.edu Thu Jan 14 13:35 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA14920 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 13:35:29 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 13:35:29 -0500 (EST) From: wpchan@socrates.berkeley.edu Date: Thu, 14 Jan 1999 10:06:25 -0800 (PST) X-Sender: wpchan@socrates To: nih-image@io.ece.drexel.edu Subject: Scion LG3 and Mac G3 In-Reply-To: <6FE6FE3338A@rna.bio.mq.edu.au> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"87gJb3.0.2U2.f8Zds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/812 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 634 A few months ago, I posted about not being able to capture at 29.97 fps with "make movie/blind capture" on a G3 tower. The problem is now solved by a hardware upgrade from Scion. After a few rounds of calling Scion's tech support which really didn't provide any useful help, Scion finally admitted that there is a hardware problem when using the LG3 in real time capture on a G3 Mac. The upgrade took about may be 2 weeks (could be faster, if not for the holidays). And now we can allocate about 500 MB to Image and capture 1000 frames per capture at 640x480 and video rate. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) From nih-image-request@io.ece.drexel.edu Thu Jan 14 16:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA05161 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 16:10:54 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 16:10:54 -0500 (EST) Date: Thu, 14 Jan 1999 12:39:33 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: Stereology In-Reply-To: <199901140856.DAA18515@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"bkFBq3.0.uD.kObds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/813 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 806 Depending upon what you need, there are a few routes for Mac stereology. A commercial package called MacStereology might still be around. there are plug-ins for Photoshop and IPLab, plus some Image macros, written by John Russ. the first versions are on the Image ftp site, there are probably updates on his image processing CD. There is another set of stereology macros in the user-contrib folder at the Image ftp site. These are entitled "Cavalieri3". 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 On Thu, 14 Jan 1999 nih-image-d-request@io.ece.drexel.edu wrote: [NON-Text Body part not included] From nih-image-request@io.ece.drexel.edu Thu Jan 14 20:24 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA04598 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 20:24:27 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 20:24:27 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: School of Biological Sciences To: pauln@usm.maine.edu, nih-image@io.ece.drexel.edu Date: Fri, 15 Jan 1999 12:03:36 GMT+1100 Subject: Re: Progressive Scan CCD and Board Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"Rks3b2.0.OR.2Dfds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/814 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 4734 >Received: from SpoolDir by RNA (Mercury 1.44); 15 Jan 99 01:33:12 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.44) with ESMTP; > 15 Jan 99 01:33:09 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id JAA07595; > Thu, 14 Jan 1999 09:32:17 -0500 (EST) >Resent-Date: Thu, 14 Jan 1999 09:32:17 -0500 (EST) >Mime-Version: 1.0 >Content-Type: text/plain; charset="us-ascii" ; format="flowed" >X-Sender: pauln@maine.maine.edu >Message-Id: >Date: Thu, 14 Jan 1999 09:15:44 -0500 >To: nih-image@io.ece.drexel.edu >From: Paul Nakroshis >Subject: Progressive Scan CCD and Board >Resent-Message-ID: <"H2Alk3.0.hG1.PmVds"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/801 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Hello, > >I am in the process of setting up a granular physics lab and need to >get a progressive scan ccd camera and a suitable board for the MAC. >Currently, I am thinking about getting a Pulnix TM-9701 camera and am >searching for a suitable capture board (not successfully yet)that >will allow me to control operation of the camera from within my own C >or C++ program. Jim Rowell from JKN Electronics told me to look for a >PCI Bus Master frame grabber board and this board would likely come >with C/C++ programming API's that I could use. > >1) Does anyone have any experience with Pulnix cameras? Can you recommend them? >2) Any advice on frame grabber boards for a PowerMac 9600 that will >allow me to digitize to disk directly and have complete control over >the camera? >3) Would I be able to simultaneously take other data from a seperate >I/O board, or will the camera take over the computer and prevent this? >4) should I give up hope finding a suitable MAC video board and get a >windows machine (where these boards are easy to find) or is their a >viable Linux alternative? > >Any wisdom is greatly appreciated! > >-paul > >================================================================= >Paul Nakroshis pauln@usm.maine.edu >Department of Physics http://www.usm.maine.edu/~pauln/ >Room 252 Science Building 207.780.4158 (OFFICE) >University of Southern Maine 207.780.5607 (FAX) >PO Box 9300 >Portland, ME 04104-9300 >================================================================= > I looked up Pulnix TM-9701 out of interest to see why you might choose it and found: "____________________ http://www.subtechnique.com/noframes/pulnix/tm_9701.html The PULNiX TM-9701 is a high resolution 768 H x 484 V black and white full frame shutter camera with asynchronous reset capability and uniform MTF (Modulation Transfer Function) characteristics. These cameras are excellent in applications such as bar code reading, on-line inspection, gauging, character reading, high definition graphics, intensified CCD cameras, and detailed surveillance. Added to the wide versatility of this camera is an 8-bit digital signal output through EIA-422. The signal is interlace (RS-170) or progressive scanning (525 lines). It has built-in frame memory for async or integration image capturing without using special frame grabbers. The built-in frame memory can maintain the asynchronously captured full frame image until next VINIT pulse comes in. The output can be either interlace or progressive scanning. Both analog RS-170 format (1 Vp-p, 75 Ohm) and 8 bit digital format ( EIA-422 ) are available from the camera. _____________________" Other sites refer to 8-bit digital output as RS422. Doesn't the existance of 8-bit digital mean that you could control the camera without a frame grabber? The writeup on the color TMC-9700 refers to and RS232 interface for more complex control as opposed to simple VINIT setting and an optional RS422 interface card. I am not a hardware person so I dont know EIA-422 but surely the statement is clear that a frame grabber is unnecessary? or am I missing something (again :-) ? In any case I would compare with camera/framefrabber combination at http://www.scioncorp.com/frames/fr_scion_products.htm 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 Jan 14 23:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA25043 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 23:23:53 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 23:23:53 -0500 (EST) From: SolamereTG@aol.com Message-ID: Date: Thu, 14 Jan 1999 23:05:15 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Progressive Scan CCD and Board Content-transfer-encoding: 7bit X-Mailer: AOL 4.0 for Windows 95 sub 226 Resent-Message-ID: <"VqI6T1.0.Sa5.cxhds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/815 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1538 The TM-9701 provides both an analog video signal out via a BNC connector and a digitized signal at 8 bit depth via a high density "airbourne connector". This camera like almost all "digital" cameras starts with the analog CCD as the sensor. Progressive scan means that the camera captures all of the vertical lines at one time (1/30 sec integration) rather than as an interlaced (alternating) set of odd and even lines. The analog charge level stored at each pixel is converted with the camera's built-in 8 bit A/D converter and shifted to a frame buffer where it can be clocked out to a digital frame grabber (yes, you still need a frame grabber of some sort to bring the 8 bit digitized image into your computer). The digitized image is also transferred to a second frame buffer where it can be held (until the next Vinit) and continuously converted at 30 fps, (60 interlaced fields per second) back to analog RS-170 video for recording, displaying and (yes) re-digitizing with your analog frame grabber. The advantage to doing this is that when you are integrating on-chip you don't need to look at a blinking display on your analog monitor. RS-422 and EIA 422 refer to a general digital format. The cables that carry these signals, the clock rates and the connectors are not standardized and seem to be different for each frame grabber and each camera. We have intensified GEN III+/ IV ICCD cameras that utilize this platform for those interested. George A. Peeters M.D. Solamere Technology Group WWW.SolamereTech.com 801 322-2645 From nih-image-request@io.ece.drexel.edu Thu Jan 14 23:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA27165 for cshtest@io.ece.drexel.edu; Thu, 14 Jan 1999 23:39:11 -0500 (EST) Resent-Date: Thu, 14 Jan 1999 23:39:11 -0500 (EST) Date: Thu, 14 Jan 1999 22:27:30 -0600 (CST) From: "Tim P. LaFave Jr." To: "DrJohnRuss@aol.com"@Sparc5.Microscopy.Com cc: it-list@sparky.uthscsa.edu, nih-image@io.ece.drexel.edu, Microscopy@Sparc5.Microscopy.Com Subject: M6 adhesive for X-sectioning. In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"-_wLC1.0.AF6.4Fids"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/816 X-Loop: nih-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 I have been told to search for "M6", an adhesive which was used in the somewhat distant past for bonding samples for cross-sectioning. ..I cannnot find a company which has even heard of this. Any suggestions as to where I can find it? __ _-==-=_,-. /--`' \_@-@.--< Tim (TJ) LaFave Jr. `--'\ \ <___/. Department of Physics \ \\ " / University of North Carolina, Charlotte >=\\_/`< Charlotte, NC 28223 ____ /= | \_|/ _' `\ _/=== \___/ (704)547-3392 [x4] `___/ //\./=/~\====\ (704)509-6622 [Hm] \ // / | ===: http://www.iit.edu/~lafatim | ._/_,__|_ ==: __ \/ \\ \\`--| / \\ ---------- +*+ ---------- | _ \\: /==:-\ `.__' `-____/ |--|==: Such that the future be theirs \ \ ===\ :==:`-' to shape and direct. _> \ ===\ /==/ ----------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Fri Jan 15 04:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05065 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 04:41:24 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 04:41:24 -0500 (EST) X-Sender: elk@129.233.21.18 Message-Id: Mime-Version: 1.0 Date: Fri, 15 Jan 1999 10:28:05 +0100 To: nih-image@io.ece.drexel.edu From: Ben Elkin Subject: digital camera tested Resent-Message-ID: <"v-Xgy2.0.Lf.Zcmds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/817 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2112 Dear imagers, a few days ago we received a CMOS PRO (TM) camera from Sound Vision Inc. ( http://www.soundvisioninc.com./ ), and I have made the (very) first tests. Actually I wanted to write more and later, but I see the topic being duscussed on the list right now. First, thanks to all who responded to my questions a couple of months ago and especially to Bill Miller who brought this modell to my attention. * This is a camera for still images only * The first impressions are good. The camera is a digital one, which means that the signal from the CCD is converted *once* into the digital form and transferred digitally to the computer via SCSI interface. This means: 1. No pixel jitter 2. You don't need any frame grabber. 3. You can use it with Mac or Wintel. 4. From 2. and 3. follows that you don't need a dedicated computer. You can use one which happens to stand where you take your pictures. The software (plugin for Photoshop) is OK, but (on a Mac) you have to allocate at least 20 MB to Photoshop. I haven't yet tested the plugin it with NIH-Image. Camera uses an internal rotating RGB filter wheel with a monochrome sensor (and trades off the aquisition speed for the image quality). The resolution (non-interpolated) is 800*960 (RGB). The camera captures with 10 bit per pixel and color channel, but normally saves as 24 bit RGB. It provides "live" (a couple of frames/sec) video for image ajustment. On a microscopy image produced with this camera I could actually see more details than looking through the microscope objective lens. The camera has C-mount and comes with reasonable accessory if you want. The camera price in USA is below $2000. The user manual is published on the company web site ( http://www.cmospro.com/images/Cp.pdf ). 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-d-request@io.ece.drexel.edu Fri Jan 15 04:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA05754; Fri, 15 Jan 1999 04:45:21 -0500 (EST) Date: Fri, 15 Jan 1999 04:45:21 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901150945.EAA05754@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #11 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/11 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: 29696 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 11 Today's Topics: Progressive Scan CCD and Board [ Paul Nakroshis ] Re: digital camera [ DrJohnRuss@aol.com ] Stereology on the Mac [ "Harvey J. Karten" ] Re: Frame grabber for new G3 towers? [ Jennifer Swann ] RE: Frame grabber for new G3 towers? [ "Heeschen, Bill (WA)" ] Re: Frame grabber for new G3 towers? [ Jeremy Brown ] ------------------------------ Date: Thu, 14 Jan 1999 09:15:44 -0500 From: Paul Nakroshis To: nih-image@io.ece.drexel.edu Subject: Progressive Scan CCD and Board Message-Id: Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hello, I am in the process of setting up a granular physics lab and need to get a progressive scan ccd camera and a suitable board for the MAC. Currently, I am thinking about getting a Pulnix TM-9701 camera and am searching for a suitable capture board (not successfully yet)that will allow me to control operation of the camera from within my own C or C++ program. Jim Rowell from JKN Electronics told me to look for a PCI Bus Master frame grabber board and this board would likely come with C/C++ programming API's that I could use. 1) Does anyone have any experience with Pulnix cameras? Can you recommend them? 2) Any advice on frame grabber boards for a PowerMac 9600 that will allow me to digitize to disk directly and have complete control over the camera? 3) Would I be able to simultaneously take other data from a seperate I/O board, or will the camera take over the computer and prevent this? 4) should I give up hope finding a suitable MAC video board and get a windows machine (where these boards are easy to find) or is their a viable Linux alternative? Any wisdom is greatly appreciated! -paul ================================================================= Paul Nakroshis pauln@usm.maine.edu Department of Physics http://www.usm.maine.edu/~pauln/ Room 252 Science Building 207.780.4158 (OFFICE) University of Southern Maine 207.780.5607 (FAX) PO Box 9300 Portland, ME 04104-9300 ================================================================= ------------------------------ Date: Thu, 14 Jan 1999 09:40:06 +0000 From: Marcia Goldfarb To: Nih-image Subject: digital camera Message-ID: <369DBB70.6804E7E5@maine.rr.com> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I use Nih-Image to quantitate spots on 2-D gels. I have purchased a digital camera (Olympus D-620L) and now use this to input the gel image into computer. I can down load directly into Photoshop 3.0. Can someone who understands the differences in computer languages help me to optimize the steps. The downloaded camera image is JPEG. I do multiple steps in Photoshop with IPTK plugins to isolate areas of interest for transfer to Nih-Image. Is it best to leave the image in JPEG or save it in Photoshop 3.0 or go directly to tiff for this work. Final product is saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. Thank you for help Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 Email: anatekep@maine.rr.com ------------------------------ Date: Thu, 14 Jan 1999 10:56:56 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: AppleScript Support Message-Id: Content-Type: text/plain; charset="us-ascii" >Is there any chance that Applescript will be supported in the future? It >would be great if we could have more flexibility automating the behaviour >of Image and its interaction with other apps. I have no plans to add Applescript support to NIH Image. I spend most of my free time these days working on ImageJ (http://rsb.info.nih.gov/ij/). -wayne ------------------------------ Date: Thu, 14 Jan 1999 09:54:36 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: digital camera Message-ID: <365d90e5.369e052c@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/14/99 9:50:36 AM, you wrote: >I use Nih-Image to quantitate spots on 2-D gels. I have purchased a >digital camera (Olympus D-620L) and now use this to input the gel image >into computer. I can down load directly into Photoshop 3.0. Can someone >who understands the differences in computer languages help me to >optimize the steps. The downloaded camera image is JPEG. I do multiple >steps in Photoshop with IPTK plugins to isolate areas of interest for >transfer to Nih-Image. Is it best to leave the image in JPEG or save it >in Photoshop 3.0 or go directly to tiff for this work. Final product is >saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. It doesn't matter. But not for a good reason. Converting the image back to tif will not recover the lost data from the jpeg compression. jpeg changes pixel values, and you will find that the brightness and dimensions of features will be altered in the process. I realize you already have this camera and probably can't return it, but PLEASE folks, don't let anyone else make this kind of mistake. Get a camera that transmits or stores images without lossy compression. jpeg is fine for pictures of the kids, but not image analysis where the pixel values are used for anything. John Russ ------------------------------ Date: Thu, 14 Jan 1999 07:13:38 -0800 From: "Harvey J. Karten" To: nih-image@io.ece.drexel.edu Subject: Stereology on the Mac Message-ID: <369E09A1.F65AA474@sdcc12.ucsd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The recent thread on Stereology on the Mac can be addressed directly by looking at NeuroZoom. This is a Freeware Program written by Warren Young his colleagues at Scripps Research Foundation. It was developed as part of the Human Brain Project, and is freely available. It is very sophisticated, with a very distinctly Mac type of interface. You will need a motorized stage (as with all such programs) to use it most efficiently. 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: Thu, 14 Jan 1999 10:22:02 -0500 From: Bill Miller To: nih-image@io.ece.drexel.edu Subject: Re: digital camera Message-Id: <3.0.5.32.19990114102202.007edd10@mohawk.net> Content-Type: text/plain; charset="us-ascii" Be VERY carful about quantifying JPEG images - it is NOT a lossless compression either spatially or intensity wise. At 09:40 AM 1/14/99 +0000, you wrote: >I use Nih-Image to quantitate spots on 2-D gels. I have purchased a >digital camera (Olympus D-620L) and now use this to input the gel image >into computer. I can down load directly into Photoshop 3.0. Can someone >who understands the differences in computer languages help me to >optimize the steps. The downloaded camera image is JPEG. I do multiple >steps in Photoshop with IPTK plugins to isolate areas of interest for >transfer to Nih-Image. Is it best to leave the image in JPEG or save it >in Photoshop 3.0 or go directly to tiff for this work. Final product is >saved in tiff for transfer to NIH-Image. Perhaps, it doesn't matter. > >Thank you for help > >Marcia Goldfarb >Anatek-EP >17 Bishop St >Portland,ME 04103 > >Email: anatekep@maine.rr.com > > > ------------------------------ Date: Thu, 14 Jan 1999 11:22:41 -0500 From: Jennifer Swann To: nih-image@io.ece.drexel.edu Subject: Re: Frame grabber for new G3 towers? Message-ID: <369E19D0.10D3@lehigh.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit I have heard that the Targas 2000 is the fram grabber that works well with apples - I do not know their copatability with the new series of G3s but you migh contac them - they have a web site! Jennifer Swann\ David Linker wrote: > > We need to digitize black and white S-VHS (NTSC) video from video tape. We > currently use a 7100AV, with the digitizer set to 8 bit gray scale images, > at 640x480, using NIHImage. This is perfectly adequate for our work, but > the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > > We received the funding, but Apple has apparently discontinued the line, > and the video capture cards. The new G3's look great in terms of > performance, but I am told that there is no video frame grabber from Apple > for them. > > I looked in the catalogs I get of Apple hardware, which used to have > several options for video capture, but see none now. > > I would appreciate any pointers to companies/hardware that would meet this > need. Also, any experiences using the hardware. Our application depends on > measuring distances on the screen, not on absolute image densities. We have > a significant number of macros that we use, so we would prefer to continue > using NIHImage. I would like to get one of the fastest new G3's, but then > will not have a very large budget for a frame grabber. We do not need to > grab continuous video. > > Thank you, > > David Linker ------------------------------ Date: Thu, 14 Jan 1999 10:57:53 -0500 From: "Heeschen, Bill (WA)" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Frame grabber for new G3 towers? Message-Id: Content-Type: text/plain David/list It does appear that Apple is leaving the built-in digitizer business, at least according to a spot check of their web page. I can readily recommend the Scion LG-3 frame grabber for $900. It only supports 8-bit grayscale and 24-bit RGB color (they do have composite color framegrabbers, too), but does it very well and is nicely supported from NIH Image. supports 4 separate video lines, plus digital control line I/O. Also works very well in Windows machines with Scion Image, just not quite as elegantly.... No commercial interest, just an obviously satisfied customer! Bill Heeschen Microscopy Group Dow Chemical ------------------------------ Date: Thu, 14 Jan 1999 18:24:55 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Object-Image and AppleScript Message-Id: Content-Type: text/plain; charset="us-ascii" I respond to the question of Alessandro Abate with a modified subject title. I have started to implement AppleScript into Object-Image1.62n9. I'll put it onto my server within a month or two. However, it can be obtained right now on request by anyone who wants to try it out and give me some feedback. The examples mentioned below are already working. There are two different methods of interaction: A) an AppleScript tells Object-Image to execute an already loaded macro. In the example below, a script asks Object-Image to say "Hello AppleScript!" B) an AppleScript is embedded into an NIH macro text and is executed from within Object-Image. In the example below, Object-Image empties the trash. The today's version has the following limitations: - Only one AppleScript can be embedded; - Besides the clipboard, no parameters can be passed - The embedded script has no access yet to the macro variables - Error messages are not yet supported, so you better try a script out with a script editor before embedding it. - RunMacro always executes the first macro, ignoring the macro name - It works only on PowerMacs Macro text in Object-Image: =========================== macro 'Say Hello'; begin PutMessage('Hello AppleScript!'); end; macro 'Empty Trash' begin PutMessage('Now emptying the trash...'); BeginScript tell application "Finder" Empty Trash end tell EndScript; PutMessage('The trash is empty'); end; Script Text in Script Editor ============================ tell application "Object-Image" activate runmacro "Say Hello" end tell 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: Thu, 14 Jan 1999 18:35:43 +0000 From: "P.M. Houpt" To: nih-image@io.ece.drexel.edu Subject: upgrading mac. 7100 AV. Message-ID: <369E38FC.79B4@wxs.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Imagers, (David) I use the 7100 AV powermac (Nubus mac)) for grabbing microscopical images. The AV card works very good for color images , (for B/W I use the LG3 card of Scion. Last summer I upgraded the 7100/AV with the SONNET CRESCENDO G3 PROCESSOR UPGRADE CARD.INCLUDED THE VIDEO ADAPTOR KIT FOR THE AV CARD. Since then I work with the 7100/AV like a modern G3 (214 MHz) with no problems at all. Look for Sonnet on the internet hhtp://www.sonnettech.com Like Bill I have no commercial interest, just an obviously satisfied customer! Best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 00703504466 ------------------------------ Date: Thu, 14 Jan 1999 17:50:06 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: Frame grabber for new G3 towers? Message-ID: <369E2E2D.57E6C9AA@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Ben Elkin wrote: > David Linker wrote: > >We need to digitize black and white S-VHS (NTSC) video from video tape. We > >currently use a 7100AV, with the digitizer set to 8 bit gray scale images, > >at 640x480, using NIHImage. This is perfectly adequate for our work, but > >the 7100 is slow, and we applied for funding for a G3 tower (333MHz). > > > >We received the funding, but Apple has apparently discontinued the line, > >and the video capture cards. The new G3's look great in terms of > >performance, but I am told that there is no video frame grabber from Apple > >for them. > > > > We have recently installed a Newer Technology ( http://www.newertech.com ) > MAXpowr G3 processor upgrade card onto an old NuBus computer. A card with 1 > MB backside cache and 240 MHz processor costs below 1000$ even in Germany. > It made a pretty fast modern computer from an old one, and we can continue > to use our NuBus framegrabber from Scion. > > The only problem you are going to have in this case: what to do with the > rest of the funding :-) > > 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 There are two Firewire ports in the new G3 macs, but have yet to hear of a scientific camera that supports firewire. Anyone know a good reason for this? ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Thu, 14 Jan 1999 10:06:25 -0800 (PST) From: wpchan@socrates.berkeley.edu To: nih-image@io.ece.drexel.edu Subject: Scion LG3 and Mac G3 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII A few months ago, I posted about not being able to capture at 29.97 fps with "make movie/blind capture" on a G3 tower. The problem is now solved by a hardware upgrade from Scion. After a few rounds of calling Scion's tech support which really didn't provide any useful help, Scion finally admitted that there is a hardware problem when using the LG3 in real time capture on a G3 Mac. The upgrade took about may be 2 weeks (could be faster, if not for the holidays). And now we can allocate about 500 MB to Image and capture 1000 frames per capture at 640x480 and video rate. --Pang (Wai Pang Chan, wpchan@socrates.berkeley.edu) ------------------------------ Date: Thu, 14 Jan 1999 12:39:33 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: Stereology Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Depending upon what you need, there are a few routes for Mac stereology. A commercial package called MacStereology might still be around. there are plug-ins for Photoshop and IPLab, plus some Image macros, written by John Russ. the first versions are on the Image ftp site, there are probably updates on his image processing CD. There is another set of stereology macros in the user-contrib folder at the Image ftp site. These are entitled "Cavalieri3". 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 On Thu, 14 Jan 1999 nih-image-d-request@io.ece.drexel.edu wrote: [NON-Text Body part not included] ------------------------------ Date: Fri, 15 Jan 1999 12:03:36 GMT+1100 From: GJOSS@rna.bio.mq.edu.au To: pauln@usm.maine.edu, nih-image@io.ece.drexel.edu Subject: Re: Progressive Scan CCD and Board Message-ID: >Received: from SpoolDir by RNA (Mercury 1.44); 15 Jan 99 01:33:12 +1100 >Return-path: >Received: from io.ece.drexel.edu (144.118.32.3) by rna.bio.mq.edu.au (Mercury >1.44) with ESMTP; > 15 Jan 99 01:33:09 +1100 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id JAA07595; > Thu, 14 Jan 1999 09:32:17 -0500 (EST) >Resent-Date: Thu, 14 Jan 1999 09:32:17 -0500 (EST) >Mime-Version: 1.0 >Content-Type: text/plain; charset="us-ascii" ; format="flowed" >X-Sender: pauln@maine.maine.edu >Message-Id: >Date: Thu, 14 Jan 1999 09:15:44 -0500 >To: nih-image@io.ece.drexel.edu >From: Paul Nakroshis >Subject: Progressive Scan CCD and Board >Resent-Message-ID: <"H2Alk3.0.hG1.PmVds"@io> >Resent-From: nih-image@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu >X-Mailing-List: archive/latest/801 >X-Loop: nih-image@biomed.drexel.edu >Precedence: list >Resent-Sender: nih-image-request@io.ece.drexel.edu >X-PMFLAGS: 34078848 0 > >Hello, > >I am in the process of setting up a granular physics lab and need to >get a progressive scan ccd camera and a suitable board for the MAC. >Currently, I am thinking about getting a Pulnix TM-9701 camera and am >searching for a suitable capture board (not successfully yet)that >will allow me to control operation of the camera from within my own C >or C++ program. Jim Rowell from JKN Electronics told me to look for a >PCI Bus Master frame grabber board and this board would likely come >with C/C++ programming API's that I could use. > >1) Does anyone have any experience with Pulnix cameras? Can you recommend them? >2) Any advice on frame grabber boards for a PowerMac 9600 that will >allow me to digitize to disk directly and have complete control over >the camera? >3) Would I be able to simultaneously take other data from a seperate >I/O board, or will the camera take over the computer and prevent this? >4) should I give up hope finding a suitable MAC video board and get a >windows machine (where these boards are easy to find) or is their a >viable Linux alternative? > >Any wisdom is greatly appreciated! > >-paul > >================================================================= >Paul Nakroshis pauln@usm.maine.edu >Department of Physics http://www.usm.maine.edu/~pauln/ >Room 252 Science Building 207.780.4158 (OFFICE) >University of Southern Maine 207.780.5607 (FAX) >PO Box 9300 >Portland, ME 04104-9300 >================================================================= > I looked up Pulnix TM-9701 out of interest to see why you might choose it and found: "____________________ http://www.subtechnique.com/noframes/pulnix/tm_9701.html The PULNiX TM-9701 is a high resolution 768 H x 484 V black and white full frame shutter camera with asynchronous reset capability and uniform MTF (Modulation Transfer Function) characteristics. These cameras are excellent in applications such as bar code reading, on-line inspection, gauging, character reading, high definition graphics, intensified CCD cameras, and detailed surveillance. Added to the wide versatility of this camera is an 8-bit digital signal output through EIA-422. The signal is interlace (RS-170) or progressive scanning (525 lines). It has built-in frame memory for async or integration image capturing without using special frame grabbers. The built-in frame memory can maintain the asynchronously captured full frame image until next VINIT pulse comes in. The output can be either interlace or progressive scanning. Both analog RS-170 format (1 Vp-p, 75 Ohm) and 8 bit digital format ( EIA-422 ) are available from the camera. _____________________" Other sites refer to 8-bit digital output as RS422. Doesn't the existance of 8-bit digital mean that you could control the camera without a frame grabber? The writeup on the color TMC-9700 refers to and RS232 interface for more complex control as opposed to simple VINIT setting and an optional RS422 interface card. I am not a hardware person so I dont know EIA-422 but surely the statement is clear that a frame grabber is unnecessary? or am I missing something (again :-) ? In any case I would compare with camera/framefrabber combination at http://www.scioncorp.com/frames/fr_scion_products.htm 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, 14 Jan 1999 23:05:15 EST From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Progressive Scan CCD and Board Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit The TM-9701 provides both an analog video signal out via a BNC connector and a digitized signal at 8 bit depth via a high density "airbourne connector". This camera like almost all "digital" cameras starts with the analog CCD as the sensor. Progressive scan means that the camera captures all of the vertical lines at one time (1/30 sec integration) rather than as an interlaced (alternating) set of odd and even lines. The analog charge level stored at each pixel is converted with the camera's built-in 8 bit A/D converter and shifted to a frame buffer where it can be clocked out to a digital frame grabber (yes, you still need a frame grabber of some sort to bring the 8 bit digitized image into your computer). The digitized image is also transferred to a second frame buffer where it can be held (until the next Vinit) and continuously converted at 30 fps, (60 interlaced fields per second) back to analog RS-170 video for recording, displaying and (yes) re-digitizing with your analog frame grabber. The advantage to doing this is that when you are integrating on-chip you don't need to look at a blinking display on your analog monitor. RS-422 and EIA 422 refer to a general digital format. The cables that carry these signals, the clock rates and the connectors are not standardized and seem to be different for each frame grabber and each camera. We have intensified GEN III+/ IV ICCD cameras that utilize this platform for those interested. George A. Peeters M.D. Solamere Technology Group WWW.SolamereTech.com 801 322-2645 ------------------------------ Date: Thu, 14 Jan 1999 22:27:30 -0600 (CST) From: "Tim P. LaFave Jr." To: "DrJohnRuss@aol.com"@Sparc5.Microscopy.Com cc: it-list@sparky.uthscsa.edu, nih-image@io.ece.drexel.edu, Microscopy@Sparc5.Microscopy.Com Subject: M6 adhesive for X-sectioning. Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I have been told to search for "M6", an adhesive which was used in the somewhat distant past for bonding samples for cross-sectioning. ..I cannnot find a company which has even heard of this. Any suggestions as to where I can find it? __ _-==-=_,-. /--`' \_@-@.--< Tim (TJ) LaFave Jr. `--'\ \ <___/. Department of Physics \ \\ " / University of North Carolina, Charlotte >=\\_/`< Charlotte, NC 28223 ____ /= | \_|/ _' `\ _/=== \___/ (704)547-3392 [x4] `___/ //\./=/~\====\ (704)509-6622 [Hm] \ // / | ===: http://www.iit.edu/~lafatim | ._/_,__|_ ==: __ \/ \\ \\`--| / \\ ---------- +*+ ---------- | _ \\: /==:-\ `.__' `-____/ |--|==: Such that the future be theirs \ \ ===\ :==:`-' to shape and direct. _> \ ===\ /==/ ----------------------------------------------------------------- ------------------------------ Date: Fri, 15 Jan 1999 10:28:05 +0100 From: Ben Elkin To: nih-image@io.ece.drexel.edu Subject: digital camera tested Message-Id: Content-Type: text/plain; charset="us-ascii" Dear imagers, a few days ago we received a CMOS PRO (TM) camera from Sound Vision Inc. ( http://www.soundvisioninc.com./ ), and I have made the (very) first tests. Actually I wanted to write more and later, but I see the topic being duscussed on the list right now. First, thanks to all who responded to my questions a couple of months ago and especially to Bill Miller who brought this modell to my attention. * This is a camera for still images only * The first impressions are good. The camera is a digital one, which means that the signal from the CCD is converted *once* into the digital form and transferred digitally to the computer via SCSI interface. This means: 1. No pixel jitter 2. You don't need any frame grabber. 3. You can use it with Mac or Wintel. 4. From 2. and 3. follows that you don't need a dedicated computer. You can use one which happens to stand where you take your pictures. The software (plugin for Photoshop) is OK, but (on a Mac) you have to allocate at least 20 MB to Photoshop. I haven't yet tested the plugin it with NIH-Image. Camera uses an internal rotating RGB filter wheel with a monochrome sensor (and trades off the aquisition speed for the image quality). The resolution (non-interpolated) is 800*960 (RGB). The camera captures with 10 bit per pixel and color channel, but normally saves as 24 bit RGB. It provides "live" (a couple of frames/sec) video for image ajustment. On a microscopy image produced with this camera I could actually see more details than looking through the microscope objective lens. The camera has C-mount and comes with reasonable accessory if you want. The camera price in USA is below $2000. The user manual is published on the company web site ( http://www.cmospro.com/images/Cp.pdf ). 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 -------------------------------- End of nih-image-d Digest V99 Issue #11 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jan 15 05:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10638 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 05:21:44 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 05:21:44 -0500 (EST) Message-ID: <369F8504.4071@bme.ym.edu.tw> Date: Fri, 15 Jan 1999 14:39:07 +0000 From: Woeichyn Chu Reply-To: wchu@bme.ym.edu.tw Organization: National Yang Ming University X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Fuji PG-3000 digital printer References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"t5nJn1.0.AA2.wEnds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/818 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=big5 Content-Length: 875 Has anyone had experience with the Fuji high resolution digital printer (model PG-3000)? We are considering buying such a printer, but do not know its performance compare to, say Kodak 8650ps or Tektronix Phaser 450? What we do know is the price for Fuji PG-3000 is about $20k, which is about 30% higher than the Kodak and 45% more than the Tektronix. Does it worth every penny we paid for? Thanks for the info. -- Sincerely yours, Woeichyn Chu, Ph.D. Associate Professor Institute of Biomedical Engineering National Yang Ming University '__|__ _ /__\__ -|=|- / Shih-Pai, Taipei, Taiwan 112 /___|___ | |'|__|__ |+| --'-. Tel: 886.2.28267025 / | \ |_| |__|__ -+- / | Fax: 886.2.28210847 / | \ |__|__ -+- / / Email: wchu@bme.ym.edu.tw ' `| ` | ---' _/ From nih-image-request@io.ece.drexel.edu Fri Jan 15 07:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA28912 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 07:50:48 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 07:50:48 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Fri, 15 Jan 1999 07:28:32 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: digital camera tested Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"9wt7M1.0.5O6.XIpds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/819 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1088 In a message dated 1/15/99 4:34:46 AM, elk@IGB.FhG.de writes: >The camera is a digital one, which means >that the signal from the CCD is converted *once* into the digital form >and transferred digitally to the computer Of course, the camera is CMOS not CCD, so there is a minor error here. But the consequence needs some testing, if the author would care to do it. CCD chips work by building up a voltage in proportion to the amount of light that arrives. CMOS works the other way, by bleeding off charge as light photons strike the detector. In a CCD camera the noise is ideally proportional to brightness, which means that dark areas are not too noisy (and in bright areas it often doesn't show up). The typical problem with CMOS is higher overall noise (especially with long exposure times), less effective dynamic range, and a lot more noise in the dark portions of the image (in a color image this is often in the blue channel where there is the least intensity). Some tests of this camera (which I have not tried myself) compared to a good CCD digital camera would be welcome. From nih-image-request@io.ece.drexel.edu Fri Jan 15 09:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA12361 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 09:40:07 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 09:40:07 -0500 (EST) Message-ID: <19990115141832.20020.qmail@hotmail.com> X-Originating-IP: [130.241.84.177] From: "Wenhua Wang" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #11 Date: Fri, 15 Jan 1999 06:18:32 PST Mime-Version: 1.0 Resent-Message-ID: <"wruU81.0.0M2.Xvqds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/820 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 2340 Hi, I am sorry to bother you. Anyhow, please tell me how to read multipart/digest. I hope this is not a stupid question. Sincerely, Wenhua Wang >From nih-image-d-request@io.ece.drexel.edu Fri Jan 15 01:39:50 1999 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id EAA03131; > Fri, 15 Jan 1999 04:29:02 -0500 (EST) >Date: Fri, 15 Jan 1999 04:29:02 -0500 (EST) >From: nih-image-d-request@io.ece.drexel.edu >Message-Id: <199901150929.EAA03131@io.ece.drexel.edu> >Subject: nih-image-d Digest V99 #11 >X-Loop: nih-image-d@biomed.drexel.edu >X-Mailing-List: archive/volume99/11 >Precedence: list >MIME-Version: 1.0 >Content-Type: multipart/digest; boundary="----------------------------" >To: nih-image-d@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu > >Content-Type: text/plain > >nih-image-d Digest Volume 99 : Issue 11 > >Today's Topics: > Progressive Scan CCD and Board [ Paul Nakroshis digital camera [ Marcia Goldfarb Re: AppleScript Support [ Wayne Rasband ] > Re: digital camera [ DrJohnRuss@aol.com ] > Stereology on the Mac [ "Harvey J. Karten" Re: digital camera [ Bill Miller ] > Re: Frame grabber for new G3 towers? [ Jennifer Swann ] > RE: Frame grabber for new G3 towers? [ "Heeschen, Bill (WA)" Object-Image and AppleScript [ Norbert Vischer upgrading mac. 7100 AV. [ "P.M. Houpt" ] > Re: Frame grabber for new G3 towers? [ Jeremy Brown Scion LG3 and Mac G3 [ wpchan@socrates.berkeley.edu ] > Re: Stereology [ "G. Macdonald" Re: Progressive Scan CCD and Board [ GJOSS@rna.bio.mq.edu.au ] > Re: Progressive Scan CCD and Board [ SolamereTG@aol.com ] > M6 adhesive for X-sectioning. [ "Tim P. LaFave Jr." digital camera tested [ Ben Elkin ] > ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Fri Jan 15 11:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA29791 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 11:59:02 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 11:59:02 -0500 (EST) Date: Fri, 15 Jan 1999 11:37:07 -0500 (EST) 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: Importing Images TIFF tags Resent-Message-ID: <"tQjP9.0.ZR6.Utsds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/821 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 779 Greg Joss's post "Re: Importing Images with fixed windows" showed how to search for text in a TIFF header. Is there a way to read TIFF tags from Image? Scanalytics 16-bit TIFFs have a tag (#281, entitled MaxSampleValue) which contains the maximum intensity value of the stack. Tiffsniff (in the NIH Image zippy) reads all the Tags in a TIFF, but doesn't pass them to Image (and gets this particular tag wrong a lot of the time). GraphicConverter displays some of the Tags. Thanks in advance. Harry 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-request@io.ece.drexel.edu Fri Jan 15 13:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA09177 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 13:16:07 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 13:16:07 -0500 (EST) X-Sender: dameh@mail.execpc.com Message-Id: In-Reply-To: <19990115141832.20020.qmail@hotmail.com> Mime-Version: 1.0 Date: Fri, 15 Jan 1999 11:47:42 -0600 To: nih-image@io.ece.drexel.edu From: "David A. Meh" Subject: Image as peak integrator Resent-Message-ID: <"uSHEa2.0.kL1.8ztds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/822 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 540 Hi, We have a very old HPLC without a peak integrator. I thought that possibly a scan of the relevant peaks could be converted using the Line Plots>Data macro and then the gel plotting mcaros would allow me to integrate the area under the peaks, but the gel plot macros don't recognize the plot. This may be more effort than it is worth, as the "old" method of cutting out the paper and weighing the peaks will work. Please give me your comments and suggestions. Thank you, David A. Meh Madness takes its toll. Please have exact change From nih-image-request@io.ece.drexel.edu Fri Jan 15 13:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA10082 for cshtest@io.ece.drexel.edu; Fri, 15 Jan 1999 13:23:02 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 13:23:02 -0500 (EST) Subject: Re: Frame grabber for new G3 towers? Date: Fri, 15 Jan 99 12:56:13 -0500 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: "david linker et al" Mime-Version: 1.0 Message-ID: <1A524540A2@qc1.qc.edu> Resent-Message-ID: <"Jk_Cp3.0.ej1.Q9uds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/823 X-Loop: nih-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 there is a new apple video capture card (reportedly much better than their older one) that DOES work with the g3. at least that's what was promised to me by our campus mac manager. From nih-image-request@io.ece.drexel.edu Fri Jan 15 19:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA19865; Fri, 15 Jan 1999 19:07:22 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 19:07:22 -0500 (EST) Date: Fri, 15 Jan 1999 18:51:51 -0400 From: Kenneth Cohen Subject: unsubscribe X-Sender: kcohen@envmed.rochester.edu To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"GQMgi2.0.aF4.YIzds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/826 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 15 --Ken From nih-image-request@io.ece.drexel.edu Fri Jan 15 19:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA20011; Fri, 15 Jan 1999 19:08:25 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 19:08:25 -0500 (EST) Message-ID: <369FC64C.91090783@mc.rochester.edu> Date: Fri, 15 Jan 1999 18:50:54 -0400 From: Kenneth Cohen Reply-To: kcohen@mc.rochester.edu Organization: University of Rochester X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: subscribe Content-Transfer-Encoding: 7bit Resent-Message-ID: <"8c-4W.0.sC4.iHzds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/825 X-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: 2 From nih-image-request@io.ece.drexel.edu Fri Jan 15 19:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA20066; Fri, 15 Jan 1999 19:08:37 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 19:08:37 -0500 (EST) Date: Fri, 15 Jan 1999 18:49:18 -0400 From: Kenneth Cohen Subject: unsubscribe X-Sender: kcohen@envmed.rochester.edu To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"KXVBo3.0.p84.0Gzds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/824 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 15 --Ken From nih-image-request@io.ece.drexel.edu Fri Jan 15 19:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA20067; Fri, 15 Jan 1999 19:08:38 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 19:08:38 -0500 (EST) Message-ID: <369FC6D0.8D0ECC7E@mc.rochester.edu> Date: Fri, 15 Jan 1999 18:53:10 -0400 From: Kenneth Cohen Reply-To: kcohen@mc.rochester.edu Organization: University of Rochester X-Mailer: Mozilla 4.05 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: subscribe Content-Transfer-Encoding: 7bit Resent-Message-ID: <"_2Cle3.0.mI4.bJzds"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/827 X-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: 2 From nih-image-d-request@io.ece.drexel.edu Fri Jan 15 21:00 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA02447; Fri, 15 Jan 1999 21:00:27 -0500 (EST) Date: Fri, 15 Jan 1999 21:00:27 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901160200.VAA02447@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #12 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/12 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: 10826 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 12 Today's Topics: Fuji PG-3000 digital printer [ Woeichyn Chu ] Re: digital camera tested [ DrJohnRuss@aol.com ] Re: nih-image-d Digest V99 #11 [ "Wenhua Wang" ] Re: Frame grabber for new G3 towers? [ "Jared L. Rifkin" To: nih-image@io.ece.drexel.edu Subject: Fuji PG-3000 digital printer Message-ID: <369F8504.4071@bme.ym.edu.tw> Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Has anyone had experience with the Fuji high resolution digital printer (model PG-3000)? We are considering buying such a printer, but do not know its performance compare to, say Kodak 8650ps or Tektronix Phaser 450? What we do know is the price for Fuji PG-3000 is about $20k, which is about 30% higher than the Kodak and 45% more than the Tektronix. Does it worth every penny we paid for? Thanks for the info. -- Sincerely yours, Woeichyn Chu, Ph.D. Associate Professor Institute of Biomedical Engineering National Yang Ming University '__|__ _ /__\__ -|=|- / Shih-Pai, Taipei, Taiwan 112 /___|___ | |'|__|__ |+| --'-. Tel: 886.2.28267025 / | \ |_| |__|__ -+- / | Fax: 886.2.28210847 / | \ |__|__ -+- / / Email: wchu@bme.ym.edu.tw ' `| ` | ---' _/ ------------------------------ Date: Fri, 15 Jan 1999 07:28:32 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: digital camera tested Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/15/99 4:34:46 AM, elk@IGB.FhG.de writes: >The camera is a digital one, which means >that the signal from the CCD is converted *once* into the digital form >and transferred digitally to the computer Of course, the camera is CMOS not CCD, so there is a minor error here. But the consequence needs some testing, if the author would care to do it. CCD chips work by building up a voltage in proportion to the amount of light that arrives. CMOS works the other way, by bleeding off charge as light photons strike the detector. In a CCD camera the noise is ideally proportional to brightness, which means that dark areas are not too noisy (and in bright areas it often doesn't show up). The typical problem with CMOS is higher overall noise (especially with long exposure times), less effective dynamic range, and a lot more noise in the dark portions of the image (in a color image this is often in the blue channel where there is the least intensity). Some tests of this camera (which I have not tried myself) compared to a good CCD digital camera would be welcome. ------------------------------ Date: Fri, 15 Jan 1999 06:18:32 PST From: "Wenhua Wang" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #11 Message-ID: <19990115141832.20020.qmail@hotmail.com> Content-Type: text/plain Hi, I am sorry to bother you. Anyhow, please tell me how to read multipart/digest. I hope this is not a stupid question. Sincerely, Wenhua Wang >From nih-image-d-request@io.ece.drexel.edu Fri Jan 15 01:39:50 1999 >Received: (from lists@localhost) > by io.ece.drexel.edu (8.8.8/8.8.8) id EAA03131; > Fri, 15 Jan 1999 04:29:02 -0500 (EST) >Date: Fri, 15 Jan 1999 04:29:02 -0500 (EST) >From: nih-image-d-request@io.ece.drexel.edu >Message-Id: <199901150929.EAA03131@io.ece.drexel.edu> >Subject: nih-image-d Digest V99 #11 >X-Loop: nih-image-d@biomed.drexel.edu >X-Mailing-List: archive/volume99/11 >Precedence: list >MIME-Version: 1.0 >Content-Type: multipart/digest; boundary="----------------------------" >To: nih-image-d@io.ece.drexel.edu >Reply-To: nih-image@io.ece.drexel.edu > >Content-Type: text/plain > >nih-image-d Digest Volume 99 : Issue 11 > >Today's Topics: > Progressive Scan CCD and Board [ Paul Nakroshis digital camera [ Marcia Goldfarb Re: AppleScript Support [ Wayne Rasband ] > Re: digital camera [ DrJohnRuss@aol.com ] > Stereology on the Mac [ "Harvey J. Karten" Re: digital camera [ Bill Miller ] > Re: Frame grabber for new G3 towers? [ Jennifer Swann ] > RE: Frame grabber for new G3 towers? [ "Heeschen, Bill (WA)" Object-Image and AppleScript [ Norbert Vischer upgrading mac. 7100 AV. [ "P.M. Houpt" ] > Re: Frame grabber for new G3 towers? [ Jeremy Brown Scion LG3 and Mac G3 [ wpchan@socrates.berkeley.edu ] > Re: Stereology [ "G. Macdonald" Re: Progressive Scan CCD and Board [ GJOSS@rna.bio.mq.edu.au ] > Re: Progressive Scan CCD and Board [ SolamereTG@aol.com ] > M6 adhesive for X-sectioning. [ "Tim P. LaFave Jr." digital camera tested [ Ben Elkin ] > ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Fri, 15 Jan 1999 11:37:07 -0500 (EST) From: hmthomas@med.cornell.edu (Henry M. Thomas) To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) Subject: Importing Images TIFF tags Message-Id: Content-Type: text/plain; charset="us-ascii" Greg Joss's post "Re: Importing Images with fixed windows" showed how to search for text in a TIFF header. Is there a way to read TIFF tags from Image? Scanalytics 16-bit TIFFs have a tag (#281, entitled MaxSampleValue) which contains the maximum intensity value of the stack. Tiffsniff (in the NIH Image zippy) reads all the Tags in a TIFF, but doesn't pass them to Image (and gets this particular tag wrong a lot of the time). GraphicConverter displays some of the Tags. Thanks in advance. Harry 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 ------------------------------ Date: Fri, 15 Jan 1999 11:47:42 -0600 From: "David A. Meh" To: nih-image@io.ece.drexel.edu Subject: Image as peak integrator Message-Id: Content-Type: text/plain; charset="us-ascii" Hi, We have a very old HPLC without a peak integrator. I thought that possibly a scan of the relevant peaks could be converted using the Line Plots>Data macro and then the gel plotting mcaros would allow me to integrate the area under the peaks, but the gel plot macros don't recognize the plot. This may be more effort than it is worth, as the "old" method of cutting out the paper and weighing the peaks will work. Please give me your comments and suggestions. Thank you, David A. Meh Madness takes its toll. Please have exact change ------------------------------ Date: Fri, 15 Jan 99 12:56:13 -0500 From: "Jared L. Rifkin" To: "david linker et al" Subject: Re: Frame grabber for new G3 towers? Message-ID: <1A524540A2@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" there is a new apple video capture card (reportedly much better than their older one) that DOES work with the g3. at least that's what was promised to me by our campus mac manager. ------------------------------ Date: Fri, 15 Jan 1999 18:49:18 -0400 From: Kenneth Cohen To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT --Ken ------------------------------ Date: Fri, 15 Jan 1999 18:50:54 -0400 From: Kenneth Cohen To: nih-image@io.ece.drexel.edu Subject: subscribe Message-ID: <369FC64C.91090783@mc.rochester.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit ------------------------------ Date: Fri, 15 Jan 1999 18:51:51 -0400 From: Kenneth Cohen To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT --Ken ------------------------------ Date: Fri, 15 Jan 1999 18:53:10 -0400 From: Kenneth Cohen To: nih-image@io.ece.drexel.edu Subject: subscribe Message-ID: <369FC6D0.8D0ECC7E@mc.rochester.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit ------------------------------ Date: Fri, 15 Jan 1999 17:42:52 -0800 From: David Linker To: nih-image@io.ece.drexel.edu cc: "Jared L. Rifkin" Subject: Re: Frame grabber for new G3 towers? Message-ID: <1964975.3125410972@huginn.medicine.washington.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline Do you have any information on the name/product number, or any other info? I cannot find anything on the web site, and our local rep says that there is nothing. Any pointers appreciated. DTL --On Fri, Jan 15, 1999 12:56 PM -0500 "Jared L. Rifkin" wrote: > there is a new apple video capture card (reportedly much better than > their older one) that DOES work with the g3. > at least that's what was promised to me by our campus mac manager. > -------------------------------- End of nih-image-d Digest V99 Issue #12 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jan 15 21:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA02647; Fri, 15 Jan 1999 21:01:43 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 21:01:43 -0500 (EST) Date: Fri, 15 Jan 1999 17:42:52 -0800 From: David Linker To: nih-image@io.ece.drexel.edu cc: "Jared L. Rifkin" Subject: Re: Frame grabber for new G3 towers? Message-ID: <1964975.3125410972@huginn.medicine.washington.edu> In-Reply-To: <1A524540A2@qc1.qc.edu> Originator-Info: login-id=dtlinker; server=dtlinker.deskmail.washington.edu X-Mailer: Mulberry (MacOS) [1.4.0, s/n U-300938] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline Resent-Message-ID: <"yRUNJ.0.ZJ7.ww-ds"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/828 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 477 Do you have any information on the name/product number, or any other info? I cannot find anything on the web site, and our local rep says that there is nothing. Any pointers appreciated. DTL --On Fri, Jan 15, 1999 12:56 PM -0500 "Jared L. Rifkin" wrote: > there is a new apple video capture card (reportedly much better than > their older one) that DOES work with the g3. > at least that's what was promised to me by our campus mac manager. > From nih-image-request@io.ece.drexel.edu Fri Jan 15 22:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA11641; Fri, 15 Jan 1999 22:23:12 -0500 (EST) Resent-Date: Fri, 15 Jan 1999 22:23:12 -0500 (EST) Message-ID: <36A00251.793B@pop.uky.edu> Date: Fri, 15 Jan 1999 22:06:56 -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: Re: Fuji PG-3000 digital printer Content-Transfer-Encoding: 7bit Resent-Message-ID: <"8k5i9.0.IM2.o80es"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/829 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 807 In my opinion, Fuji's printer is much better. We have Kodak DS 8650 dye-sub, and I have spent a good part of last month trying to get a decent printout of double-labeled confocal images, without much success. Eventually, I just used Fuji printer in the lab next door. Even though the nominal resolution was the same, the results with Fuji were way better. In addition, Fuji printer has color calibrator, which is a lot of help if you are trying to get exactly what you see on the screen. I don't know what monetary value to put on it (since I didn't have to pay a cent to use it;), but the lack of frustration with Fuji printer might be worth $5k. Besides, per print cost is less with Fuji at close to $2 per half-page compared to around $4 per print on Kodak (including CMYK ribbon). Alex Gimelbrant From nih-image-request@io.ece.drexel.edu Sat Jan 16 11:34 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA12629; Sat, 16 Jan 1999 11:34:14 -0500 (EST) Resent-Date: Sat, 16 Jan 1999 11:34:14 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Sat, 16 Jan 1999 11:21:00 -0500 To: nih-image@io.ece.drexel.edu From: Louie Kerr Subject: Summer Biology Microscopy Technician Position Resent-Message-ID: <"Ghh9N.0.fd2.unBes"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/830 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1528 SUMMER MICROSCOPY TECHNICIAN POSITION AVAILABLE A three month (June, July, and August) position is open for a microscopy oriented technician at the Marine Biological Laboratory, Woods Hole, MA. We would like to attract someone with some knowledge of biological preparative techniques and experience in laser scanning confocal microscopy, TEM, SEM, and/or LM. The technician will assist in the Central Microscopy Facility. The technician's duties will be to check out incoming investigators in the usage of our equipment and then to supervise its continuing usage and to perform contract work for investigators. This may include fixation, embedding, sectioning, scope use, darkroom work, etc. The technician will also provide routine maintenance. This is a short term and scientifically rewarding position. Salary will be in the $7 to $10/hour range. Housing may be available to rent through MBL. For more information, including a more detailed position description, please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. Please apply to: Human Resources, MBL, 7 MBL Street, Woods Hole, MA 02543. or resume@mbl.edu. An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. Louie Kerr Research and Education Support Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 508-289-7273 508-540-6902 (FAX) VISIT OUR WEB SITE: http://www.mbl.edu From nih-image-d-request@io.ece.drexel.edu Sun Jan 17 06:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA28307; Sun, 17 Jan 1999 06:13:45 -0500 (EST) Date: Sun, 17 Jan 1999 06:13:45 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901171113.GAA28307@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #13 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/13 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: 3336 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 13 Today's Topics: Re: Fuji PG-3000 digital printer [ alex gimelbrant ] ------------------------------ Date: Fri, 15 Jan 1999 22:06:56 -0500 From: alex gimelbrant To: NIH-Image mailing list Subject: Re: Fuji PG-3000 digital printer Message-ID: <36A00251.793B@pop.uky.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In my opinion, Fuji's printer is much better. We have Kodak DS 8650 dye-sub, and I have spent a good part of last month trying to get a decent printout of double-labeled confocal images, without much success. Eventually, I just used Fuji printer in the lab next door. Even though the nominal resolution was the same, the results with Fuji were way better. In addition, Fuji printer has color calibrator, which is a lot of help if you are trying to get exactly what you see on the screen. I don't know what monetary value to put on it (since I didn't have to pay a cent to use it;), but the lack of frustration with Fuji printer might be worth $5k. Besides, per print cost is less with Fuji at close to $2 per half-page compared to around $4 per print on Kodak (including CMYK ribbon). Alex Gimelbrant ------------------------------ Date: Sat, 16 Jan 1999 11:21:00 -0500 From: Louie Kerr To: nih-image@io.ece.drexel.edu Subject: Summer Biology Microscopy Technician Position Message-Id: Content-Type: text/plain; charset="us-ascii" SUMMER MICROSCOPY TECHNICIAN POSITION AVAILABLE A three month (June, July, and August) position is open for a microscopy oriented technician at the Marine Biological Laboratory, Woods Hole, MA. We would like to attract someone with some knowledge of biological preparative techniques and experience in laser scanning confocal microscopy, TEM, SEM, and/or LM. The technician will assist in the Central Microscopy Facility. The technician's duties will be to check out incoming investigators in the usage of our equipment and then to supervise its continuing usage and to perform contract work for investigators. This may include fixation, embedding, sectioning, scope use, darkroom work, etc. The technician will also provide routine maintenance. This is a short term and scientifically rewarding position. Salary will be in the $7 to $10/hour range. Housing may be available to rent through MBL. For more information, including a more detailed position description, please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. Please apply to: Human Resources, MBL, 7 MBL Street, Woods Hole, MA 02543. or resume@mbl.edu. An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. Louie Kerr Research and Education Support Coordinator Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 508-289-7273 508-540-6902 (FAX) VISIT OUR WEB SITE: http://www.mbl.edu -------------------------------- End of nih-image-d Digest V99 Issue #13 *************************************** From nih-image-request@io.ece.drexel.edu Sun Jan 17 15:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA09319 for cshtest@io.ece.drexel.edu; Sun, 17 Jan 1999 15:54:50 -0500 (EST) Resent-Date: Sun, 17 Jan 1999 15:54:50 -0500 (EST) Date: Sun, 17 Jan 1999 14:39:41 -0600 (CST) From: Heidi Guetschow Subject: vesicle size distribution To: nih-image@io.ece.drexel.edu Message-id: <01J6NFKO9Q9E8WZDP8@carleton.edu> X-VMS-To: IN::"nih-image@biomed.drexel.edu" MIME-version: 1.0 Resent-Message-ID: <"3pH7z.0.Bu1.agaes"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/831 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 685 Greetings, fellow particle counters. Has anyone figured out a good solution to the problem of counting individual particles on images with grey-dark grey backgrounds (such as SEM images of basalt, pumice, etc)? I've been working with various macros and kernels I've found on the web, but none of them give me quite the results I'm looking for, and it seems like many people have faced similar problems. I am trying to do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need to somehow define the edges of the vesicles apart from the background grey. I'd appreciate any ideas. Thanks! Heidi Guetschow Carleton College 300 N. College St. Northfield, MN 55057 From nih-image-request@io.ece.drexel.edu Sun Jan 17 18:03 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA23000 for cshtest@io.ece.drexel.edu; Sun, 17 Jan 1999 18:03:19 -0500 (EST) Resent-Date: Sun, 17 Jan 1999 18:03:19 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: dameh@execpc.com, nih-image@io.ece.drexel.edu Date: Mon, 18 Jan 1999 9:53:19 +1100 Subject: Re: Image as peak integrator Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"PQWrA2.0.vB5.Laces"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/832 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1651 >Date: Fri, 15 Jan 1999 11:47:42 -0600 >To: nih-image@io.ece.drexel.edu >From: "David A. Meh" >Subject: Image as peak integrator > >We have a very old HPLC without a peak integrator. I thought that possibly >a scan of the relevant peaks could be converted using the Line Plots>Data >macro and then the gel plotting mcaros would allow me to integrate the area >under the peaks, but the gel plot macros don't recognize the plot. This may >be more effort than it is worth, as the "old" method of cutting out the >paper and weighing the peaks will work. >Please give me your comments and suggestions. >Thank you, >David A. Meh > >Madness takes its toll. Please have exact change ? As you already have a line plot and want to measure the "area under the graph" ie the area between the graph and the X axis, all you need to do is to ensure that the X axis and droplines from the graph to X axis exist (you can draw using shift key to make vertical/horizoontal) and to then measure the area directly. There is no point in Line Plots>Data macro. It is probably necessary to threshold or density slice to convert the graph to a binary (ie black and white 255/0) image first. You could use the fill bucket tool to ensure that the space is enclosed without break in the graph. Apart from the touchup procedure, a simple wand tool to select the internal space enclosed by the graph, x axis and droplines; followed by 'measure'; will give the area. 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 Sun Jan 17 23:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA28623 for cshtest@io.ece.drexel.edu; Sun, 17 Jan 1999 23:15:25 -0500 (EST) Resent-Date: Sun, 17 Jan 1999 23:15:25 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: hmthomas@med.cornell.edu, nih-image@io.ece.drexel.edu Date: Mon, 18 Jan 1999 15:04:19 +1100 Subject: Re: Importing Images TIFF tags Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"R5mY52.0.dV6.h7hes"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/833 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 10492 >To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) >From: hmthomas@med.cornell.edu (Henry M. Thomas) >Subject: Importing Images TIFF tags > >Greg Joss's post "Re: Importing Images with fixed windows" showed how to >search for text in a TIFF header. > >Is there a way to read TIFF tags from Image? Scanalytics 16-bit TIFFs have >a tag (#281, entitled MaxSampleValue) which contains the maximum intensity >value of the stack. Tiffsniff (in the NIH Image zippy) reads all the Tags >in a TIFF, but doesn't pass them to Image (and gets this particular tag >wrong a lot of the time). GraphicConverter displays some of the Tags. > >Thanks in advance. >Harry > >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 > Harry, If what you say re " Scanalytics 16-bit TIFFs have a tag (#281, entitled MaxSampleValue) which contains the maximum intensity value of the stack." it is at odds with " TIFF 5.0 An Aldus/Microsoft Technical Memorandum: 8/8/88 Page 1 Preface This memorandum has been prepared jointly by Aldus and Microsoft in conjunction with leading scanner vendors and other interested parties. " "_______________________ MaxSampleValue Tag = 281 (119) Type = SHORT N = SamplesPerPixel The maximum used sample value. For example, if the image consists of 6-bit data low-order-justified into 8-bit bytes, MaxSampleValue will be no greater than 63. This is field is not to be used to affect the visual appearance of the image when displayed. Nor should the values of this field affect the interpretation of any other field. Use it for statistical purposes only. Default is 2**(BitsPerSample) - 1. MinSampleValue Tag = 280 (118) Type = SHORT N = SamplesPerPixel The minimum used sample value. This field is not to be used to affect the visual appearance of the image when displayed. See the comments for MaxSampleValue. Default is 0. ______________________" However, As you can import any section of an image file as an image and you can read that image into LineBuffer using getRow, it should be a straightforward to locate a particular tag entry in a particular tiff format. You can find your way around the file by converting address offsets to image offsets by statements such as hdrOffset:=lineBuffer[7]+lineBuffer[6]*256+lineBuffer[5]*256*256; {Bytes 4-7 This long word contains the offset (in bytes) of the first Image File Directory.} You can see sample Pascal code to access TIFF header info in file2.p of NIH-Image source in OpenTiffHeader. However, in practice, rather than chase pointers in the generalised TIFF file format, it is much simpler and ususally quite effective to take a simple pragmatic approach. I dont know Scanalytics 16-bit TIFFs but I suspect that all you need to do in practice is to locate tag #281 in one header by inspection and it is likely to be at the same offset in all the image files from the same source. You can probably make use of some of the macro code appended below. (another version of that posted recently) If you have difficulty, send me a sample Scanalytics image (or 2) and I will check macro code. {_______________________________________________________________} { DirectAccessToTiffFramesMacro incremental or direct access by frame to uncompressed TIFF stack or uncompressed Quicktime Fully automatic for 256 gray level, No compression, TIFF stacks in that frame Width and Height is found in header but for Quicktime movie: to set PicSize for macro to "know" framesize; either use NEW(File menu ([N] to create a dummy image of correct size or load sample image or terminate full load of actual TIFF stack or Quicktime movie with [.] to get palette etc then invoke macro with model window current. else respond to queries. Load and invoke macro'/0Sample Tiff or QT unCompressed Movie'; It will allow file selection via import dialogue window. Dont change custom entries. 256 gray level No compression Quicktime has an 8 byte header Tiff 768 Import offset allows access to a sequence in middle of the stack or QuickTime Movie Writen by: Greg Joss, 1997-12-17 last Modified 1999-1-18 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 } procedure ImportSlices(fromSlice,slices:integer); var setoff,p,i,n:integer;begin SetImport('Custom 8-bits'); if (trailerLen<>0) or (headerLen<>0) then begin setNewSize(width,height);makeNewStack(movieName);p:=pidNumber; for i:=1 to slices do begin n:=fromSlice-1+i; setoff:=offset+(n-1)*width*height; if n>1 then setoff:=setoff+(trailerLen+headerLen)*(n-1)+trailerLen-8; SetCustom(width,height,setoff,1); Import(movieName);selectAll;copy;dispose; selectPic(p);paste;invert;addSlice; end;deleteSlice;selectSlice(1);killRoi; end else begin setoff:=offset+(fromSlice-1)*width*height; SetCustom(width,height,setoff,slices); Import(movieName); end; showMessage(movieName,'\from slice ',fromSlice,' for ' slices ,'\WxH: ',width,height ,'\offset: ',offset,'\slice at: ',setoff); end function matchLine(s:string,i):boolean;var m:boolean;begin m:=true; showmessage(chr(lineBuffer[i]),chr(lineBuffer[i+1]) ,lineBuffer[i+2],chr(lineBuffer[i+3])); while (length(s)>0) and (m=true) do begin if ord(s)=ord(nullChr)then begin if lineBuffer[i]<>0 then m:=false; end else if lineBuffer[i]<>ord(s) then m:=false; delete(s,1,1);i:=i+1;end; matchLine:=m; end function tagField(i,t):integer;begin if swapBytes then begin if (lineBuffer[i+1]=trunc(t/256)) and (lineBuffer[i]=t mod 256) and (lineBuffer[i+3]=3) then tagField:=lineBuffer[i+9]*256+lineBuffer[i+8] else exit(concat('unexpected tagField',lineBuffer[i+1]*256+lineBuffer[i])); end else begin if (lineBuffer[i]=trunc(t/256)) and (lineBuffer[i+1]=t mod 256) and (lineBuffer[i+3]=3) then tagField:=lineBuffer[i+8]*256+lineBuffer[i+9] else exit(concat('unexpected tagField',lineBuffer[i]*256+lineBuffer[i+1])); end end procedure tiffHeader;var nullChr:string; hdrOffset:integer;begin { else if matchLine('....mdat',0) then FileType:='MooV'; redundant now GetFileInfo available but header content is accessible} GetRow(0,0,8); nullChr:='.'; swapBytes:=matchLine('II*.',0); if not (matchLine('MM.*',0) or swapBytes)then begin showMessage('ensure invert not set in import dialogue'); exit ('FileType:=TIFF but not MM.* or II*. ?');end; if swapBytes then hdrOffset:=lineBuffer[4]+lineBuffer[5]*256+lineBuffer[6]*256*256 else hdrOffset:=lineBuffer[7]+lineBuffer[6]*256+lineBuffer[5]*256*256; if hdrOffset=8 then begin GetRow(8,0,256);offset:=768;end else begin offset:=hdrOffset;dispose; height:=1;ImportSlices(1,1);GetRow(0,0,256); offset:=8;trailerLen:=94;headerLen:=236{-40 }; {-40 works for bau2406aa.tif. see OpenTiffDirectory in file2.p for code} end; end macro'/1 ShowTags'; var fromSlice,i,n,m,stack,t,tag:integer;{macro variables} {variables used by functions} width,height,offset,FileSize,mslices,trailerLen,headerLen:integer; swapBytes:boolean; movieName,directory,FullPath,FileType:string; begin width:=256; height:=8; ImportSlices(1,1); movieName:=windowTitle; directory:=GetPath('window'); fullPath:=concat(directory,windowTitle); GetFileInfo(FullPath, FileType, FileSize); if FileType<>'TIFF' then {exit}putMessage('not seen as TIFF by NiH-Image'); tiffHeader; if swapBytes then n:=lineBuffer[0] else n:=lineBuffer[1]; newTextWindow(concat(windowTitle,'tags')); i:=2; for t:=1 to n-1 do begin if swapBytes then tag:=lineBuffer[i+1]*256+lineBuffer[i] else tag:=lineBuffer[i]*256+lineBuffer[i+1]; write(t,':',tag); if tag=256 then write(' width:',tagField(i,tag)); if tag=257 then write(' height:',tagField(i,tag)); writeln; i:=i+12; end end procedure getFileType;{Check Header tiff or QTMoov} var w,h:integer;s:string; begin getPicSize(w,h); width:=256; height:=8; ImportSlices(1,1); movieName:=windowTitle; directory:=GetPath('window'); fullPath:=concat(directory,windowTitle); GetFileInfo(FullPath, FileType, FileSize); if FileType='TIFF' then begin tiffHeader; width:=tagField(2+12,256); height:=tagField(2+12*2,257);end else if FileType='MooV' then offset:=8 else offset:=0; if FileType<>'TIFF' then if (w=0) or (h=0) then begin putMessage('no model window for QTMoov dimensions'); width:=getNumber('width in pixels',768); height:=getNumber('height in pixels',512); end else begin width:=w; height:=h; end; if width*height<>0 then mslices:=trunc((FileSize-offset)/(width*height+trailerLen+headerLen)); if trailerLen<>0 then s:='INDY origin?' else s:=''; showMessage(FullPath,'\FileType: ',FileType,s,'\FileSize: ',FileSize ,'\Offset: ',offset,'\WxH: ',width,'x',height,'\expected slices:',mslices); SetPicName(windowTitle,' header.',FileType); dispose;{oooo comment out if want header info} SetNewSize(w,h); end; macro'/0 Sample Tiff or QT unCompressed Movie'; var fromSlice,i,n,m,stack:integer;{macro variables} {variables used by functions} width,height,offset,FileSize,mslices,trailerLen,headerLen:integer; movieName,directory,FullPath,FileType:string; begin getFileType; fromSlice:=GetNumber('fromSlice',1); n:=GetNumber('every n th slice',1); m:=GetNumber('number of slices in extract',1+trunc((mslices-fromSlice)/n)); if n=1 then ImportSlices(fromSlice,m) else for i:=1 to m do begin ImportSlices(fromSlice,1);SelectAll;Copy;Dispose; if i=1 then begin MakeNewStack(movieName);stack:=pidNumber;end else begin ChoosePic(stack);addSlice;end; paste; fromSlice:=fromSlice+n; end; setPicName(GetString('output name',concat(windowtitle,'.',FileType,'.Extract'))); 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 Mon Jan 18 06:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA18663 for cshtest@io.ece.drexel.edu; Mon, 18 Jan 1999 06:23:12 -0500 (EST) Resent-Date: Mon, 18 Jan 1999 06:23:12 -0500 (EST) Message-ID: <000b01be42d2$200f6dc0$99efe18f@amendola.unina.it> From: "Eugenio Amendola" To: "NIH-Image mailing list" Subject: Arc integration Date: Mon, 18 Jan 1999 12:03:05 +0100 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: <"uTyJF1.0.f04.7Mnes"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/834 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_0008_01BE42DA.81878A80" Content-Length: 4543 This is a multi-part message in MIME format. ------=_NextPart_000_0008_01BE42DA.81878A80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable >From digest V98#145 Dr. Russ wrote: 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 I'm interested in arc integration indeed. I'd like to scan a X-ray = diffraction image obtained from polymeric samples and evaluate molecular = orientation in the sample through the calculation of the order = parameter. I've figured out a tentative procedure involving: 1 scanning of Xray film; 2 converting into OD; 3 locating the center of the diffraction halo (it could be a = cicorference or arcs) using Hough transform; 4 identifing the radius of diffraction halo; 5 performing arc integration (and averaging if needed); 6 outputting integrated data into Excell for further analysis. I can do steps 1-4 and 6, but help for arc integration would very = welcome. Thamk you for the help. Sincerely Eugenio Amendola _________________________________________ _________________________________________ Dr. Eugenio Amendola Italian National Council of Research Institute of Composite Material Technology P.le Tecchio 80, 80125 - Naples, ITALY Tel. 39 (0) 81 7682511 fax 39 (0) 81 7682404 email amendola@unina.it URL http:\\143.225.239.86 ------=_NextPart_000_0008_01BE42DA.81878A80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

From digest V98#145 Dr. Russ = wrote:
In a message = dated 12/18/98=20 12:56:15 PM, you wrote:
 
> Are there any capablities on nih-image to do = arc=20 integration along the
>angular direction and to plot the data as = a=20 function of radial direction ?
 
I have a macro that will do that, and will post it = if enough=20 people are
interested.
John Russ
 
 
I'm interested in arc integration indeed. I'd like = to scan a=20 X-ray diffraction image obtained from polymeric samples and evaluate = molecular=20 orientation in the sample through the calculation of the order=20 parameter.
I've figured out a tentative procedure = involving:
1 scanning of Xray film;
2 converting into OD;
3 locating the center of the diffraction halo (it = could be a=20 cicorference or arcs) using Hough transform;
4 identifing the radius of diffraction = halo;
5 performing arc integration (and averaging if=20 needed);
6 outputting integrated data into Excell for further = analysis.
I can do steps 1-4 and 6, but help = for arc=20 integration would very welcome.
Thamk you for = the=20 help.
Sincerely
Eugenio Amendola
_________________________________________
___________________= ______________________
 
Dr. Eugenio Amendola
Italian = National Council=20 of Research
Institute of Composite Material Technology
P.le = Tecchio 80,=20 80125 - Naples, ITALY
Tel.     39 (0) 81=20 7682511
fax      39 (0) 81=20 7682404
email   amendola@unina.it
URL  = ; =20 http:\\143.225.239.86
------=_NextPart_000_0008_01BE42DA.81878A80-- From nih-image-request@io.ece.drexel.edu Mon Jan 18 11:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA21147 for cshtest@io.ece.drexel.edu; Mon, 18 Jan 1999 11:08:44 -0500 (EST) Resent-Date: Mon, 18 Jan 1999 11:08:44 -0500 (EST) Date: Mon, 18 Jan 1999 10:38:52 -0500 From: Michael Klug Subject: Fuji vs. Kodak DS 8650 dye-sub To: nih-image@io.ece.drexel.edu Cc: aagime0@pop.uky.edu, wchu@bme.ym.edu.tw Message-id: <052566FD.0055F88D.00@aammta1.d51.lilly.com> MIME-version: 1.0 Content-disposition: inline X-Lotus-FromDomain: LILLY Resent-Message-ID: <"2YFLw3.0.rT4.3Tres"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/835 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1308 Regarding the Fuji vs Kodak printer, I too had a lot of problems setting up the Kodak printer, but they were network related. It turned out that the problems were both Kodak problems and network administrator problems (here). In terms of color matching, I have found the Kodak excellent, except that I have to alter the brightness and contrast for transparencies. I do print out double-labelled immunofluorescent images. DO NOT GET THE CMYK RIBBON--I found it impossible to match screen colors. Kodak did include color matching software with the printer, although I do not have the hardware to try to do so. I compared the Kodak to the Tektronix 450 and thought that the Kodak was much better in several aspects. I have not tried the Fuji printer. I could add a lot more specifics about the Kodak, if anyone is interested (reply to me directly to save bandwith?). Also, try the customer service #'s for both--I don't know about Fuji at all or Kodak now, but Kodak was terrible 12 months ago. Part of why I stopped considering the Tektronix was that even their sales people were unresponsive to scientific imaging applications of their machines (so I assumed that service would be even worse). --Michael G. Klug, Ph.D. Postdoctoral Fellow Eli Lilly and Company klug_michael@lilly.com 317-276-6951 From nih-image-d-request@io.ece.drexel.edu Mon Jan 18 11:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA22006; Mon, 18 Jan 1999 11:15:36 -0500 (EST) Date: Mon, 18 Jan 1999 11:15:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901181615.LAA22006@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #14 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/14 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: 20739 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 14 Today's Topics: vesicle size distribution [ Heidi Guetschow To: nih-image@io.ece.drexel.edu Subject: vesicle size distribution Message-id: <01J6NFKO9Q9E8WZDP8@carleton.edu> Greetings, fellow particle counters. Has anyone figured out a good solution to the problem of counting individual particles on images with grey-dark grey backgrounds (such as SEM images of basalt, pumice, etc)? I've been working with various macros and kernels I've found on the web, but none of them give me quite the results I'm looking for, and it seems like many people have faced similar problems. I am trying to do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need to somehow define the edges of the vesicles apart from the background grey. I'd appreciate any ideas. Thanks! Heidi Guetschow Carleton College 300 N. College St. Northfield, MN 55057 ------------------------------ Date: Mon, 18 Jan 1999 9:53:19 +1100 From: GJOSS@rna.bio.mq.edu.au To: dameh@execpc.com, nih-image@io.ece.drexel.edu Subject: Re: Image as peak integrator Message-ID: >Date: Fri, 15 Jan 1999 11:47:42 -0600 >To: nih-image@io.ece.drexel.edu >From: "David A. Meh" >Subject: Image as peak integrator > >We have a very old HPLC without a peak integrator. I thought that possibly >a scan of the relevant peaks could be converted using the Line Plots>Data >macro and then the gel plotting mcaros would allow me to integrate the area >under the peaks, but the gel plot macros don't recognize the plot. This may >be more effort than it is worth, as the "old" method of cutting out the >paper and weighing the peaks will work. >Please give me your comments and suggestions. >Thank you, >David A. Meh > >Madness takes its toll. Please have exact change ? As you already have a line plot and want to measure the "area under the graph" ie the area between the graph and the X axis, all you need to do is to ensure that the X axis and droplines from the graph to X axis exist (you can draw using shift key to make vertical/horizoontal) and to then measure the area directly. There is no point in Line Plots>Data macro. It is probably necessary to threshold or density slice to convert the graph to a binary (ie black and white 255/0) image first. You could use the fill bucket tool to ensure that the space is enclosed without break in the graph. Apart from the touchup procedure, a simple wand tool to select the internal space enclosed by the graph, x axis and droplines; followed by 'measure'; will give the area. 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, 18 Jan 1999 15:04:19 +1100 From: GJOSS@rna.bio.mq.edu.au To: hmthomas@med.cornell.edu, nih-image@io.ece.drexel.edu Subject: Re: Importing Images TIFF tags Message-ID: >To: nih-image@io.ece.drexel.edu (Drexel Computer Vision Center) >From: hmthomas@med.cornell.edu (Henry M. Thomas) >Subject: Importing Images TIFF tags > >Greg Joss's post "Re: Importing Images with fixed windows" showed how to >search for text in a TIFF header. > >Is there a way to read TIFF tags from Image? Scanalytics 16-bit TIFFs have >a tag (#281, entitled MaxSampleValue) which contains the maximum intensity >value of the stack. Tiffsniff (in the NIH Image zippy) reads all the Tags >in a TIFF, but doesn't pass them to Image (and gets this particular tag >wrong a lot of the time). GraphicConverter displays some of the Tags. > >Thanks in advance. >Harry > >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 > Harry, If what you say re " Scanalytics 16-bit TIFFs have a tag (#281, entitled MaxSampleValue) which contains the maximum intensity value of the stack." it is at odds with " TIFF 5.0 An Aldus/Microsoft Technical Memorandum: 8/8/88 Page 1 Preface This memorandum has been prepared jointly by Aldus and Microsoft in conjunction with leading scanner vendors and other interested parties. " "_______________________ MaxSampleValue Tag = 281 (119) Type = SHORT N = SamplesPerPixel The maximum used sample value. For example, if the image consists of 6-bit data low-order-justified into 8-bit bytes, MaxSampleValue will be no greater than 63. This is field is not to be used to affect the visual appearance of the image when displayed. Nor should the values of this field affect the interpretation of any other field. Use it for statistical purposes only. Default is 2**(BitsPerSample) - 1. MinSampleValue Tag = 280 (118) Type = SHORT N = SamplesPerPixel The minimum used sample value. This field is not to be used to affect the visual appearance of the image when displayed. See the comments for MaxSampleValue. Default is 0. ______________________" However, As you can import any section of an image file as an image and you can read that image into LineBuffer using getRow, it should be a straightforward to locate a particular tag entry in a particular tiff format. You can find your way around the file by converting address offsets to image offsets by statements such as hdrOffset:=lineBuffer[7]+lineBuffer[6]*256+lineBuffer[5]*256*256; {Bytes 4-7 This long word contains the offset (in bytes) of the first Image File Directory.} You can see sample Pascal code to access TIFF header info in file2.p of NIH-Image source in OpenTiffHeader. However, in practice, rather than chase pointers in the generalised TIFF file format, it is much simpler and ususally quite effective to take a simple pragmatic approach. I dont know Scanalytics 16-bit TIFFs but I suspect that all you need to do in practice is to locate tag #281 in one header by inspection and it is likely to be at the same offset in all the image files from the same source. You can probably make use of some of the macro code appended below. (another version of that posted recently) If you have difficulty, send me a sample Scanalytics image (or 2) and I will check macro code. {_______________________________________________________________} { DirectAccessToTiffFramesMacro incremental or direct access by frame to uncompressed TIFF stack or uncompressed Quicktime Fully automatic for 256 gray level, No compression, TIFF stacks in that frame Width and Height is found in header but for Quicktime movie: to set PicSize for macro to "know" framesize; either use NEW(File menu ([N] to create a dummy image of correct size or load sample image or terminate full load of actual TIFF stack or Quicktime movie with [.] to get palette etc then invoke macro with model window current. else respond to queries. Load and invoke macro'/0Sample Tiff or QT unCompressed Movie'; It will allow file selection via import dialogue window. Dont change custom entries. 256 gray level No compression Quicktime has an 8 byte header Tiff 768 Import offset allows access to a sequence in middle of the stack or QuickTime Movie Writen by: Greg Joss, 1997-12-17 last Modified 1999-1-18 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 } procedure ImportSlices(fromSlice,slices:integer); var setoff,p,i,n:integer;begin SetImport('Custom 8-bits'); if (trailerLen<>0) or (headerLen<>0) then begin setNewSize(width,height);makeNewStack(movieName);p:=pidNumber; for i:=1 to slices do begin n:=fromSlice-1+i; setoff:=offset+(n-1)*width*height; if n>1 then setoff:=setoff+(trailerLen+headerLen)*(n-1)+trailerLen-8; SetCustom(width,height,setoff,1); Import(movieName);selectAll;copy;dispose; selectPic(p);paste;invert;addSlice; end;deleteSlice;selectSlice(1);killRoi; end else begin setoff:=offset+(fromSlice-1)*width*height; SetCustom(width,height,setoff,slices); Import(movieName); end; showMessage(movieName,'\from slice ',fromSlice,' for ' slices ,'\WxH: ',width,height ,'\offset: ',offset,'\slice at: ',setoff); end function matchLine(s:string,i):boolean;var m:boolean;begin m:=true; showmessage(chr(lineBuffer[i]),chr(lineBuffer[i+1]) ,lineBuffer[i+2],chr(lineBuffer[i+3])); while (length(s)>0) and (m=true) do begin if ord(s)=ord(nullChr)then begin if lineBuffer[i]<>0 then m:=false; end else if lineBuffer[i]<>ord(s) then m:=false; delete(s,1,1);i:=i+1;end; matchLine:=m; end function tagField(i,t):integer;begin if swapBytes then begin if (lineBuffer[i+1]=trunc(t/256)) and (lineBuffer[i]=t mod 256) and (lineBuffer[i+3]=3) then tagField:=lineBuffer[i+9]*256+lineBuffer[i+8] else exit(concat('unexpected tagField',lineBuffer[i+1]*256+lineBuffer[i])); end else begin if (lineBuffer[i]=trunc(t/256)) and (lineBuffer[i+1]=t mod 256) and (lineBuffer[i+3]=3) then tagField:=lineBuffer[i+8]*256+lineBuffer[i+9] else exit(concat('unexpected tagField',lineBuffer[i]*256+lineBuffer[i+1])); end end procedure tiffHeader;var nullChr:string; hdrOffset:integer;begin { else if matchLine('....mdat',0) then FileType:='MooV'; redundant now GetFileInfo available but header content is accessible} GetRow(0,0,8); nullChr:='.'; swapBytes:=matchLine('II*.',0); if not (matchLine('MM.*',0) or swapBytes)then begin showMessage('ensure invert not set in import dialogue'); exit ('FileType:=TIFF but not MM.* or II*. ?');end; if swapBytes then hdrOffset:=lineBuffer[4]+lineBuffer[5]*256+lineBuffer[6]*256*256 else hdrOffset:=lineBuffer[7]+lineBuffer[6]*256+lineBuffer[5]*256*256; if hdrOffset=8 then begin GetRow(8,0,256);offset:=768;end else begin offset:=hdrOffset;dispose; height:=1;ImportSlices(1,1);GetRow(0,0,256); offset:=8;trailerLen:=94;headerLen:=236{-40 }; {-40 works for bau2406aa.tif. see OpenTiffDirectory in file2.p for code} end; end macro'/1 ShowTags'; var fromSlice,i,n,m,stack,t,tag:integer;{macro variables} {variables used by functions} width,height,offset,FileSize,mslices,trailerLen,headerLen:integer; swapBytes:boolean; movieName,directory,FullPath,FileType:string; begin width:=256; height:=8; ImportSlices(1,1); movieName:=windowTitle; directory:=GetPath('window'); fullPath:=concat(directory,windowTitle); GetFileInfo(FullPath, FileType, FileSize); if FileType<>'TIFF' then {exit}putMessage('not seen as TIFF by NiH-Image'); tiffHeader; if swapBytes then n:=lineBuffer[0] else n:=lineBuffer[1]; newTextWindow(concat(windowTitle,'tags')); i:=2; for t:=1 to n-1 do begin if swapBytes then tag:=lineBuffer[i+1]*256+lineBuffer[i] else tag:=lineBuffer[i]*256+lineBuffer[i+1]; write(t,':',tag); if tag=256 then write(' width:',tagField(i,tag)); if tag=257 then write(' height:',tagField(i,tag)); writeln; i:=i+12; end end procedure getFileType;{Check Header tiff or QTMoov} var w,h:integer;s:string; begin getPicSize(w,h); width:=256; height:=8; ImportSlices(1,1); movieName:=windowTitle; directory:=GetPath('window'); fullPath:=concat(directory,windowTitle); GetFileInfo(FullPath, FileType, FileSize); if FileType='TIFF' then begin tiffHeader; width:=tagField(2+12,256); height:=tagField(2+12*2,257);end else if FileType='MooV' then offset:=8 else offset:=0; if FileType<>'TIFF' then if (w=0) or (h=0) then begin putMessage('no model window for QTMoov dimensions'); width:=getNumber('width in pixels',768); height:=getNumber('height in pixels',512); end else begin width:=w; height:=h; end; if width*height<>0 then mslices:=trunc((FileSize-offset)/(width*height+trailerLen+headerLen)); if trailerLen<>0 then s:='INDY origin?' else s:=''; showMessage(FullPath,'\FileType: ',FileType,s,'\FileSize: ',FileSize ,'\Offset: ',offset,'\WxH: ',width,'x',height,'\expected slices:',mslices); SetPicName(windowTitle,' header.',FileType); dispose;{oooo comment out if want header info} SetNewSize(w,h); end; macro'/0 Sample Tiff or QT unCompressed Movie'; var fromSlice,i,n,m,stack:integer;{macro variables} {variables used by functions} width,height,offset,FileSize,mslices,trailerLen,headerLen:integer; movieName,directory,FullPath,FileType:string; begin getFileType; fromSlice:=GetNumber('fromSlice',1); n:=GetNumber('every n th slice',1); m:=GetNumber('number of slices in extract',1+trunc((mslices-fromSlice)/n)); if n=1 then ImportSlices(fromSlice,m) else for i:=1 to m do begin ImportSlices(fromSlice,1);SelectAll;Copy;Dispose; if i=1 then begin MakeNewStack(movieName);stack:=pidNumber;end else begin ChoosePic(stack);addSlice;end; paste; fromSlice:=fromSlice+n; end; setPicName(GetString('output name',concat(windowtitle,'.',FileType,'.Extract'))); 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: Mon, 18 Jan 1999 12:03:05 +0100 From: "Eugenio Amendola" To: "NIH-Image mailing list" Subject: Arc integration Message-ID: <000b01be42d2$200f6dc0$99efe18f@amendola.unina.it> Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01BE42DA.81878A80" This is a multi-part message in MIME format. ------=_NextPart_000_0008_01BE42DA.81878A80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable >From digest V98#145 Dr. Russ wrote: 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 I'm interested in arc integration indeed. I'd like to scan a X-ray = diffraction image obtained from polymeric samples and evaluate molecular = orientation in the sample through the calculation of the order = parameter. I've figured out a tentative procedure involving: 1 scanning of Xray film; 2 converting into OD; 3 locating the center of the diffraction halo (it could be a = cicorference or arcs) using Hough transform; 4 identifing the radius of diffraction halo; 5 performing arc integration (and averaging if needed); 6 outputting integrated data into Excell for further analysis. I can do steps 1-4 and 6, but help for arc integration would very = welcome. Thamk you for the help. Sincerely Eugenio Amendola _________________________________________ _________________________________________ Dr. Eugenio Amendola Italian National Council of Research Institute of Composite Material Technology P.le Tecchio 80, 80125 - Naples, ITALY Tel. 39 (0) 81 7682511 fax 39 (0) 81 7682404 email amendola@unina.it URL http:\\143.225.239.86 ------=_NextPart_000_0008_01BE42DA.81878A80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
From digest V98#145 Dr. Russ = wrote:
In a message = dated 12/18/98=20 12:56:15 PM, you wrote:
 
> Are there any capablities on nih-image to do = arc=20 integration along the
>angular direction and to plot the data as = a=20 function of radial direction ?
 
I have a macro that will do that, and will post it = if enough=20 people are
interested.
John Russ
 
 
I'm interested in arc integration indeed. I'd like = to scan a=20 X-ray diffraction image obtained from polymeric samples and evaluate = molecular=20 orientation in the sample through the calculation of the order=20 parameter.
I've figured out a tentative procedure = involving:
1 scanning of Xray film;
2 converting into OD;
3 locating the center of the diffraction halo (it = could be a=20 cicorference or arcs) using Hough transform;
4 identifing the radius of diffraction = halo;
5 performing arc integration (and averaging if=20 needed);
6 outputting integrated data into Excell for further = analysis.
I can do steps 1-4 and 6, but help = for arc=20 integration would very welcome.
Thamk you for = the=20 help.
Sincerely
Eugenio Amendola
_________________________________________
___________________= ______________________
 
Dr. Eugenio Amendola
Italian = National Council=20 of Research
Institute of Composite Material Technology
P.le = Tecchio 80,=20 80125 - Naples, ITALY
Tel.     39 (0) 81=20 7682511
fax      39 (0) 81=20 7682404
email   amendola@unina.it
URL  = ; =20 http:\\143.225.239.86
------=_NextPart_000_0008_01BE42DA.81878A80-- ------------------------------ Date: Mon, 18 Jan 1999 10:38:52 -0500 From: Michael Klug To: nih-image@io.ece.drexel.edu Cc: aagime0@pop.uky.edu, wchu@bme.ym.edu.tw Subject: Fuji vs. Kodak DS 8650 dye-sub Message-id: <052566FD.0055F88D.00@aammta1.d51.lilly.com> Content-type: text/plain; charset=us-ascii Content-disposition: inline Regarding the Fuji vs Kodak printer, I too had a lot of problems setting up the Kodak printer, but they were network related. It turned out that the problems were both Kodak problems and network administrator problems (here). In terms of color matching, I have found the Kodak excellent, except that I have to alter the brightness and contrast for transparencies. I do print out double-labelled immunofluorescent images. DO NOT GET THE CMYK RIBBON--I found it impossible to match screen colors. Kodak did include color matching software with the printer, although I do not have the hardware to try to do so. I compared the Kodak to the Tektronix 450 and thought that the Kodak was much better in several aspects. I have not tried the Fuji printer. I could add a lot more specifics about the Kodak, if anyone is interested (reply to me directly to save bandwith?). Also, try the customer service #'s for both--I don't know about Fuji at all or Kodak now, but Kodak was terrible 12 months ago. Part of why I stopped considering the Tektronix was that even their sales people were unresponsive to scientific imaging applications of their machines (so I assumed that service would be even worse). --Michael G. Klug, Ph.D. Postdoctoral Fellow Eli Lilly and Company klug_michael@lilly.com 317-276-6951 -------------------------------- End of nih-image-d Digest V99 Issue #14 *************************************** From nih-image-request@io.ece.drexel.edu Mon Jan 18 17:19 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05570 for cshtest@io.ece.drexel.edu; Mon, 18 Jan 1999 17:19:07 -0500 (EST) Resent-Date: Mon, 18 Jan 1999 17:19:07 -0500 (EST) Message-Id: <3.0.1.32.19990118171055.00686510@email.psu.edu> X-Sender: cdm7@email.psu.edu (Unverified) X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 18 Jan 1999 17:10:55 -0500 To: nih-image@io.ece.drexel.edu From: Colleen Merritt Subject: How do I set a timer/trigger for a mercury lamp fluorescent microscope imaging using Scion Image? Mime-Version: 1.0 Resent-Message-ID: <"zfyi31.0.rw.G-wes"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/836 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1257 Dear Colleagues, I am observing green fluorescent protein production in plant roots with a Nikon SMZ dissecting microscope while illuminating my sample with filtered ultraviolet light from a mercury lamp. The image is captured by an Optronics DEI 750 system and saved and analyzed via Scion Image 1.60 on a Macintosh 8600/200 computer. I am currently attempting to set up this system to collect images over a 24/48 hour period every 2 hours. A macro program can be written to trigger the camera and save the image every 2 hours in Scion. However, I'm not sure how to handle triggering the mercury lamp to turn on and off for those intervals; the lamp must be externally ignited each time the power is turned off. Prolonged exposure of my sample to the light source will result in extreme stresses, not to mention the expense of the mercury bulbs. Does anyone know how I can work the mercury lamp timing and ignition into the Scion image program? Or does anyone have an idea of how I can separately time the mercury lamp? Also, if I desire to convert my images from Mac format to PC-format using MacLink Plus, and then use Scion Image software to analyze them, do I risk loss of information/data in the conversion? Thank you. Colleen Merritt From nih-image-request@io.ece.drexel.edu Tue Jan 19 07:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA09157 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 07:23:58 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 07:23:58 -0500 (EST) Message-Id: <3.0.5.32.19990119121010.007e76f0@wingate> X-Sender: brh#krokur.is@wingate X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Tue, 19 Jan 1999 12:10:10 +0000 To: nih-image@io.ece.drexel.edu From: Broddi Reyr Hansen Subject: is it practical to make color pictures from gray ones (composite) Mime-Version: 1.0 Resent-Message-ID: <"q6cLy2.0.Vm1.EO7fs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/837 X-Loop: nih-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 Hello all NIH users, this is my first letter to this mailinglist in 12 months. I just wanted to know if it is possible to make color pictures from stacks of gray pictures (using color filters on the camera etc.), gray(RGB) --> color(RBG)??? Thanks in advance, Broddi Reyr Hansen BSc Holar Agricultual College, 551 Saudarkrokur, Iceland email: brh@krokur.is web: www.krokur.is/~holar/main.html =========================================== From nih-image-d-request@io.ece.drexel.edu Tue Jan 19 08:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA20660; Tue, 19 Jan 1999 08:59:49 -0500 (EST) Date: Tue, 19 Jan 1999 08:59:49 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901191359.IAA20660@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #15 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/15 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: 3926 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 15 Today's Topics: How do I set a timer/trigger for a m [ Colleen Merritt ] is it practical to make color pictur [ Broddi Reyr Hansen ] Re: is it practical to make color pi [ "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: How do I set a timer/trigger for a mercury lamp fluorescent microscope imaging using Scion Image? Message-Id: <3.0.1.32.19990118171055.00686510@email.psu.edu> Content-Type: text/plain; charset="us-ascii" Dear Colleagues, I am observing green fluorescent protein production in plant roots with a Nikon SMZ dissecting microscope while illuminating my sample with filtered ultraviolet light from a mercury lamp. The image is captured by an Optronics DEI 750 system and saved and analyzed via Scion Image 1.60 on a Macintosh 8600/200 computer. I am currently attempting to set up this system to collect images over a 24/48 hour period every 2 hours. A macro program can be written to trigger the camera and save the image every 2 hours in Scion. However, I'm not sure how to handle triggering the mercury lamp to turn on and off for those intervals; the lamp must be externally ignited each time the power is turned off. Prolonged exposure of my sample to the light source will result in extreme stresses, not to mention the expense of the mercury bulbs. Does anyone know how I can work the mercury lamp timing and ignition into the Scion image program? Or does anyone have an idea of how I can separately time the mercury lamp? Also, if I desire to convert my images from Mac format to PC-format using MacLink Plus, and then use Scion Image software to analyze them, do I risk loss of information/data in the conversion? Thank you. Colleen Merritt ------------------------------ Date: Tue, 19 Jan 1999 12:10:10 +0000 From: Broddi Reyr Hansen To: nih-image@io.ece.drexel.edu Subject: is it practical to make color pictures from gray ones (composite) Message-Id: <3.0.5.32.19990119121010.007e76f0@wingate> Content-Type: text/plain; charset="us-ascii" Hello all NIH users, this is my first letter to this mailinglist in 12 months. I just wanted to know if it is possible to make color pictures from stacks of gray pictures (using color filters on the camera etc.), gray(RGB) --> color(RBG)??? Thanks in advance, Broddi Reyr Hansen BSc Holar Agricultual College, 551 Saudarkrokur, Iceland email: brh@krokur.is web: www.krokur.is/~holar/main.html =========================================== ------------------------------ Date: Tue, 19 Jan 1999 08:38:49 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: is it practical to make color pictures from gray ones(composite) Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Yes, it certainly is possible. The RGB stack in a 24-bit color TIFF is precisely just 3 greyscale images. I believe some people use 3 filters and a 1-ccd camera to get better resolution than a 3-ccd camera would produce, in fact. Wade >>> Broddi Reyr Hansen 01/19 7:23 AM >>> Hello all NIH users, this is my first letter to this mailinglist in 12 months. I just wanted to know if it is possible to make color pictures from stacks of gray pictures (using color filters on the camera etc.), gray(RGB) --> color(RBG)??? Thanks in advance, Broddi Reyr Hansen BSc Holar Agricultual College, 551 Saudarkrokur, Iceland email: brh@krokur.is web: www.krokur.is/~holar/main.html =========================================== -------------------------------- End of nih-image-d Digest V99 Issue #15 *************************************** From nih-image-request@io.ece.drexel.edu Tue Jan 19 09:00 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA20755 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 09:00:34 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 09:00:34 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Tue, 19 Jan 1999 08:38:49 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: is it practical to make color pictures from gray ones(composite) Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"N5VKI1.0.IN4.xh8fs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/838 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 743 Yes, it certainly is possible. The RGB stack in a 24-bit color TIFF is precisely just 3 greyscale images. I believe some people use 3 filters and a 1-ccd camera to get better resolution than a 3-ccd camera would produce, in fact. Wade >>> Broddi Reyr Hansen 01/19 7:23 AM >>> Hello all NIH users, this is my first letter to this mailinglist in 12 months. I just wanted to know if it is possible to make color pictures from stacks of gray pictures (using color filters on the camera etc.), gray(RGB) --> color(RBG)??? Thanks in advance, Broddi Reyr Hansen BSc Holar Agricultual College, 551 Saudarkrokur, Iceland email: brh@krokur.is web: www.krokur.is/~holar/main.html =========================================== From nih-image-request@io.ece.drexel.edu Tue Jan 19 11:24 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA07966 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 11:24:19 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 11:24:19 -0500 (EST) Message-Id: In-Reply-To: <01J6NFKO9Q9E8WZDP8@carleton.edu> Mime-Version: 1.0 Date: Tue, 19 Jan 1999 07:59:47 -0800 To: nih-image@io.ece.drexel.edu From: Margaret Mangan Subject: Re: vesicle size distribution Resent-Message-ID: <"9hLdw1.0.2D1.BlAfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/839 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1164 Make the greyscale into a binary image after using the threshold utility, (vesicles black, matrix white); use the analyze particles command to measure the area of each vesicles (designate "area" in the options menu). See Mangan & Cashman, JVGR 1996 v 73, p 1-18. >Greetings, fellow particle counters. > >Has anyone figured out a good solution to the problem of counting individual >particles on images with grey-dark grey backgrounds (such as SEM images of >basalt, pumice, etc)? I've been working with various macros and kernels I've >found on the web, but none of them give me quite the results I'm looking for, >and it seems like many people have faced similar problems. I am trying to >do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need >to somehow define the edges of the vesicles apart from the background grey. >I'd appreciate any ideas. > >Thanks! > >Heidi Guetschow >Carleton College >300 N. College St. >Northfield, MN 55057 Margaret Mangan telephone:(650)329-5738 U.S. Geological Survey fax:(650)329-5203 Volcano Hazards Team MS 910 email:mmangan@mojave.wr.usgs.gov 345 Middlefield Road Menlo Park, CA 94025 USA From nih-image-request@io.ece.drexel.edu Tue Jan 19 11:57 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11830 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 11:57:00 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 11:57:00 -0500 (EST) Date: Tue, 19 Jan 1999 17:29:14 +0100 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Mark Wunsch Subject: Radius Photo DV Resent-Message-ID: <"zaRN22.0.G92.rDBfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/840 X-Loop: nih-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 Dear Imagers, I would like to grab images from digital videotape with NIH-Image. I am using a Radius PhotoDV card with Firewire input. Radius supplies a Photoshop plug-in which works well with Photoshop or ColorIt software but is not recognized by NIH. Does anybody know why? Is there any chance to change this! Greetings Mark ******************************** NEW TELEPHONE NEW TELEPHONE Mark Wunsch Centre for Tropical Marine Ecology Fahrenheitstr. 1 28359 Bremen Phone ++49-421-23800-25 Phone Secretary ++49-421-23800-21 Fax ++49-421-2208330 mwunsch@uni-bremen.de ******************************** From nih-image-request@io.ece.drexel.edu Tue Jan 19 12:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA13120 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 12:07:08 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 12:07:08 -0500 (EST) Message-ID: <36A4B517.E224496B@starlab.net> Date: Tue, 19 Jan 1999 17:38:48 +0100 From: gregoire X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Margaret Mangan , nih-image@io.ece.drexel.edu Subject: Re: vesicle size distribution --> JVGR References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"MMmKd2.0.6L2.eJBfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/841 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1682 Hi! I was just wondering.... what does JVGR stands for? Thanks Gregoire Margaret Mangan wrote: > Make the greyscale into a binary image after using the threshold utility, > (vesicles black, matrix white); use the analyze particles command to > measure the area of each vesicles (designate "area" in the options menu). > See Mangan & Cashman, JVGR 1996 v 73, p 1-18. > > >Greetings, fellow particle counters. > > > >Has anyone figured out a good solution to the problem of counting individual > >particles on images with grey-dark grey backgrounds (such as SEM images of > >basalt, pumice, etc)? I've been working with various macros and kernels I've > >found on the web, but none of them give me quite the results I'm looking for, > >and it seems like many people have faced similar problems. I am trying to > >do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need > >to somehow define the edges of the vesicles apart from the background grey. > >I'd appreciate any ideas. > > > >Thanks! > > > >Heidi Guetschow > >Carleton College > >300 N. College St. > >Northfield, MN 55057 > > Margaret Mangan telephone:(650)329-5738 > U.S. Geological Survey fax:(650)329-5203 > Volcano Hazards Team MS 910 email:mmangan@mojave.wr.usgs.gov > 345 Middlefield Road > Menlo Park, CA 94025 > USA -- ======================================================== Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-53-80 http://www.starlab.org email:gregoire@starlab.net ======================================================== From nih-image-request@io.ece.drexel.edu Tue Jan 19 13:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA21039 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 13:15:53 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 13:15:53 -0500 (EST) X-Sender: bruckner@bruckner.deskmail.washington.edu Message-Id: In-Reply-To: <199901191402.JAA21036@io.ece.drexel.edu> Mime-Version: 1.0 X-Face: ,5-1`[.GWu}Gki.@O4TcoJhGF6#|nery_y7r1rD2hcNr&wc=q(lM_x Y$66Oe)MYC*)Mar76RpUIgnbJn!<[ Subject: trigger for Hg lamp fluorescence imaging Resent-Message-ID: <"vkPzF1.0.WA4._FCfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/842 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1446 >I am observing green fluorescent protein production in plant roots with a >Nikon SMZ dissecting microscope while illuminating my sample with filtered >ultraviolet light from a mercury lamp. > > However, I'm not sure how to handle triggering the mercury >lamp to turn on and off for those intervals; the lamp must be externally >ignited each time the power is turned off. Prolonged exposure of my sample >to the light source will result in extreme stresses, not to mention the >expense of the mercury bulbs. Does anyone know how I can work the mercury >lamp timing and ignition into the Scion image program? Or does anyone have >an idea of how I can separately time the mercury lamp? Mercury lamps have a warm-up time of at least 5 minutes to full power. If you have some flexibility with light sources, how about using a Xenon flashlamp (strobes and camera flashes use this). Scientific Xenon flashlamps (EG&G, Hamamatsu, Strobotac) are designed to flash off an external trigger. I realize that Xenon isn't as intense in the UV as Hg lamps. By pulsing the light source, however, you get a bright intensity light for the duration of 1 camera exposure. With filters, I use the blue light from Xenon flashlamps to excite green fluorescence with my system (not a microscope setup). ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- From nih-image-request@io.ece.drexel.edu Tue Jan 19 14:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA26283 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 14:01:38 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 14:01:38 -0500 (EST) Subject: trigger for Hg lamp fluorescence imaging Date: Tue, 19 Jan 99 13:38:29 -0500 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: Mime-Version: 1.0 Message-ID: <7AF9862B4B@qc1.qc.edu> Resent-Message-ID: <"pKHPO3.0.hn5.S5Dfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/843 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 1068 if you can leave the lamp on for the duration of the experiment (24 hrs?) that would be the easiest thing: insert a shutter in the light path (piece of black posterboard attached to the hourhand of a electric alarm clock- take the face and other hands off and use toothpick or paperclip and tape to secure the shutter; or- secure the shutter to a timer-actuated solenoid- fancier but just as effective - better if space is limited.) the width of the piece of board will dictate the illumination-on time. yes- the prep will be lit every hour but so-what. if leaving the lamp on for the ex4ended time is not good ( i realize that mercury lamps have a limited life but doesn't turning them on and off considerably shorten that life??)- then the question is how to trigger the 'ignition' circuit directly from a timer. send me the circuit and i'll try to help. i've had considerable experience building timers and shutters and time-ramped turn circuits for microscope illuminators- i've learned that the 'too simple' is often the best and most reliable. From nih-image-request@io.ece.drexel.edu Tue Jan 19 14:33 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA00379 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 14:33:04 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 14:33:04 -0500 (EST) Date: Tue, 19 Jan 1999 19:10:32 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: Help with copying results in macro Message-ID: X-MIME-Autoconverted: from 8bit to quoted-printable by thor.cf.ac.uk id TAA12994 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id OAA27458 Resent-Message-ID: <"4UFrX2.0.Dj6.XZDfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/844 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: 2218 Dear all, today I've written my first macros and of course there are problems. The macro (susan) works well for one image but the stack version (susanstack) is somehow wrong. The results of slice n are overwritten by the results of slice n+1. I want to collect all the results of all particles in one clipboard buffer or file (doesn't matter which). At the bottom is my macro file. Can someone spot the error in the last macro called susanstack. I tried different places for ShowResults and CopyResults to no avail. Thanks in advance, 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 ------------------------------- macro file begins here macro 'susan [j]'; {for final analysis of susan edge images} var n, mean, mode, min, max: integer; begin; SelectAll; Measure; GetResults(n,mean,mode,min,max); SetThreshold(max); MakeBinary; ResetCounter; SetScale(24.11396947,'µm',0.9799); SetOptions('Area, X-Y Center, Perimeter, Major, Minor'); SetPrecision(5); LabelParticles(false); OutlineParticles(false); IgnoreParticlesTouchingEdge(true); IncludeInteriorHoles(true); SetParticleSize(200,10000); AnalyzeParticles; ShowResults; CopyResults; end; macro 'dispose [d]'; {dispose without confirmation or warning} begin; Dispose; end; procedure CheckForStack; begin if nPics=0 then begin PutMessage('This macro requires a stack.'); exit; end; if nSlices=0 then begin PutMessage('This window is not a stack.'); exit end; end; macro 'susanstack [s]'; {for final analysis of susan edge images in a stack} var i, n, mean, mode, min, max: integer; begin; CheckForStack; ResetCounter; SetScale(24.11396947,'µm',0.9799); SetOptions('Area, X-Y Center, Perimeter, Major, Minor'); SetPrecision(5); LabelParticles(false); OutlineParticles(false); IgnoreParticlesTouchingEdge(true); IncludeInteriorHoles(true); SetParticleSize(200,10000); for i:= 1 to nSlices do begin SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SetThreshold(max); MakeBinary; AnalyzeParticles; ShowResults; end; CopyResults; end; From nih-image-request@io.ece.drexel.edu Tue Jan 19 17:47 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA21953 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 17:47:21 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 17:47:21 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: Kreft@cardiff.ac.uk, nih-image@io.ece.drexel.edu Date: Wed, 20 Jan 1999 9:23:34 +1100 Subject: Re: Help with copying results in macro Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <116FE0B7A4D@rna.bio.mq.edu.au> Resent-Message-ID: <"55fGX.0.sd4.XOGfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/845 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1814 >Date: Tue, 19 Jan 1999 19:10:32 +0000 (GMT) >From: Jan Kreft >To: nih-image@io.ece.drexel.edu >Subject: Help with copying results in macro > >Dear all, > >today I've written my first macros and of course there are problems. The >macro (susan) works well for one image but the stack version (susanstack) >is somehow wrong. The results of slice n are overwritten by the results o= >f >slice n+1. I want to collect all the results of all particles in one >clipboard buffer or file (doesn't matter which).=20 > >At the bottom is my macro file. Can someone spot the error in the last >macro called susanstack. I tried different places for ShowResults and >CopyResults to no avail.=20 > >Thanks in advance, > >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 > Fortunately, few commonly made macro programming mistakes are as obscure as this one but I did battle with it long ago. :-) >From Object-Image Help file (and in NIH-Image manual): "_______________ AnalyzeParticles('options') Does particle analysis, where 'options' (optional) contains some combination of 'label', 'outline', 'ignore', 'include' and 'reset'. Any option not listed is disabled. Use "AnalyzeParticles('dialog')" to display the dialog box using the existing settings. ________________" So AnalyzeParticles; implies reset of results counter. To accumulate results for stack, change AnalyzeParticles; to: AnalyzeParticles(''); As 'reset' is not listed, then it will then be disabled :-) 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 19 18:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA29427 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 18:52:13 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 18:52:13 -0500 (EST) Mime-Version: 1.0 Message-Id: In-Reply-To: <3.0.5.32.19990119121010.007e76f0@wingate> Date: Tue, 19 Jan 1999 18:29:10 -0500 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: Re: is it practical to make color pictures from gray ones (composite) Resent-Message-ID: <"lmT9o1.0.hW6.ELHfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/846 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 762 With a good camera for initial camera, the results can be better than any mid range color camera!! Definitely worth it. >Hello all NIH users, this is my first letter to this mailinglist in >12 months. I just wanted to know if it is possible to make color pictures >from stacks of gray pictures (using color filters on the camera etc.), >gray(RGB) --> color(RBG)??? > >Thanks in advance, > >Broddi Reyr Hansen BSc >Holar Agricultual College, >551 Saudarkrokur, >Iceland >email: brh@krokur.is >web: www.krokur.is/~holar/main.html >=========================================== 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 Tue Jan 19 19:31 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA04462 for cshtest@io.ece.drexel.edu; Tue, 19 Jan 1999 19:31:42 -0500 (EST) Resent-Date: Tue, 19 Jan 1999 19:31:42 -0500 (EST) Message-Id: <3.0.5.32.19990119191212.00c2a200@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: Tue, 19 Jan 1999 19:12:12 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: How do I set a timer/trigger for a mercury lamp fluorescent In-Reply-To: <3.0.1.32.19990118171055.00686510@email.psu.edu> Mime-Version: 1.0 Resent-Message-ID: <"IUFTB.0.dV.e-Hfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/847 X-Loop: nih-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 Or does anyone have >an idea of how I can separately time the mercury lamp? > There are various commercial remote-control power outlets that can be controlled by ethernet, telephone, serial ports, etc. (cost $250 US and up, depending on what you want.) See for example http://www.baytechdcd.com/rpc1.hthml or http://www.dataprobe.com I'd think their technical staff could help you find a product that would do the job. Wade Schuette Ann Arbor, MI Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Wed Jan 20 03:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA07616 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 03:28:12 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 03:28:12 -0500 (EST) Message-ID: <19990120080802.15769.qmail@hotmail.com> X-Originating-IP: [139.165.30.104] From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: DEM grayscale 16 bit Date: Wed, 20 Jan 1999 00:08:01 PST Mime-Version: 1.0 Resent-Message-ID: <"nEjq11.0.I71.7yOfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/848 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 899 Dear Imagers I need to import a USGS Digital Elevation Model (EROS DATA CENTER DAAC_GTOPO30) composed of 6000x4800 pixel, with a deep of 16 bit grayscale, BIL, in Image (NIH, SXM or Scion) on Macintosh, but in reponse I've the message that I'm limited on 4092 pixel for images with 16 bit... otherwise on PC (ScionImage) is possible to import the image without problem. Someone can explain me why? And how can I import the DEM on NIH-Image? Thanks in advance Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV -> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-d-request@io.ece.drexel.edu Wed Jan 20 03:32 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA08224; Wed, 20 Jan 1999 03:32:01 -0500 (EST) Date: Wed, 20 Jan 1999 03:32:01 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901200832.DAA08224@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #16 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/16 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: 16219 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 16 Today's Topics: Re: vesicle size distribution [ Margaret Mangan ] Re: vesicle size distribution --> JV [ gregoire ] trigger for Hg lamp fluorescence ima [ bruckner ] Re: Help with copying results in mac [ GJOSS@rna.bio.mq.edu.au ] Re: is it practical to make color pi [ Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: Re: vesicle size distribution Message-Id: Content-Type: text/plain; charset="us-ascii" Make the greyscale into a binary image after using the threshold utility, (vesicles black, matrix white); use the analyze particles command to measure the area of each vesicles (designate "area" in the options menu). See Mangan & Cashman, JVGR 1996 v 73, p 1-18. >Greetings, fellow particle counters. > >Has anyone figured out a good solution to the problem of counting individual >particles on images with grey-dark grey backgrounds (such as SEM images of >basalt, pumice, etc)? I've been working with various macros and kernels I've >found on the web, but none of them give me quite the results I'm looking for, >and it seems like many people have faced similar problems. I am trying to >do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need >to somehow define the edges of the vesicles apart from the background grey. >I'd appreciate any ideas. > >Thanks! > >Heidi Guetschow >Carleton College >300 N. College St. >Northfield, MN 55057 Margaret Mangan telephone:(650)329-5738 U.S. Geological Survey fax:(650)329-5203 Volcano Hazards Team MS 910 email:mmangan@mojave.wr.usgs.gov 345 Middlefield Road Menlo Park, CA 94025 USA ------------------------------ Date: Tue, 19 Jan 1999 17:29:14 +0100 From: Mark Wunsch To: nih-image@io.ece.drexel.edu Subject: Radius Photo DV Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Imagers, I would like to grab images from digital videotape with NIH-Image. I am using a Radius PhotoDV card with Firewire input. Radius supplies a Photoshop plug-in which works well with Photoshop or ColorIt software but is not recognized by NIH. Does anybody know why? Is there any chance to change this! Greetings Mark ******************************** NEW TELEPHONE NEW TELEPHONE Mark Wunsch Centre for Tropical Marine Ecology Fahrenheitstr. 1 28359 Bremen Phone ++49-421-23800-25 Phone Secretary ++49-421-23800-21 Fax ++49-421-2208330 mwunsch@uni-bremen.de ******************************** ------------------------------ Date: Tue, 19 Jan 1999 17:38:48 +0100 From: gregoire To: Margaret Mangan , nih-image@io.ece.drexel.edu Subject: Re: vesicle size distribution --> JVGR Message-ID: <36A4B517.E224496B@starlab.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! I was just wondering.... what does JVGR stands for? Thanks Gregoire Margaret Mangan wrote: > Make the greyscale into a binary image after using the threshold utility, > (vesicles black, matrix white); use the analyze particles command to > measure the area of each vesicles (designate "area" in the options menu). > See Mangan & Cashman, JVGR 1996 v 73, p 1-18. > > >Greetings, fellow particle counters. > > > >Has anyone figured out a good solution to the problem of counting individual > >particles on images with grey-dark grey backgrounds (such as SEM images of > >basalt, pumice, etc)? I've been working with various macros and kernels I've > >found on the web, but none of them give me quite the results I'm looking for, > >and it seems like many people have faced similar problems. I am trying to > >do a vesicle size distribution analysis on a rhyolite dome in Alaska. I need > >to somehow define the edges of the vesicles apart from the background grey. > >I'd appreciate any ideas. > > > >Thanks! > > > >Heidi Guetschow > >Carleton College > >300 N. College St. > >Northfield, MN 55057 > > Margaret Mangan telephone:(650)329-5738 > U.S. Geological Survey fax:(650)329-5203 > Volcano Hazards Team MS 910 email:mmangan@mojave.wr.usgs.gov > 345 Middlefield Road > Menlo Park, CA 94025 > USA -- ======================================================== Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-53-80 http://www.starlab.org email:gregoire@starlab.net ======================================================== ------------------------------ Date: Tue, 19 Jan 1999 09:41:11 -0800 From: bruckner To: nih-image@io.ece.drexel.edu Subject: trigger for Hg lamp fluorescence imaging Message-Id: Content-Type: text/plain; charset="us-ascii" >I am observing green fluorescent protein production in plant roots with a >Nikon SMZ dissecting microscope while illuminating my sample with filtered >ultraviolet light from a mercury lamp. > > However, I'm not sure how to handle triggering the mercury >lamp to turn on and off for those intervals; the lamp must be externally >ignited each time the power is turned off. Prolonged exposure of my sample >to the light source will result in extreme stresses, not to mention the >expense of the mercury bulbs. Does anyone know how I can work the mercury >lamp timing and ignition into the Scion image program? Or does anyone have >an idea of how I can separately time the mercury lamp? Mercury lamps have a warm-up time of at least 5 minutes to full power. If you have some flexibility with light sources, how about using a Xenon flashlamp (strobes and camera flashes use this). Scientific Xenon flashlamps (EG&G, Hamamatsu, Strobotac) are designed to flash off an external trigger. I realize that Xenon isn't as intense in the UV as Hg lamps. By pulsing the light source, however, you get a bright intensity light for the duration of 1 camera exposure. With filters, I use the blue light from Xenon flashlamps to excite green fluorescence with my system (not a microscope setup). ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- ------------------------------ Date: Tue, 19 Jan 99 13:38:29 -0500 From: "Jared L. Rifkin" To: Subject: trigger for Hg lamp fluorescence imaging Message-ID: <7AF9862B4B@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" if you can leave the lamp on for the duration of the experiment (24 hrs?) that would be the easiest thing: insert a shutter in the light path (piece of black posterboard attached to the hourhand of a electric alarm clock- take the face and other hands off and use toothpick or paperclip and tape to secure the shutter; or- secure the shutter to a timer-actuated solenoid- fancier but just as effective - better if space is limited.) the width of the piece of board will dictate the illumination-on time. yes- the prep will be lit every hour but so-what. if leaving the lamp on for the ex4ended time is not good ( i realize that mercury lamps have a limited life but doesn't turning them on and off considerably shorten that life??)- then the question is how to trigger the 'ignition' circuit directly from a timer. send me the circuit and i'll try to help. i've had considerable experience building timers and shutters and time-ramped turn circuits for microscope illuminators- i've learned that the 'too simple' is often the best and most reliable. ------------------------------ Date: Tue, 19 Jan 1999 19:10:32 +0000 (GMT) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: Help with copying results in macro Message-ID: Content-type: text/PLAIN; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Dear all, today I've written my first macros and of course there are problems. The macro (susan) works well for one image but the stack version (susanstack) is somehow wrong. The results of slice n are overwritten by the results of slice n+1. I want to collect all the results of all particles in one clipboard buffer or file (doesn't matter which). At the bottom is my macro file. Can someone spot the error in the last macro called susanstack. I tried different places for ShowResults and CopyResults to no avail. Thanks in advance, 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 ------------------------------- macro file begins here macro 'susan [j]'; {for final analysis of susan edge images} var n, mean, mode, min, max: integer; begin; SelectAll; Measure; GetResults(n,mean,mode,min,max); SetThreshold(max); MakeBinary; ResetCounter; SetScale(24.11396947,'µm',0.9799); SetOptions('Area, X-Y Center, Perimeter, Major, Minor'); SetPrecision(5); LabelParticles(false); OutlineParticles(false); IgnoreParticlesTouchingEdge(true); IncludeInteriorHoles(true); SetParticleSize(200,10000); AnalyzeParticles; ShowResults; CopyResults; end; macro 'dispose [d]'; {dispose without confirmation or warning} begin; Dispose; end; procedure CheckForStack; begin if nPics=0 then begin PutMessage('This macro requires a stack.'); exit; end; if nSlices=0 then begin PutMessage('This window is not a stack.'); exit end; end; macro 'susanstack [s]'; {for final analysis of susan edge images in a stack} var i, n, mean, mode, min, max: integer; begin; CheckForStack; ResetCounter; SetScale(24.11396947,'µm',0.9799); SetOptions('Area, X-Y Center, Perimeter, Major, Minor'); SetPrecision(5); LabelParticles(false); OutlineParticles(false); IgnoreParticlesTouchingEdge(true); IncludeInteriorHoles(true); SetParticleSize(200,10000); for i:= 1 to nSlices do begin SelectSlice(i); SelectAll; Measure; GetResults(n,mean,mode,min,max); SetThreshold(max); MakeBinary; AnalyzeParticles; ShowResults; end; CopyResults; end; ------------------------------ Date: Wed, 20 Jan 1999 9:23:34 +1100 From: GJOSS@rna.bio.mq.edu.au To: Kreft@cardiff.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Help with copying results in macro Message-ID: <116FE0B7A4D@rna.bio.mq.edu.au> >Date: Tue, 19 Jan 1999 19:10:32 +0000 (GMT) >From: Jan Kreft >To: nih-image@io.ece.drexel.edu >Subject: Help with copying results in macro > >Dear all, > >today I've written my first macros and of course there are problems. The >macro (susan) works well for one image but the stack version (susanstack) >is somehow wrong. The results of slice n are overwritten by the results o= >f >slice n+1. I want to collect all the results of all particles in one >clipboard buffer or file (doesn't matter which).=20 > >At the bottom is my macro file. Can someone spot the error in the last >macro called susanstack. I tried different places for ShowResults and >CopyResults to no avail.=20 > >Thanks in advance, > >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 > Fortunately, few commonly made macro programming mistakes are as obscure as this one but I did battle with it long ago. :-) >From Object-Image Help file (and in NIH-Image manual): "_______________ AnalyzeParticles('options') Does particle analysis, where 'options' (optional) contains some combination of 'label', 'outline', 'ignore', 'include' and 'reset'. Any option not listed is disabled. Use "AnalyzeParticles('dialog')" to display the dialog box using the existing settings. ________________" So AnalyzeParticles; implies reset of results counter. To accumulate results for stack, change AnalyzeParticles; to: AnalyzeParticles(''); As 'reset' is not listed, then it will then be disabled :-) 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, 19 Jan 1999 18:29:10 -0500 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: Re: is it practical to make color pictures from gray ones (composite) Message-Id: Content-Type: text/plain; charset="us-ascii" With a good camera for initial camera, the results can be better than any mid range color camera!! Definitely worth it. >Hello all NIH users, this is my first letter to this mailinglist in >12 months. I just wanted to know if it is possible to make color pictures >from stacks of gray pictures (using color filters on the camera etc.), >gray(RGB) --> color(RBG)??? > >Thanks in advance, > >Broddi Reyr Hansen BSc >Holar Agricultual College, >551 Saudarkrokur, >Iceland >email: brh@krokur.is >web: www.krokur.is/~holar/main.html >=========================================== 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: Tue, 19 Jan 1999 19:12:12 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: How do I set a timer/trigger for a mercury lamp fluorescent Message-Id: <3.0.5.32.19990119191212.00c2a200@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" Or does anyone have >an idea of how I can separately time the mercury lamp? > There are various commercial remote-control power outlets that can be controlled by ethernet, telephone, serial ports, etc. (cost $250 US and up, depending on what you want.) See for example http://www.baytechdcd.com/rpc1.hthml or http://www.dataprobe.com I'd think their technical staff could help you find a product that would do the job. Wade Schuette Ann Arbor, MI Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Wed, 20 Jan 1999 00:08:01 PST From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: DEM grayscale 16 bit Message-ID: <19990120080802.15769.qmail@hotmail.com> Content-Type: text/plain Dear Imagers I need to import a USGS Digital Elevation Model (EROS DATA CENTER DAAC_GTOPO30) composed of 6000x4800 pixel, with a deep of 16 bit grayscale, BIL, in Image (NIH, SXM or Scion) on Macintosh, but in reponse I've the message that I'm limited on 4092 pixel for images with 16 bit... otherwise on PC (ScionImage) is possible to import the image without problem. Someone can explain me why? And how can I import the DEM on NIH-Image? Thanks in advance Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV -> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com -------------------------------- End of nih-image-d Digest V99 Issue #16 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 20 03:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA12184 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 03:58:08 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 03:58:08 -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: <116FE0B7A4D@rna.bio.mq.edu.au> Mime-Version: 1.0 Date: Wed, 20 Jan 1999 09:45:43 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Help with copying results in macro Resent-Message-ID: <"Ee-Xs1.0.LN2.XRPfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/849 X-Loop: nih-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 >So > AnalyzeParticles; >implies reset of results counter. It seems that AnalyzeParticles; leaves the current settings untouched, i.e. it doesn't necessarily reset the counter. 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 Jan 20 05:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA23998 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 05:23:52 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 05:23:52 -0500 (EST) Date: Wed, 20 Jan 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199901201005.FAA21166@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"1aZNC.0.sA5.FfQfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/850 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. 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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 Wed Jan 20 09:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24754 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 09:08:06 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 09:08:06 -0500 (EST) X-Sender: ajonker.public.amc@reddwarf.amc.uva.nl Message-Id: In-Reply-To: <199901200816.DAA05659@io.ece.drexel.edu> Mime-Version: 1.0 Date: Wed, 20 Jan 1999 14:39:48 +0100 To: nih-image@io.ece.drexel.edu From: Ard Jonker Subject: Re: trigger for Hg lamp fluorescence imaging Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id IAA20689 Resent-Message-ID: <"a_f9-1.0.e35.RpTfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/851 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1074 >considerably shorten that life??)- then the question is how to trigger >the 'ignition' circuit directly from a timer. You can trigger with the digital output lines of the Scion LG-3. That drives e.g. a BUZ-11 FET directly for powering a solenoid, as far as we experience it. An alternative could be a photodiode that is stuck to a piece of the screen. Blank that part (put a black NIH-Image window over it) and display a white block in it when you want an exposure.... The potodiode will come to conductivity and you trigger is there. We made a macro that does time lapse recording and that also records the number of seconds elapsed since the start of the time lapse measurement in the first few pixels of the image, so that in retrospect these times can be extracted, even after years. Ard dr A.Jonker |Academic Medical Centre Dep of Cell Biology and Histology |Meibergdreef 15 Faculty of Medicine |1105 AZ Amsterdam University of Amsterdam |The Netherlands tel +31 20 566 5304 |fax +31 20 697 4156 From nih-image-request@io.ece.drexel.edu Wed Jan 20 10:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA08891 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 10:52:27 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 10:52:27 -0500 (EST) Message-ID: <19990120153227.24612.rocketmail@web507.yahoomail.com> Date: Wed, 20 Jan 1999 07:32:27 -0800 (PST) From: Mark Vivino Subject: Re: Help with copying results in macro To: nih-image@io.ece.drexel.edu MIME-Version: 1.0 Resent-Message-ID: <"qRTCb3.0.RO1.zRVfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/852 X-Loop: nih-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 If I understand what you are asking then you have to do all this in your loop: Copy results select a different window which is a text window paste the results select the stack == Mark A. Vivino 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 Jan 20 11:31 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA13980 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 11:31:01 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 11:31:01 -0500 (EST) Message-Id: <3.0.6.32.19990120111707.008e0800@crab.rutgers.edu> X-Sender: saidel@crab.rutgers.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 20 Jan 1999 11:17:07 -0500 To: nih-image@io.ece.drexel.edu From: Bill Saidel Subject: doubling video capture rate? Mime-Version: 1.0 Resent-Message-ID: <"wAaNL3.0.In2.G0Wfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/853 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1412 Hi, Since my understanding of video technology is limited, please excuse the ignorance inherent in this question. Is it possible to send the odd & even lines of a video captured image to NIH-Image separately during movie acquisition? This would, as I understand the sequence of odd-line/even-line acquisition or perhaps misunderstand it, double the 30 images/sec rate limitation inherent in straight movie capture since odd lines are acquired before the even lines (Is this true?. If it were possible, would the trade-off be a reduced image size since the line number/image would be effectively cut in half. Since ignorance drives this question (and lack of money for a sophisticated system), if it cannot be done, could an explanation be provided? Looking forward to reducing my personal entropy, Bill ********************************************************************** 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 "Between the approximation of the idea and the precision of reality, there is a small gap of the unimaginable." Milan Kundera - "The Unbearable Lightness of Being" From nih-image-request@io.ece.drexel.edu Wed Jan 20 13:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA27867 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 13:23:56 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 13:23:56 -0500 (EST) Message-Id: <3.0.5.32.19990120105119.00944740@NMT.EDU> X-Sender: grawling@NMT.EDU X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 20 Jan 1999 10:51:19 -0700 To: nih-image@io.ece.drexel.edu From: "Geoffrey C. Rawling" Subject: Save blank field macro? Mime-Version: 1.0 Resent-Message-ID: <"bVQLO3.0.Mp5.xUXfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/854 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1330 Hi imagers, I have been trying to write a macro that reproduces the action of the "Save Blank Field" menu command during image capture. I would like to collect an rgb stack of the illumination, and then use the macro to correct the captured rgb image (of rock thin sections) for the uneven illumination, slice by slice in the stack. The algorithm as described in the help manual that the menu command uses seems simple, but I can't reproduce the results in a macro, even on a one pass greyscale image. I've been using real image math to do the calculations. Any thoughts on this? Related to this, I only get uneven illumination on the lowest power (2x) objective on our scope. The image through the oculars looks fine but the image on the screen is dim around the edges. Something in the optical path I should change? BTW, Thanks to all who responded to my query last fall about setting up a petrographic image analysis system. The info from the list was invaluble. We now have a Hitachi KPD-50 RGB camera mounted on our scope with a DiagInc. adaptor and connected to a PC with a Scion VG-5 board, and I'm very happy with it. Thanks ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* From nih-image-request@io.ece.drexel.edu Wed Jan 20 14:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA08761 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 14:56:52 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 14:56:52 -0500 (EST) From: SolamereTG@aol.com Message-ID: <948361e0.36a62e77@aol.com> Date: Wed, 20 Jan 1999 14:28:55 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Save blank field macro? Content-transfer-encoding: 7bit X-Mailer: AOL 3.0.1 for Mac sub 78 Resent-Message-ID: <"baTt-.0.HU1.NyYfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/855 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 877 With regard to uneven illumination using the 2x lens.: "Related to this, I only get uneven illumination on the lowest power (2x) objective on our scope. The image through the oculars looks fine but the image on the screen is dim around the edges. Something in the optical path I should change? " I Assume you are using epi-illumination (through the lens): It sounds like you are not "overfilling" the rear aperture of the objective with your illumination beam. Compare the rear aperture diameters of your 10x and 2x lens and compare it with the beam size from your source measured at a distance equivalent to the rear aperture. The beam size may be limited by your microscopes filter cube or the epi-illumination path in your microscope. Good Luck, George Peeters Solamere Technology Group WWW.Solameretech.com 801 322-2645 Good Luck Depending on your epi-illumination From nih-image-request@io.ece.drexel.edu Wed Jan 20 15:49 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA18239 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 15:49:12 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 15:49:12 -0500 (EST) Mime-Version: 1.0 X-Sender: gehoffma@umaryland.edu (Unverified) Message-Id: In-Reply-To: <948361e0.36a62e77@aol.com> Date: Wed, 20 Jan 1999 15:17:17 -0500 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: Re: Save blank field macro? Resent-Message-ID: <"CQsMk2.0.qi3.JoZfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/856 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1524 the uneven illumination is a common problem with brightfield low power images. With Nikon Scopes there is a low power condensor that evens out the illumination and solves the problem. If you don't have such a component, with Photoshop, you can correct the unevenness by capturing a blank field and then subtracting the blank from the desired image. If the result is inverted, then you simply invert that image and the problem is solved. >With regard to uneven illumination using the 2x lens.: >"Related to this, I only get uneven illumination on the lowest power (2x) >objective on our scope. The image through the oculars looks fine but the >image on the screen is dim around the edges. Something in the optical path >I should change? " > >I Assume you are using epi-illumination (through the lens): >It sounds like you are not "overfilling" the rear aperture of the objective >with your illumination beam. Compare the rear aperture diameters of your 10x >and 2x lens and compare it with the beam size from your source measured at a >distance equivalent to the rear aperture. The beam size may be limited by your >microscopes filter cube or the epi-illumination path in your microscope. > >Good Luck, >George Peeters >Solamere Technology Group >WWW.Solameretech.com >801 322-2645 > > >Good Luck > >Depending on your epi-illumination 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 Jan 20 17:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA02092 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 17:41:51 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 17:41:51 -0500 (EST) Message-ID: <36A5E757.42E9@thurston.com> Date: Wed, 20 Jan 1999 14:25:27 +0000 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: Re: nih-image-d Digest V99 #16 References: <199901200816.DAA05789@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"71_pD3.0.l57.CPbfs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/857 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 124 JVGR=Journal of Volcanology and Geothermal Research. This journal is subscribed to by most major universities. Pat Pringle From nih-image-request@io.ece.drexel.edu Wed Jan 20 18:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA07497 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 18:21:56 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 18:21:56 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Date: Thu, 21 Jan 1999 9:55:26 +1100 Subject: Re: Save blank field macro? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <12F7805325F@rna.bio.mq.edu.au> Resent-Message-ID: <"NZHY4.0.M-.hybfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/858 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1651 >Date: Wed, 20 Jan 1999 10:51:19 -0700 >To: nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: Save blank field macro? >...... > I have been trying to write a macro that reproduces the action of the >"Save Blank Field" menu command during image capture. I would like to >collect an rgb stack of the illumination, and then use the macro to correct >the captured rgb image (of rock thin sections) for the uneven illumination, >slice by slice in the stack. The algorithm as described in the help manual >that the menu command uses seems simple, but I can't reproduce the results >in a macro, even on a one pass greyscale image. I've been using real image >math to do the calculations. Any thoughts on this? >...... The easiest trap to fall into with macro subtraction of background is to omit Scalemath(false); but this shouldn't apply to real imageMath. Another is that blankfields are generally much brighter than those containing a subject and many cameras will adjust to this but your post implies that "Save Blank Field" menu command works OK so the problem is presumeably not in capture. However the fact that you refer to REAL imagemath has me wondering. I cant see the need for REAL math unless you are attempting to accomodate for greater dynamic range in the blank field which would leave you open to nonlinearities. Perhaps, if you posted your macro, it would be possible to see how it diverges from built-in code. 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 Jan 20 18:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA07715 for cshtest@io.ece.drexel.edu; Wed, 20 Jan 1999 18:23:19 -0500 (EST) Resent-Date: Wed, 20 Jan 1999 18:23:19 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: saidel@crab.rutgers.edu, nih-image@io.ece.drexel.edu Date: Thu, 21 Jan 1999 9:52:10 +1100 Subject: Re: doubling video capture rate? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <12F6A9D1322@rna.bio.mq.edu.au> Resent-Message-ID: <"aqzu_3.0.K41.6_bfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/859 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1831 >Date: Wed, 20 Jan 1999 11:17:07 -0500 >To: nih-image@io.ece.drexel.edu >From: Bill Saidel >Subject: doubling video capture rate? >Hi, > Since my understanding of video technology is limited, please excuse the >ignorance inherent in this question. Is it possible to send the odd & even >lines of a video captured image to NIH-Image separately during movie >acquisition? This would, as I understand the sequence of >odd-line/even-line acquisition or perhaps misunderstand it, double the 30 >images/sec rate limitation inherent in straight movie capture since odd >lines are acquired before the even lines (Is this true?. If it were >possible, would the trade-off be a reduced image size since the line >number/image would be effectively cut in half. > Since ignorance drives this question (and lack of money for a >sophisticated system), if it cannot be done, could an explanation be >provided? > >Looking forward to reducing my personal entropy, > Bill, It is indeed possible and practical to effectively double framerate in video capture by spliting even and odd fields of video. There is (was?) a sample macro in video macros as supplied with NIH-Image to do this for a single frame. I presume you would be satisfied to do this as a postcapture process. You can take the approach of alternately taking even/odd field frames so that you effectively halve the vertical resolution and double framerate but maintain aspect ratio by duplicating the interleaved lines. In some applications (horizontal motion), you can improve image clarity by shifting one field relative to the other to compensate for motion. 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 Jan 21 00:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA20629; Thu, 21 Jan 1999 00:07:35 -0500 (EST) Date: Thu, 21 Jan 1999 00:07:35 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901210507.AAA20629@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #17 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/17 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: 18848 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 17 Today's Topics: Re: Help with copying results in mac [ Norbert Vischer ] Re: Help with copying results in mac [ Mark Vivino ] doubling video capture rate? [ Bill Saidel To: nih-image@io.ece.drexel.edu Subject: Re: Help with copying results in macro Message-Id: Content-Type: text/plain; charset="us-ascii" >So > AnalyzeParticles; >implies reset of results counter. It seems that AnalyzeParticles; leaves the current settings untouched, i.e. it doesn't necessarily reset the counter. 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, 20 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: <199901201005.FAA21166@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". 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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: Wed, 20 Jan 1999 14:39:48 +0100 From: Ard Jonker To: nih-image@io.ece.drexel.edu Subject: Re: trigger for Hg lamp fluorescence imaging Message-Id: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit >considerably shorten that life??)- then the question is how to trigger >the 'ignition' circuit directly from a timer. You can trigger with the digital output lines of the Scion LG-3. That drives e.g. a BUZ-11 FET directly for powering a solenoid, as far as we experience it. An alternative could be a photodiode that is stuck to a piece of the screen. Blank that part (put a black NIH-Image window over it) and display a white block in it when you want an exposure.... The potodiode will come to conductivity and you trigger is there. We made a macro that does time lapse recording and that also records the number of seconds elapsed since the start of the time lapse measurement in the first few pixels of the image, so that in retrospect these times can be extracted, even after years. Ard dr A.Jonker |Academic Medical Centre Dep of Cell Biology and Histology |Meibergdreef 15 Faculty of Medicine |1105 AZ Amsterdam University of Amsterdam |The Netherlands tel +31 20 566 5304 |fax +31 20 697 4156 ------------------------------ Date: Wed, 20 Jan 1999 07:32:27 -0800 (PST) From: Mark Vivino To: nih-image@io.ece.drexel.edu Subject: Re: Help with copying results in macro Message-ID: <19990120153227.24612.rocketmail@web507.yahoomail.com> Content-Type: text/plain; charset=us-ascii If I understand what you are asking then you have to do all this in your loop: Copy results select a different window which is a text window paste the results select the stack == Mark A. Vivino Consulting Biomedical Engineer _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ------------------------------ Date: Wed, 20 Jan 1999 11:17:07 -0500 From: Bill Saidel To: nih-image@io.ece.drexel.edu Subject: doubling video capture rate? Message-Id: <3.0.6.32.19990120111707.008e0800@crab.rutgers.edu> Content-Type: text/plain; charset="us-ascii" Hi, Since my understanding of video technology is limited, please excuse the ignorance inherent in this question. Is it possible to send the odd & even lines of a video captured image to NIH-Image separately during movie acquisition? This would, as I understand the sequence of odd-line/even-line acquisition or perhaps misunderstand it, double the 30 images/sec rate limitation inherent in straight movie capture since odd lines are acquired before the even lines (Is this true?. If it were possible, would the trade-off be a reduced image size since the line number/image would be effectively cut in half. Since ignorance drives this question (and lack of money for a sophisticated system), if it cannot be done, could an explanation be provided? Looking forward to reducing my personal entropy, Bill ********************************************************************** 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 "Between the approximation of the idea and the precision of reality, there is a small gap of the unimaginable." Milan Kundera - "The Unbearable Lightness of Being" ------------------------------ Date: Wed, 20 Jan 1999 10:51:19 -0700 From: "Geoffrey C. Rawling" To: nih-image@io.ece.drexel.edu Subject: Save blank field macro? Message-Id: <3.0.5.32.19990120105119.00944740@NMT.EDU> Content-Type: text/plain; charset="us-ascii" Hi imagers, I have been trying to write a macro that reproduces the action of the "Save Blank Field" menu command during image capture. I would like to collect an rgb stack of the illumination, and then use the macro to correct the captured rgb image (of rock thin sections) for the uneven illumination, slice by slice in the stack. The algorithm as described in the help manual that the menu command uses seems simple, but I can't reproduce the results in a macro, even on a one pass greyscale image. I've been using real image math to do the calculations. Any thoughts on this? Related to this, I only get uneven illumination on the lowest power (2x) objective on our scope. The image through the oculars looks fine but the image on the screen is dim around the edges. Something in the optical path I should change? BTW, Thanks to all who responded to my query last fall about setting up a petrographic image analysis system. The info from the list was invaluble. We now have a Hitachi KPD-50 RGB camera mounted on our scope with a DiagInc. adaptor and connected to a PC with a Scion VG-5 board, and I'm very happy with it. Thanks ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* ------------------------------ Date: Wed, 20 Jan 1999 14:28:55 EST From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Save blank field macro? Message-ID: <948361e0.36a62e77@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit With regard to uneven illumination using the 2x lens.: "Related to this, I only get uneven illumination on the lowest power (2x) objective on our scope. The image through the oculars looks fine but the image on the screen is dim around the edges. Something in the optical path I should change? " I Assume you are using epi-illumination (through the lens): It sounds like you are not "overfilling" the rear aperture of the objective with your illumination beam. Compare the rear aperture diameters of your 10x and 2x lens and compare it with the beam size from your source measured at a distance equivalent to the rear aperture. The beam size may be limited by your microscopes filter cube or the epi-illumination path in your microscope. Good Luck, George Peeters Solamere Technology Group WWW.Solameretech.com 801 322-2645 Good Luck Depending on your epi-illumination ------------------------------ Date: Wed, 20 Jan 1999 15:17:17 -0500 From: Gloria Hoffman To: nih-image@io.ece.drexel.edu Subject: Re: Save blank field macro? Message-Id: Content-Type: text/plain; charset="us-ascii" the uneven illumination is a common problem with brightfield low power images. With Nikon Scopes there is a low power condensor that evens out the illumination and solves the problem. If you don't have such a component, with Photoshop, you can correct the unevenness by capturing a blank field and then subtracting the blank from the desired image. If the result is inverted, then you simply invert that image and the problem is solved. >With regard to uneven illumination using the 2x lens.: >"Related to this, I only get uneven illumination on the lowest power (2x) >objective on our scope. The image through the oculars looks fine but the >image on the screen is dim around the edges. Something in the optical path >I should change? " > >I Assume you are using epi-illumination (through the lens): >It sounds like you are not "overfilling" the rear aperture of the objective >with your illumination beam. Compare the rear aperture diameters of your 10x >and 2x lens and compare it with the beam size from your source measured at a >distance equivalent to the rear aperture. The beam size may be limited by your >microscopes filter cube or the epi-illumination path in your microscope. > >Good Luck, >George Peeters >Solamere Technology Group >WWW.Solameretech.com >801 322-2645 > > >Good Luck > >Depending on your epi-illumination 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, 20 Jan 1999 14:25:27 +0000 From: "Patrick T. Pringle" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #16 Message-ID: <36A5E757.42E9@thurston.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit JVGR=Journal of Volcanology and Geothermal Research. This journal is subscribed to by most major universities. Pat Pringle ------------------------------ Date: Thu, 21 Jan 1999 9:55:26 +1100 From: GJOSS@rna.bio.mq.edu.au To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Subject: Re: Save blank field macro? Message-ID: <12F7805325F@rna.bio.mq.edu.au> >Date: Wed, 20 Jan 1999 10:51:19 -0700 >To: nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: Save blank field macro? >...... > I have been trying to write a macro that reproduces the action of the >"Save Blank Field" menu command during image capture. I would like to >collect an rgb stack of the illumination, and then use the macro to correct >the captured rgb image (of rock thin sections) for the uneven illumination, >slice by slice in the stack. The algorithm as described in the help manual >that the menu command uses seems simple, but I can't reproduce the results >in a macro, even on a one pass greyscale image. I've been using real image >math to do the calculations. Any thoughts on this? >...... The easiest trap to fall into with macro subtraction of background is to omit Scalemath(false); but this shouldn't apply to real imageMath. Another is that blankfields are generally much brighter than those containing a subject and many cameras will adjust to this but your post implies that "Save Blank Field" menu command works OK so the problem is presumeably not in capture. However the fact that you refer to REAL imagemath has me wondering. I cant see the need for REAL math unless you are attempting to accomodate for greater dynamic range in the blank field which would leave you open to nonlinearities. Perhaps, if you posted your macro, it would be possible to see how it diverges from built-in code. 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, 21 Jan 1999 9:52:10 +1100 From: GJOSS@rna.bio.mq.edu.au To: saidel@crab.rutgers.edu, nih-image@io.ece.drexel.edu Subject: Re: doubling video capture rate? Message-ID: <12F6A9D1322@rna.bio.mq.edu.au> >Date: Wed, 20 Jan 1999 11:17:07 -0500 >To: nih-image@io.ece.drexel.edu >From: Bill Saidel >Subject: doubling video capture rate? >Hi, > Since my understanding of video technology is limited, please excuse the >ignorance inherent in this question. Is it possible to send the odd & even >lines of a video captured image to NIH-Image separately during movie >acquisition? This would, as I understand the sequence of >odd-line/even-line acquisition or perhaps misunderstand it, double the 30 >images/sec rate limitation inherent in straight movie capture since odd >lines are acquired before the even lines (Is this true?. If it were >possible, would the trade-off be a reduced image size since the line >number/image would be effectively cut in half. > Since ignorance drives this question (and lack of money for a >sophisticated system), if it cannot be done, could an explanation be >provided? > >Looking forward to reducing my personal entropy, > Bill, It is indeed possible and practical to effectively double framerate in video capture by spliting even and odd fields of video. There is (was?) a sample macro in video macros as supplied with NIH-Image to do this for a single frame. I presume you would be satisfied to do this as a postcapture process. You can take the approach of alternately taking even/odd field frames so that you effectively halve the vertical resolution and double framerate but maintain aspect ratio by duplicating the interleaved lines. In some applications (horizontal motion), you can improve image clarity by shifting one field relative to the other to compensate for motion. 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: Wed, 20 Jan 1999 23:45:44 -0500 From: Ross Nakatsuji To: nih-image@io.ece.drexel.edu Subject: Re: is it practical to make color pictures from gray ones (composite) Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Broddi, Yes. It is practical and often done these days for quantitative imaging. Most imaging packages like NIH Image, IPLab, or ImagePro Plus have a "merge" function that can make a color 24-bit, 36-bit, or 48-bit image from 8-bit, 12-bit, or 16-bit grayscale "planes" taken with RGB filters. The company I work for, CRI, even sells a liquid crystal RGB filter to take these pictures in quick succession and combine them. You've hit on a technique that makes possible high resolution, outstanding color if you do your merge right, and low cost (no 3-CCD camera). The beauty is that each pixel, instead of having the interpolated color of a color "mosiac" chip or having low resolution because 3 CCDs are needed, has full color information. Of course, remember that if the sample is moving, the cycle from R to G to B needs to be fast! >Hello all NIH users, this is my first letter to this mailinglist in >12 months. I just wanted to know if it is possible to make color pictures >from stacks of gray pictures (using color filters on the camera etc.), >gray(RGB) --> color(RBG)??? > >Thanks in advance, > >Broddi Reyr Hansen BSc >Holar Agricultual College, >551 Saudarkrokur, >Iceland >email: brh@krokur.is >web: www.krokur.is/~holar/main.html >=========================================== ========================================== Ross Nakatsuji, Technical Sales Support Cambridge Research & Instrumentation, Inc. 80 Ashford Street Boston, MA 02134 TEL: 617.787.5700 FAX: 617.787.4488 website: http://www.cri-inc.com e-mail (CRI): techsupport@cri-inc.com e-mail (home): pp002736@mindspring.com -------------------------------- End of nih-image-d Digest V99 Issue #17 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jan 21 00:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA20677 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 00:07:50 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 00:07:50 -0500 (EST) Mime-Version: 1.0 X-Sender: pp002736@mail.mindspring.com Message-Id: In-Reply-To: <3.0.5.32.19990119121010.007e76f0@wingate> Date: Wed, 20 Jan 1999 23:45:44 -0500 To: nih-image@io.ece.drexel.edu From: Ross Nakatsuji Subject: Re: is it practical to make color pictures from gray ones (composite) Resent-Message-ID: <"Q7i--.0.yP4.88hfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/860 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1606 Dear Broddi, Yes. It is practical and often done these days for quantitative imaging. Most imaging packages like NIH Image, IPLab, or ImagePro Plus have a "merge" function that can make a color 24-bit, 36-bit, or 48-bit image from 8-bit, 12-bit, or 16-bit grayscale "planes" taken with RGB filters. The company I work for, CRI, even sells a liquid crystal RGB filter to take these pictures in quick succession and combine them. You've hit on a technique that makes possible high resolution, outstanding color if you do your merge right, and low cost (no 3-CCD camera). The beauty is that each pixel, instead of having the interpolated color of a color "mosiac" chip or having low resolution because 3 CCDs are needed, has full color information. Of course, remember that if the sample is moving, the cycle from R to G to B needs to be fast! >Hello all NIH users, this is my first letter to this mailinglist in >12 months. I just wanted to know if it is possible to make color pictures >from stacks of gray pictures (using color filters on the camera etc.), >gray(RGB) --> color(RBG)??? > >Thanks in advance, > >Broddi Reyr Hansen BSc >Holar Agricultual College, >551 Saudarkrokur, >Iceland >email: brh@krokur.is >web: www.krokur.is/~holar/main.html >=========================================== ========================================== Ross Nakatsuji, Technical Sales Support Cambridge Research & Instrumentation, Inc. 80 Ashford Street Boston, MA 02134 TEL: 617.787.5700 FAX: 617.787.4488 website: http://www.cri-inc.com e-mail (CRI): techsupport@cri-inc.com e-mail (home): pp002736@mindspring.com From nih-image-request@io.ece.drexel.edu Thu Jan 21 02:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA10350 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 02:41:56 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 02:41:56 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Thu, 21 Jan 1999 09:15:26 +0200 To: nih-image@io.ece.drexel.edu From: golomb@cc.huji.ac.il (Gershon Golomb) Subject: restenosis histomorphometry Resent-Message-ID: <"lmraG3.0.Le1.5Fjfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/861 X-Loop: nih-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 Hi, Is there a macro for performing histomorphometry measurments on arterial segments for calculating areas of neointima, lumen etc.? Thanks Prof. Gershon Golomb, Head, Dept. of Pharmaceutics School of Pharmacy, The Hebrew University of Jerusalem POBOX 12065, Jerusalem 91120, Israel FAX - 972-2-6436246 Phone - 972-2-6757014 e-mail - golomb@cc.huji.ac.il From nih-image-request@io.ece.drexel.edu Thu Jan 21 09:32 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA04938 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 09:32:25 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 09:32:25 -0500 (EST) Message-ID: <36A73556.FD656155@starlab.net> Date: Thu, 21 Jan 1999 15:10:32 +0100 From: gregoire X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: 'Filter' macro command References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"Pda-e1.0.dQ.QKpfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/862 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 482 Hello! Just wondering if anybody knows how to change the number of iterations for the Rank Filters from a macro (I'm using "Filter('min');"). TIA Gregoire -- ======================================================== Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-53-80 http://www.starlab.org/ email:gregoire@starlab.net ======================================================== From nih-image-request@io.ece.drexel.edu Thu Jan 21 13:49 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA08804 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 13:49:38 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 13:49:38 -0500 (EST) Message-Id: <3.0.5.32.19990121111040.0093fdd0@NMT.EDU> X-Sender: grawling@NMT.EDU X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 21 Jan 1999 11:10:40 -0700 To: nih-image@io.ece.drexel.edu From: "Geoffrey C. Rawling" Subject: more save blank field macro Mime-Version: 1.0 Resent-Message-ID: <"bhKgx1.0._u.kssfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/863 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1862 Here's the (nonworking) macro I wrote to perform the save blank field menu command. This was just for a greyscale image, not a stack. Doing the imagemath without the 'real' changes the result, but it doesn't reproduce the menu command. Geff MACRO 'background correction'; VAR OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string n, mode, min, max, b1, t1, cfw1, cfw2 : integer mean, invmean : real BEGIN {This section asks for the image names and directory} PutMessage('This macro requires a background image and the t-sect image. ', 'They must be in the same directory'); OpPath := GetString('Enter the path to the images','d:\images\practice\'); BackImage := GetString('Enter the background image name','gsblankfield.tif'); TsectImage := GetString('Enter the t-sect image image name','gsuncorrected.tif'); BackImagePath := Concat(OpPath, BackImage); Open(BackImagePath); b1 := PidNumber; TsectImagePath := Concat(OpPath, TsectImage); Open(TsectImagePath); t1 := PidNumber; {get mean of background} SelectPic(b1); Measure; GetResults(n,mean,mode,min,max); invmean := (1/mean); {make window of ones} Duplicate('correction factor window'); cfw1 := PidNumber; ChangeValues(0,255,1); {create image with pixel by pixel correction factors} ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); cfw2 := PidNumber; SelectPic(cfw1); Dispose; PutMessage('invmean = ',invmean); {divide t-sect image by window with correction factors} ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); END; ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* From nih-image-request@io.ece.drexel.edu Thu Jan 21 17:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA04631 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 17:18:55 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 17:18:55 -0500 (EST) Date: Thu, 21 Jan 1999 13:49:32 -0800 (PST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: vera@physics.ucla.edu (Moin Vera) Subject: unsubscribe Resent-Message-ID: <"_PZrd2.0.X8.k4wfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/864 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3 From nih-image-request@io.ece.drexel.edu Thu Jan 21 17:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA05543 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 17:25:41 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 17:25:41 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gregoire@starlab.net, nih-image@io.ece.drexel.edu Date: Fri, 22 Jan 1999 9:04:34 +1100 Subject: Re: 'Filter' macro command Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <146A0F0618B@rna.bio.mq.edu.au> Resent-Message-ID: <"GR-641.0.8W.9Fwfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/865 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 541 >Date: Thu, 21 Jan 1999 15:10:32 +0100 >From: gregoire >To: nih-image@io.ece.drexel.edu >Subject: 'Filter' macro command >Just wondering if anybody knows how to change the number of iterations for >the Rank Filters from a macro (I'm using "Filter('min');"). >TIA >Gregoire var i,n:integer; n:=3; for i:=1 to n do Filter('min'); :-) 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 Jan 21 19:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA18943 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 19:10:25 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 19:10:25 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Date: Fri, 22 Jan 1999 10:49:10 +1100 Subject: Re: more save blank field macro Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <1485F0630E2@rna.bio.mq.edu.au> Resent-Message-ID: <"nfvVR3.0.8n3.Snxfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/866 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 4478 >Date: Thu, 21 Jan 1999 11:10:40 -0700 >To: nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: more save blank field macro Geff, It appears your macro for 'background correction' is not quite as sophisticated as Wayne's code. I also had not previously appreciated how much "save blank field" in menu did and will pay more attention to it in future. The manual states: "_______________________ Save Blank Field Saves (in a window named "Blank Field") a background image that will be used to correct for uneven illumination. The Stop Capturing command will use this reference image to correct shading errors in newly acquired images. It does this by dividing each pixel in the newly acquired image by a correction factor computed for each pixel in the blank field. This correction factor is generated by dividing each gray value in the blank field by the mean gray value. You can capture a single frame without shading correction by holding down the option key while selecting Stop Capturing. Close the "Blank Field" window to stop doing shading correction. _________________________" but the crux of the code: "________________________ procedure CorrectShadingOfLine (PicPtr, BFPtr: ptr; width, BFMean: integer); VAR PicLine,BFLine:LinePtr; i,value:LongInt; BEGIN PicLine:=LinePtr(PicPtr); BFLine:=LinePtr(BFPtr); FOR i:=0 TO width-1 DO BEGIN value:=PicLine^[i]; value:=255-value; value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; IF value>254 THEN value:=254; IF value<1 THEN value:=1; PicLine^[i]:=255-value; END; END; ___________________________" actually does more that the manual suggests. Pixel "value" is inverted : value:=255-value; and brightness increased in ratio of BFMean/BFPixelValue but a "toneing down" fudge? factor of BFPixelValue/2 is added first. Pixel "value" is then re-inverted. Someone on the maillist with more understanding of these matters might offer an explanation of the choice of the BFPixelValue/2 fudge? factor. I will need to give it more thought. Note also that your: ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); line which uses an image of 1's to do inversion can be replaced by ImageMath('copy real',b1,b1,invmean,0,'correction factor window 2'); and you can avoid playing with cfw1. > >Here's the (nonworking) macro I wrote to perform the save blank field menu >command. This was just for a greyscale image, not a stack. Doing the >imagemath without the 'real' changes the result, but it doesn't reproduce >the menu command. > >Geff > >MACRO 'background correction'; > > >VAR > > OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string > n, mode, min, max, b1, t1, cfw1, cfw2 : integer > mean, invmean : real > > > >BEGIN > > {This section asks for the image names and directory} > > PutMessage('This macro requires a background image and the t-sect image. ', > 'They must be in the same directory'); > OpPath := GetString('Enter the path to the images','d:\images\practice\'); > BackImage := GetString('Enter the background image >name','gsblankfield.tif'); > TsectImage := GetString('Enter the t-sect image image >name','gsuncorrected.tif'); > > BackImagePath := Concat(OpPath, BackImage); > Open(BackImagePath); > b1 := PidNumber; > TsectImagePath := Concat(OpPath, TsectImage); > Open(TsectImagePath); > t1 := PidNumber; > > {get mean of background} > > SelectPic(b1); > Measure; > GetResults(n,mean,mode,min,max); > invmean := (1/mean); > > {make window of ones} > > Duplicate('correction factor window'); > cfw1 := PidNumber; > ChangeValues(0,255,1); > > {create image with pixel by pixel correction factors} > > ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); > cfw2 := PidNumber; > > SelectPic(cfw1); > Dispose; > > PutMessage('invmean = ',invmean); > > {divide t-sect image by window with correction factors} > > ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); > >END; > >************************************* >Geoffrey C. Rawling >Earth and Environmental Science Dept. >New Mexico Tech >Socorro, NM 87801 >grawling@nmt.edu >************************************* > > 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 Jan 21 19:11 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA19080 for cshtest@io.ece.drexel.edu; Thu, 21 Jan 1999 19:11:09 -0500 (EST) Resent-Date: Thu, 21 Jan 1999 19:11:09 -0500 (EST) Message-Id: <199901212352.SAA16193@io.ece.drexel.edu> X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Date: Fri, 22 Jan 1999 13:02:30 +1200 To: nih-image@io.ece.drexel.edu From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian) Subject: unsubscribe Resent-Message-ID: <"PtbGA1.0.Ez3.gsxfs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/867 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 153 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-d-request@io.ece.drexel.edu Thu Jan 21 19:12 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA19333; Thu, 21 Jan 1999 19:12:58 -0500 (EST) Date: Thu, 21 Jan 1999 19:12:58 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901220012.TAA19333@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #18 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/18 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: 10028 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 18 Today's Topics: restenosis histomorphometry [ golomb@cc.huji.ac.il (Gershon Golom ] 'Filter' macro command [ gregoire ] more save blank field macro [ "Geoffrey C. Rawling" Content-Type: text/plain; charset="us-ascii" Hi, Is there a macro for performing histomorphometry measurments on arterial segments for calculating areas of neointima, lumen etc.? Thanks Prof. Gershon Golomb, Head, Dept. of Pharmaceutics School of Pharmacy, The Hebrew University of Jerusalem POBOX 12065, Jerusalem 91120, Israel FAX - 972-2-6436246 Phone - 972-2-6757014 e-mail - golomb@cc.huji.ac.il ------------------------------ Date: Thu, 21 Jan 1999 15:10:32 +0100 From: gregoire To: nih-image@io.ece.drexel.edu Subject: 'Filter' macro command Message-ID: <36A73556.FD656155@starlab.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello! Just wondering if anybody knows how to change the number of iterations for the Rank Filters from a macro (I'm using "Filter('min');"). TIA Gregoire -- ======================================================== Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-53-80 http://www.starlab.org/ email:gregoire@starlab.net ======================================================== ------------------------------ Date: Thu, 21 Jan 1999 11:10:40 -0700 From: "Geoffrey C. Rawling" To: nih-image@io.ece.drexel.edu Subject: more save blank field macro Message-Id: <3.0.5.32.19990121111040.0093fdd0@NMT.EDU> Content-Type: text/plain; charset="us-ascii" Here's the (nonworking) macro I wrote to perform the save blank field menu command. This was just for a greyscale image, not a stack. Doing the imagemath without the 'real' changes the result, but it doesn't reproduce the menu command. Geff MACRO 'background correction'; VAR OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string n, mode, min, max, b1, t1, cfw1, cfw2 : integer mean, invmean : real BEGIN {This section asks for the image names and directory} PutMessage('This macro requires a background image and the t-sect image. ', 'They must be in the same directory'); OpPath := GetString('Enter the path to the images','d:\images\practice\'); BackImage := GetString('Enter the background image name','gsblankfield.tif'); TsectImage := GetString('Enter the t-sect image image name','gsuncorrected.tif'); BackImagePath := Concat(OpPath, BackImage); Open(BackImagePath); b1 := PidNumber; TsectImagePath := Concat(OpPath, TsectImage); Open(TsectImagePath); t1 := PidNumber; {get mean of background} SelectPic(b1); Measure; GetResults(n,mean,mode,min,max); invmean := (1/mean); {make window of ones} Duplicate('correction factor window'); cfw1 := PidNumber; ChangeValues(0,255,1); {create image with pixel by pixel correction factors} ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); cfw2 := PidNumber; SelectPic(cfw1); Dispose; PutMessage('invmean = ',invmean); {divide t-sect image by window with correction factors} ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); END; ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* ------------------------------ Date: Thu, 21 Jan 1999 13:49:32 -0800 (PST) From: vera@physics.ucla.edu (Moin Vera) To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" ------------------------------ Date: Fri, 22 Jan 1999 9:04:34 +1100 From: GJOSS@rna.bio.mq.edu.au To: gregoire@starlab.net, nih-image@io.ece.drexel.edu Subject: Re: 'Filter' macro command Message-ID: <146A0F0618B@rna.bio.mq.edu.au> >Date: Thu, 21 Jan 1999 15:10:32 +0100 >From: gregoire >To: nih-image@io.ece.drexel.edu >Subject: 'Filter' macro command >Just wondering if anybody knows how to change the number of iterations for >the Rank Filters from a macro (I'm using "Filter('min');"). >TIA >Gregoire var i,n:integer; n:=3; for i:=1 to n do Filter('min'); :-) 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, 22 Jan 1999 10:49:10 +1100 From: GJOSS@rna.bio.mq.edu.au To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Subject: Re: more save blank field macro Message-ID: <1485F0630E2@rna.bio.mq.edu.au> >Date: Thu, 21 Jan 1999 11:10:40 -0700 >To: nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: more save blank field macro Geff, It appears your macro for 'background correction' is not quite as sophisticated as Wayne's code. I also had not previously appreciated how much "save blank field" in menu did and will pay more attention to it in future. The manual states: "_______________________ Save Blank Field Saves (in a window named "Blank Field") a background image that will be used to correct for uneven illumination. The Stop Capturing command will use this reference image to correct shading errors in newly acquired images. It does this by dividing each pixel in the newly acquired image by a correction factor computed for each pixel in the blank field. This correction factor is generated by dividing each gray value in the blank field by the mean gray value. You can capture a single frame without shading correction by holding down the option key while selecting Stop Capturing. Close the "Blank Field" window to stop doing shading correction. _________________________" but the crux of the code: "________________________ procedure CorrectShadingOfLine (PicPtr, BFPtr: ptr; width, BFMean: integer); VAR PicLine,BFLine:LinePtr; i,value:LongInt; BEGIN PicLine:=LinePtr(PicPtr); BFLine:=LinePtr(BFPtr); FOR i:=0 TO width-1 DO BEGIN value:=PicLine^[i]; value:=255-value; value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; IF value>254 THEN value:=254; IF value<1 THEN value:=1; PicLine^[i]:=255-value; END; END; ___________________________" actually does more that the manual suggests. Pixel "value" is inverted : value:=255-value; and brightness increased in ratio of BFMean/BFPixelValue but a "toneing down" fudge? factor of BFPixelValue/2 is added first. Pixel "value" is then re-inverted. Someone on the maillist with more understanding of these matters might offer an explanation of the choice of the BFPixelValue/2 fudge? factor. I will need to give it more thought. Note also that your: ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); line which uses an image of 1's to do inversion can be replaced by ImageMath('copy real',b1,b1,invmean,0,'correction factor window 2'); and you can avoid playing with cfw1. > >Here's the (nonworking) macro I wrote to perform the save blank field menu >command. This was just for a greyscale image, not a stack. Doing the >imagemath without the 'real' changes the result, but it doesn't reproduce >the menu command. > >Geff > >MACRO 'background correction'; > > >VAR > > OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string > n, mode, min, max, b1, t1, cfw1, cfw2 : integer > mean, invmean : real > > > >BEGIN > > {This section asks for the image names and directory} > > PutMessage('This macro requires a background image and the t-sect image. ', > 'They must be in the same directory'); > OpPath := GetString('Enter the path to the images','d:\images\practice\'); > BackImage := GetString('Enter the background image >name','gsblankfield.tif'); > TsectImage := GetString('Enter the t-sect image image >name','gsuncorrected.tif'); > > BackImagePath := Concat(OpPath, BackImage); > Open(BackImagePath); > b1 := PidNumber; > TsectImagePath := Concat(OpPath, TsectImage); > Open(TsectImagePath); > t1 := PidNumber; > > {get mean of background} > > SelectPic(b1); > Measure; > GetResults(n,mean,mode,min,max); > invmean := (1/mean); > > {make window of ones} > > Duplicate('correction factor window'); > cfw1 := PidNumber; > ChangeValues(0,255,1); > > {create image with pixel by pixel correction factors} > > ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); > cfw2 := PidNumber; > > SelectPic(cfw1); > Dispose; > > PutMessage('invmean = ',invmean); > > {divide t-sect image by window with correction factors} > > ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); > >END; > >************************************* >Geoffrey C. Rawling >Earth and Environmental Science Dept. >New Mexico Tech >Socorro, NM 87801 >grawling@nmt.edu >************************************* > > 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 V99 Issue #18 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jan 22 13:06 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA05739 for cshtest@io.ece.drexel.edu; Fri, 22 Jan 1999 13:06:33 -0500 (EST) Resent-Date: Fri, 22 Jan 1999 13:06:33 -0500 (EST) From: sandra.corr@bbsrc.ac.uk Alternate-Recipient: allowed Auto-Forwarded: prohibited Content-Return: allowed Disclose-Recipients: prohibited Conversion: allowed Importance: normal Priority: normal Sensitivity: Company-Confidential Subject: unsuscribe Sandra Corr To: nih-image@io.ece.drexel.edu Message-Id: <990122173256.681@mserv.ri.bbsrc.ac.uk.0> X-Dmw-Body-Names: unsuscribe Sandra Corr Date: Fri, 22 Jan 99 17:32:57 +0000 X-Mailer: MailWorks 2.0-4 Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"CQiFE2.0.4j.pZBgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/868 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; Type = Text; name = "unsuscribe_Sandra_Corr.TXT"; x-dmw-oid = 2A864886F70F0301; x-dmw-btname = "PlainText" Content-Length: 67 I'd like to unsuscribe from this list please. Thanks, Sandra Corr From nih-image-d-request@io.ece.drexel.edu Fri Jan 22 13:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA05863; Fri, 22 Jan 1999 13:07:12 -0500 (EST) Date: Fri, 22 Jan 1999 13:07:12 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901221807.NAA05863@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #19 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/19 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: 1309 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 19 Today's Topics: unsubscribe [ C.J.Trevillian@massey.ac.nz (Cristy ] unsuscribe Sandra Corr [ sandra.corr@bbsrc.ac.uk ] ------------------------------ Date: Fri, 22 Jan 1999 13:02:30 +1200 From: C.J.Trevillian@massey.ac.nz (Cristy Trevillian) To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <199901212352.SAA16193@io.ece.drexel.edu> Content-Type: text/plain; charset="us-ascii" Cristy Trevillian BSc BVMS Assistant Lecturer Equine Studies Massey University Private Bag 11222 Palmerston North, New Zealand 64 6 350 5329 extn 7494 ------------------------------ Date: Fri, 22 Jan 99 17:32:57 +0000 From: sandra.corr@bbsrc.ac.uk To: nih-image@io.ece.drexel.edu Subject: unsuscribe Sandra Corr Message-Id: <990122173256.681@mserv.ri.bbsrc.ac.uk.0> Content-Return: allowed Content-Type: text/plain; charset = ISO-8859-1; Type = Text; name = "unsuscribe_Sandra_Corr.TXT"; x-dmw-oid = 2A864886F70F0301; x-dmw-btname = "PlainText" Content-Transfer-Encoding: 7bit I'd like to unsuscribe from this list please. Thanks, Sandra Corr -------------------------------- End of nih-image-d Digest V99 Issue #19 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jan 22 13:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA11101 for cshtest@io.ece.drexel.edu; Fri, 22 Jan 1999 13:41:07 -0500 (EST) Resent-Date: Fri, 22 Jan 1999 13:41:07 -0500 (EST) Message-Id: <4.1.19990122101931.00a59750@uclink4.berkeley.edu> X-Sender: nicholeg@uclink4.berkeley.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 22 Jan 1999 10:20:02 -0800 To: nih-image@io.ece.drexel.edu From: Nichole Goeden Subject: unsubscribe In-Reply-To: <199901220014.TAA19543@io.ece.drexel.edu> Mime-Version: 1.0 Resent-Message-ID: <"6ln7o1.0.Z-1.I8Cgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/869 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="=====================_926729075==_.ALT" Content-Length: 1153 --=====================_926729075==_.ALT Content-Type: text/plain; charset="us-ascii" unsubscribe please ---------------------------------------------------------------------------- --------------- Nichole L. Goeden Department of Chemical Engineering Lab: (510) 642-8354 201 Gilman Hall, Keasling Laboratory Fax: (510) 643-1228 University of California, Berkeley 94720-1462 nicholeg@uclink4.berkeley.edu --=====================_926729075==_.ALT Content-Type: text/html; charset="us-ascii"
unsubscribe please




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Nichole L. Goeden          Department of Chemical Engineering
Lab: (510) 642-8354         201 Gilman Hall, Keasling Laboratory
Fax:  (510) 643-1228        University of California, Berkeley 94720-1462

nicholeg@uclink4.berkeley.edu
--=====================_926729075==_.ALT-- From nih-image-request@io.ece.drexel.edu Fri Jan 22 14:20 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA15158 for cshtest@io.ece.drexel.edu; Fri, 22 Jan 1999 14:20:53 -0500 (EST) Resent-Date: Fri, 22 Jan 1999 14:20:53 -0500 (EST) Date: Fri, 22 Jan 1999 12:58:50 -0600 From: "Mark R. Molenda" Subject: Re: unsubscribe To: nih-image@io.ece.drexel.edu Message-id: <0F5Z0061M5ZSED@PM05SM.PMM.CW.NET> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express for Macintosh - 4.0c (197) Content-transfer-encoding: 7bit X-Priority: 3 Resent-Message-ID: <"OuuFr3.0.T53.yeCgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/870 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 524 Dear list: I have a couple of questions. 1. Is NIH Image Y2K compatible? 2. We have been having some trouble with NIH Image Integration on a Mac G3. There is no pattern to this, but when we issue an integration command sometimes it won't integrate as it should. It simply shows the picture as it was. Then, for no apparent reason, it will integrate as it should. Is this a bug that anyone else has encountered?? Do we need to allocate more memory to Image?? Any suggestions........... Thanks for any help!! From nih-image-request@io.ece.drexel.edu Fri Jan 22 16:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA27344 for cshtest@io.ece.drexel.edu; Fri, 22 Jan 1999 16:08:37 -0500 (EST) Resent-Date: Fri, 22 Jan 1999 16:08:37 -0500 (EST) From: SolamereTG@aol.com Message-ID: <29711e74.36a8e297@aol.com> Date: Fri, 22 Jan 1999 15:41:59 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: integrate on G-3 Content-transfer-encoding: 7bit X-Mailer: AOL 4.0 for Windows 95 sub 226 Resent-Message-ID: <"TyKKD2.0.bz5.RCEgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/871 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1206 In a message dated 1/22/99 12:09:43 PM Mountain Standard Time, scidi@mci2000.com writes: << We have been having some trouble with NIH Image Integration on a Mac G3. There is no pattern to this, but when we issue an integration command sometimes it won't integrate as it should. It simply shows the picture as it was. Then, for no apparent reason, it will integrate as it should. Is this a bug that anyone else has encountered?? Do we need to allocate more memory to Image?? Any suggestions........... Thanks for any help! >> I tested the integrate command from the (Average frames window submenu) on our G-3 allocating 128 MB to Image and see a similar problem. Also; when it does integrate it seems to limit to 2 frames of integration. (we tested with an LG-3, and scion image 1.62a) Increasing the requested integration to 5, 10 ,20 doesn't change the image returned which has values 1/2 that (twice as white) as the live image. Perhaps Scion could help. We use integrate on-chip with our cameras, this can reduce the readout noise in the integrated image and is faster if you are using an LG-3, or CG-7. Dr. George A. Peeters Solamere Technology Group WWW.SolamereTech.com 801 322-2645 From nih-image-request@io.ece.drexel.edu Sat Jan 23 00:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA24747 for cshtest@io.ece.drexel.edu; Sat, 23 Jan 1999 00:13:32 -0500 (EST) Resent-Date: Sat, 23 Jan 1999 00:13:32 -0500 (EST) Message-Id: <199901230505.QAA16331@redback.ne.com.au> Subject: Averaging video slices Date: Sat, 23 Jan 99 16:00:55 +1100 x-mailer: Claris Emailer 1.1 From: gecko To: Mime-Version: 1.0 Resent-Message-ID: <"1vgog1.0.cc5.bULgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/872 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 1156 Hello all, (Re: the 3-colour filters and a b/w camera - this is used extensively in astronomical applications with very high quality results.) I am writing a macro to average short video sequences, but when I use imagemath to add slices I get white pictures. I assume that this is because the pictures are 8-bit. Should I be using 'real' to fix the problem? Can I just add them without div/numslice if I'm using 'real'? ... ImageMath('op',pic1,pic2,scale,offset,result) Where 'op' is one of 'add', 'sub', 'mul', 'div', 'and', 'or', 'xor', 'min', 'max' or 'copy'. Add the keyword 'real' (e.g. 'add real') to generate a 32-bit real result ... The second part of the problem is that the image in the video sequence is shifting and I want to do a 'shift and combine' type operation. Selecting a reference point on the first and last slices is no problem, but can anyone tell me how to 'shift' an image by a set number of pixels in x and y? The application is a cheap CCD board video camera on a telescope. Integration of short video sequences could give very nice results. Thanks-for any help. Doug Rolfe Geelong, Australia gecko@ne.com.au From nih-image-d-request@io.ece.drexel.edu Sat Jan 23 06:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA09321; Sat, 23 Jan 1999 06:09:42 -0500 (EST) Date: Sat, 23 Jan 1999 06:09:42 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901231109.GAA09321@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #20 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/20 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: 5720 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 20 Today's Topics: unsubscribe [ Nichole Goeden ] ------------------------------ Date: Fri, 22 Jan 1999 10:20:02 -0800 From: Nichole Goeden To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <4.1.19990122101931.00a59750@uclink4.berkeley.edu> Content-Type: multipart/alternative; boundary="=====================_926729075==_.ALT" --=====================_926729075==_.ALT Content-Type: text/plain; charset="us-ascii" unsubscribe please ---------------------------------------------------------------------------- --------------- Nichole L. Goeden Department of Chemical Engineering Lab: (510) 642-8354 201 Gilman Hall, Keasling Laboratory Fax: (510) 643-1228 University of California, Berkeley 94720-1462 nicholeg@uclink4.berkeley.edu --=====================_926729075==_.ALT Content-Type: text/html; charset="us-ascii"
unsubscribe please




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Nichole L. Goeden          Department of Chemical Engineering
Lab: (510) 642-8354         201 Gilman Hall, Keasling Laboratory
Fax:  (510) 643-1228        University of California, Berkeley 94720-1462

nicholeg@uclink4.berkeley.edu
--=====================_926729075==_.ALT-- ------------------------------ Date: Fri, 22 Jan 1999 12:58:50 -0600 From: "Mark R. Molenda" To: nih-image@io.ece.drexel.edu Subject: Re: unsubscribe Message-id: <0F5Z0061M5ZSED@PM05SM.PMM.CW.NET> Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear list: I have a couple of questions. 1. Is NIH Image Y2K compatible? 2. We have been having some trouble with NIH Image Integration on a Mac G3. There is no pattern to this, but when we issue an integration command sometimes it won't integrate as it should. It simply shows the picture as it was. Then, for no apparent reason, it will integrate as it should. Is this a bug that anyone else has encountered?? Do we need to allocate more memory to Image?? Any suggestions........... Thanks for any help!! ------------------------------ Date: Fri, 22 Jan 1999 15:41:59 EST From: SolamereTG@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: integrate on G-3 Message-ID: <29711e74.36a8e297@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/22/99 12:09:43 PM Mountain Standard Time, scidi@mci2000.com writes: << We have been having some trouble with NIH Image Integration on a Mac G3. There is no pattern to this, but when we issue an integration command sometimes it won't integrate as it should. It simply shows the picture as it was. Then, for no apparent reason, it will integrate as it should. Is this a bug that anyone else has encountered?? Do we need to allocate more memory to Image?? Any suggestions........... Thanks for any help! >> I tested the integrate command from the (Average frames window submenu) on our G-3 allocating 128 MB to Image and see a similar problem. Also; when it does integrate it seems to limit to 2 frames of integration. (we tested with an LG-3, and scion image 1.62a) Increasing the requested integration to 5, 10 ,20 doesn't change the image returned which has values 1/2 that (twice as white) as the live image. Perhaps Scion could help. We use integrate on-chip with our cameras, this can reduce the readout noise in the integrated image and is faster if you are using an LG-3, or CG-7. Dr. George A. Peeters Solamere Technology Group WWW.SolamereTech.com 801 322-2645 ------------------------------ Date: Sat, 23 Jan 99 16:00:55 +1100 From: gecko To: Subject: Averaging video slices Message-Id: <199901230505.QAA16331@redback.ne.com.au> Content-Type: text/plain; charset="US-ASCII" Hello all, (Re: the 3-colour filters and a b/w camera - this is used extensively in astronomical applications with very high quality results.) I am writing a macro to average short video sequences, but when I use imagemath to add slices I get white pictures. I assume that this is because the pictures are 8-bit. Should I be using 'real' to fix the problem? Can I just add them without div/numslice if I'm using 'real'? ... ImageMath('op',pic1,pic2,scale,offset,result) Where 'op' is one of 'add', 'sub', 'mul', 'div', 'and', 'or', 'xor', 'min', 'max' or 'copy'. Add the keyword 'real' (e.g. 'add real') to generate a 32-bit real result ... The second part of the problem is that the image in the video sequence is shifting and I want to do a 'shift and combine' type operation. Selecting a reference point on the first and last slices is no problem, but can anyone tell me how to 'shift' an image by a set number of pixels in x and y? The application is a cheap CCD board video camera on a telescope. Integration of short video sequences could give very nice results. Thanks-for any help. Doug Rolfe Geelong, Australia gecko@ne.com.au -------------------------------- End of nih-image-d Digest V99 Issue #20 *************************************** From nih-image-request@io.ece.drexel.edu Sat Jan 23 08:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA26736 for cshtest@io.ece.drexel.edu; Sat, 23 Jan 1999 08:26:32 -0500 (EST) Resent-Date: Sat, 23 Jan 1999 08:26:32 -0500 (EST) Message-Id: <3.0.5.32.19990123081518.00955210@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: Sat, 23 Jan 1999 08:15:18 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Averaging video slices In-Reply-To: <199901230505.QAA16331@redback.ne.com.au> Mime-Version: 1.0 Resent-Message-ID: <"HgFXW.0.wA6.vkSgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/873 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1658 At 04:00 PM 1/23/99 +1100, you wrote: >Hello all, > >(Re: the 3-colour filters and a b/w camera - this is used extensively in >astronomical applications with very high quality results.) > >I am writing a macro to average short video sequences, but when I use >imagemath to add slices I get white pictures. I assume that this is >because the pictures are 8-bit. Should I be using 'real' to fix the >problem? Can I just add them without div/numslice if I'm using 'real'? > >... ImageMath('op',pic1,pic2,scale,offset,result) >Where 'op' is one of 'add', 'sub', 'mul', 'div', 'and', 'or', 'xor', >'min', 'max' or 'copy'. Add the keyword 'real' (e.g. 'add real') to >generate a 32-bit real result ... If all the images are in a stack as they would be if you use MakeMovie, you can use the pulldown-menu Stacks/Average to generate your average. It's compiled so it runs faster than any macro you could write. (I'm assuming that average to the nearest integer is adequate). Animating the stack isn't a bad way to do a fast eyeball check that the images are all aligned. >The second part of the problem is that the image in the video sequence is >shifting and I want to do a 'shift and combine' type operation. Selecting >a reference point on the first and last slices is no problem, but can >anyone tell me how to 'shift' an image by a set number of pixels in x and >y? Try something like: dx=5; dy=10; {whatever} SelectAll; Copy; SetBackgroundColor(255); {whatever the background fill is} Clear; MoveROI(dx,dy); Paste; Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-d-request@io.ece.drexel.edu Sun Jan 24 01:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA26673; Sun, 24 Jan 1999 01:13:30 -0500 (EST) Date: Sun, 24 Jan 1999 01:13:30 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901240613.BAA26673@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #21 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/21 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: 6493 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 21 Today's Topics: Re: Averaging video slices [ Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Averaging video slices Message-Id: <3.0.5.32.19990123081518.00955210@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" At 04:00 PM 1/23/99 +1100, you wrote: >Hello all, > >(Re: the 3-colour filters and a b/w camera - this is used extensively in >astronomical applications with very high quality results.) > >I am writing a macro to average short video sequences, but when I use >imagemath to add slices I get white pictures. I assume that this is >because the pictures are 8-bit. Should I be using 'real' to fix the >problem? Can I just add them without div/numslice if I'm using 'real'? > >... ImageMath('op',pic1,pic2,scale,offset,result) >Where 'op' is one of 'add', 'sub', 'mul', 'div', 'and', 'or', 'xor', >'min', 'max' or 'copy'. Add the keyword 'real' (e.g. 'add real') to >generate a 32-bit real result ... If all the images are in a stack as they would be if you use MakeMovie, you can use the pulldown-menu Stacks/Average to generate your average. It's compiled so it runs faster than any macro you could write. (I'm assuming that average to the nearest integer is adequate). Animating the stack isn't a bad way to do a fast eyeball check that the images are all aligned. >The second part of the problem is that the image in the video sequence is >shifting and I want to do a 'shift and combine' type operation. Selecting >a reference point on the first and last slices is no problem, but can >anyone tell me how to 'shift' an image by a set number of pixels in x and >y? Try something like: dx=5; dy=10; {whatever} SelectAll; Copy; SetBackgroundColor(255); {whatever the background fill is} Clear; MoveROI(dx,dy); Paste; Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Sat, 23 Jan 1999 22:46:07 -0700 From: "Geoffrey C. Rawling" To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu Subject: Re: more save blank field macro Message-Id: <3.0.5.32.19990123224607.00932820@NMT.EDU> Content-Type: text/plain; charset="us-ascii" Greg and the list, Here's an attempt at a macro to do the "save blank field" operation as described below in the bit of source code. I don't claim to understand the "fudge factor". It gives a result that looks very similar to the result from the menu command but comparing the two results with image math shows differences of +/- 20 pixel values. Is precision being lost somewhere? Of course its real slow too! Geff >but the crux of the code: >"________________________ >procedure CorrectShadingOfLine (PicPtr, BFPtr: ptr; width, BFMean: integer); >VAR > PicLine,BFLine:LinePtr; > i,value:LongInt; >BEGIN > PicLine:=LinePtr(PicPtr); > BFLine:=LinePtr(BFPtr); > FOR i:=0 TO width-1 DO BEGIN > value:=PicLine^[i]; > value:=255-value; > value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; > IF value>254 THEN value:=254; > IF value<1 THEN value:=1; > PicLine^[i]:=255-value; > END; >END; >___________________________" >actually does more that the manual suggests. > >Pixel "value" is inverted : value:=255-value; >and brightness increased in ratio of BFMean/BFPixelValue >but a "toneing down" fudge? factor of BFPixelValue/2 is added first. >Pixel "value" is then re-inverted. > >Someone on the maillist with more understanding of these matters might offer an >explanation of the choice of the BFPixelValue/2 fudge? factor. >I will need to give it more thought. MACRO 'background correction 2' VAR OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string width, height, n, mean, mode, min, max : integer b1, t1, cti1 : integer i, j, k, l : integer BEGIN {This section asks for the image names and directory} PutMessage('This macro requires a background image and the t-sect image. ', 'They must be in the same directory'); OpPath := GetString('Enter the path to the images','d:\images\practice\'); BackImage := GetString('Enter the background image name','gsblankfield.tif'); TsectImage := GetString('Enter the t-sect image image name','gsuncorrected.tif'); BackImagePath := Concat(OpPath, BackImage); Open(BackImagePath); b1 := PidNumber; TsectImagePath := Concat(OpPath, TsectImage); Open(TsectImagePath); t1 := PidNumber; SelectPic(b1); Invert; ApplyLUT; Measure; GetResults(n,mean,mode,min,max); SelectPic(t1); GetPicSize(width,height); SetNewSize(width, height); MakeNewWindow('Corrected T-sect Image'); cti1 := PidNumber; FOR i := 0 TO width-1 DO BEGIN ChoosePic(b1); GetColumn(i,0,height); {get column of pixel data from background image} FOR j:= 0 TO height-1 DO BEGIN rUser1[j+1] := LineBuffer[j]; {write that column to the rUser1 array} END; ChoosePic(t1); GetColumn(i,0,height); {get column of pixel data from tsect image} {it goes into the line buffer} {do calculations on the tsect pixel data column in the line buffer array} FOR k := 0 TO height-1 DO BEGIN LineBuffer[k] := 255-LineBuffer[k]; rUser2[k+1] := (LineBuffer[k] * mean + (rUser1[k+1] DIV 2)) DIV rUser1[k+1]; IF rUser2[k+1] > 254 THEN rUser2[k+1] := 254; IF rUser2[k+1] < 1 THEN rUser2[k+1] := 1; rUser2[k+1] := 255 - rUser2[k+1]; LineBuffer[k] := rUser2[k+1] END; {write column of background-corrected pixel values to the corrected image window} ChoosePic(cti1); PutColumn(i,0,height); ResetCounter; END; END; ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* -------------------------------- End of nih-image-d Digest V99 Issue #21 *************************************** From nih-image-request@io.ece.drexel.edu Sun Jan 24 01:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA27356 for cshtest@io.ece.drexel.edu; Sun, 24 Jan 1999 01:17:55 -0500 (EST) Resent-Date: Sun, 24 Jan 1999 01:17:55 -0500 (EST) Message-Id: <3.0.5.32.19990123224607.00932820@NMT.EDU> X-Sender: grawling@NMT.EDU X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sat, 23 Jan 1999 22:46:07 -0700 To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu From: "Geoffrey C. Rawling" Subject: Re: more save blank field macro In-Reply-To: <1485F0630E2@rna.bio.mq.edu.au> Mime-Version: 1.0 Resent-Message-ID: <"1jezN1.0.Zd5.oEhgs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/874 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3814 Greg and the list, Here's an attempt at a macro to do the "save blank field" operation as described below in the bit of source code. I don't claim to understand the "fudge factor". It gives a result that looks very similar to the result from the menu command but comparing the two results with image math shows differences of +/- 20 pixel values. Is precision being lost somewhere? Of course its real slow too! Geff >but the crux of the code: >"________________________ >procedure CorrectShadingOfLine (PicPtr, BFPtr: ptr; width, BFMean: integer); >VAR > PicLine,BFLine:LinePtr; > i,value:LongInt; >BEGIN > PicLine:=LinePtr(PicPtr); > BFLine:=LinePtr(BFPtr); > FOR i:=0 TO width-1 DO BEGIN > value:=PicLine^[i]; > value:=255-value; > value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; > IF value>254 THEN value:=254; > IF value<1 THEN value:=1; > PicLine^[i]:=255-value; > END; >END; >___________________________" >actually does more that the manual suggests. > >Pixel "value" is inverted : value:=255-value; >and brightness increased in ratio of BFMean/BFPixelValue >but a "toneing down" fudge? factor of BFPixelValue/2 is added first. >Pixel "value" is then re-inverted. > >Someone on the maillist with more understanding of these matters might offer an >explanation of the choice of the BFPixelValue/2 fudge? factor. >I will need to give it more thought. MACRO 'background correction 2' VAR OpPath, BackImage, TsectImage, BackImagePath, TsectImagePath : string width, height, n, mean, mode, min, max : integer b1, t1, cti1 : integer i, j, k, l : integer BEGIN {This section asks for the image names and directory} PutMessage('This macro requires a background image and the t-sect image. ', 'They must be in the same directory'); OpPath := GetString('Enter the path to the images','d:\images\practice\'); BackImage := GetString('Enter the background image name','gsblankfield.tif'); TsectImage := GetString('Enter the t-sect image image name','gsuncorrected.tif'); BackImagePath := Concat(OpPath, BackImage); Open(BackImagePath); b1 := PidNumber; TsectImagePath := Concat(OpPath, TsectImage); Open(TsectImagePath); t1 := PidNumber; SelectPic(b1); Invert; ApplyLUT; Measure; GetResults(n,mean,mode,min,max); SelectPic(t1); GetPicSize(width,height); SetNewSize(width, height); MakeNewWindow('Corrected T-sect Image'); cti1 := PidNumber; FOR i := 0 TO width-1 DO BEGIN ChoosePic(b1); GetColumn(i,0,height); {get column of pixel data from background image} FOR j:= 0 TO height-1 DO BEGIN rUser1[j+1] := LineBuffer[j]; {write that column to the rUser1 array} END; ChoosePic(t1); GetColumn(i,0,height); {get column of pixel data from tsect image} {it goes into the line buffer} {do calculations on the tsect pixel data column in the line buffer array} FOR k := 0 TO height-1 DO BEGIN LineBuffer[k] := 255-LineBuffer[k]; rUser2[k+1] := (LineBuffer[k] * mean + (rUser1[k+1] DIV 2)) DIV rUser1[k+1]; IF rUser2[k+1] > 254 THEN rUser2[k+1] := 254; IF rUser2[k+1] < 1 THEN rUser2[k+1] := 1; rUser2[k+1] := 255 - rUser2[k+1]; LineBuffer[k] := rUser2[k+1] END; {write column of background-corrected pixel values to the corrected image window} ChoosePic(cti1); PutColumn(i,0,height); ResetCounter; END; END; ************************************* Geoffrey C. Rawling Earth and Environmental Science Dept. New Mexico Tech Socorro, NM 87801 grawling@nmt.edu ************************************* From nih-image-request@io.ece.drexel.edu Sun Jan 24 16:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10998 for cshtest@io.ece.drexel.edu; Sun, 24 Jan 1999 16:15:21 -0500 (EST) Resent-Date: Sun, 24 Jan 1999 16:15:21 -0500 (EST) X-Sender: ad1054@unix.worldpath.net Message-Id: Mime-Version: 1.0 Date: Sun, 24 Jan 1999 15:48:51 -0500 To: nih-image@io.ece.drexel.edu From: ad1054@worldpath.net (Dr. Christopher Coulon) Subject: Re: Summer Biology Microscopy Technician Position Resent-Message-ID: <"u9AdA1.0.k_1.ESugs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/875 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2720 Dear Louie, I am interested in this position. My last position was running the image laboratory for the Los Alamos National Laboratory (LANL) Life Science Division's Human Genome Project. I ran the laser confocal microscope and the epifluorescence microscopes and got involved in automating image analysis. I have been a professional photographer and have extensive experience in darkroom work as well as image processing. Getting my Ph.D. caused LANL to terminate my position there, since they didn't have funds for the mandatory pay increase. Since that time I have discovered I am over-qualified for local positions and am forced to work as an apprentice electrician here in New Hampshire (I have been a master electrician elsewhere). I would love the opportunity to be your summer microscopy technician, and if you would consider hiring me, I will send my resume. Sincerely, Chris Coulon > SUMMER MICROSCOPY TECHNICIAN > POSITION AVAILABLE > >A three month (June, July, and August) position is open for a microscopy >oriented technician at the Marine Biological Laboratory, Woods Hole, MA. >We would like to attract someone with some knowledge of biological >preparative techniques and experience in laser scanning confocal >microscopy, TEM, SEM, and/or LM. > >The technician will assist in the Central Microscopy Facility. The >technician's duties will be to check out incoming investigators in the >usage of our equipment and then to supervise its continuing usage and to >perform contract work for investigators. This may include fixation, >embedding, sectioning, scope use, darkroom work, etc. The technician will >also provide routine maintenance. > >This is a short term and scientifically rewarding position. Salary will be >in the $7 to $10/hour range. Housing may be available to rent through MBL. > >For more information, including a more detailed position description, >please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. >Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. >Please apply to: Human Resources, MBL, 7 MBL Street, >Woods Hole, MA 02543. or resume@mbl.edu. > >An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. > >Louie Kerr >Research and Education Support Coordinator >Marine Biological Laboratory >7 MBL Street >Woods Hole, MA 02543 >508-289-7273 >508-540-6902 (FAX) > >VISIT OUR WEB SITE: >http://www.mbl.edu * * * * * * * * * * * * * * * * * * * 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 Jan 25 00:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01766 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 00:14:27 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 00:14:27 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Date: Mon, 25 Jan 1999 15:50:15 +1100 Subject: Re: more save blank field macro Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <3E6BA01B86@rna.bio.mq.edu.au> Resent-Message-ID: <"bOc801.0.1w6.nS_gs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/876 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 5288 >Date: Sat, 23 Jan 1999 22:46:07 -0700 >To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: Re: more save blank field macro > >Greg and the list, > > Here's an attempt at a macro to do the "save blank field" operation as >described below in the bit of source code. I don't claim to understand the >"fudge factor". It gives a result that looks very similar to the result >from the menu command but comparing the two results with image math shows >differences of +/- 20 pixel values. Is precision being lost somewhere? Of >course its real slow too! Geff, Doing macro operations on an image on a pixel by pixel basis IS VERY SLOW. Fortunately, many operations can be done via macro on an image (rather than pixel) basis. Your code doesn't show the capture/origin of the save'd blank field but note that when NIH-Image does "Save Blank Field", the Blank Field is in fact the Camera field inverted. This can be easlily seen by comparing Blank Field and Camera images and/or their histograms. I suspect that you would have stored the image as captured for Blank Field rather than an intensity inverted image and that this might be a source of difference in this version. With some reflection on the Pascal source code statement: value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; I realised that the + (BFLine^[i] div 2) term is simply a means of achieving rounding to the nearest integer in integer arithmetic. The fractions would otherwise be lost in the integer mode divison and adding 0.5 to the result is not effective in integer arithmetic. (note that all macro arithmetic is actually done as Pascal float). I now recall querying Wayne on a similar operation in the HSV coversion routine. A difference in the macro as you posted it originally and the operation via menu lies in the limits in Wayne's code: IF value>254 THEN value:=254; IF value<1 THEN value:=1; versus the real arithmetic in your macro ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); Your real image as displayed of as converted to integer will cause the real image pixel values to be scaled rather than limited to 1<>254. Your comment "Doing the imagemath without the 'real' changes the result, but it doesn't reproduce the menu command." is a little ambiguous in that there was also the ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); which would presumably overflow substancially without the "real". I dont know why Wayne would choose to store the Blank Field as inverted and then invert the camera values forward and back. However, I have convinced myself that the appended macro achieves the same result and the menu operation. If you would like to pursue further the problems your code or if you dispute that the following works correctly, it might be better to take our exchange offine rather than bore others and for you to email a sample image set to me as attachments. The whole function (ie division, scaleing by mean, and limiting by truncation to 8-bit integer) is effectively done in imageMath('divide',pid,bid,mean,0,pid); in the appended macro. __________________________cut________________________________________ { blankFieldMacro NIH-Image macro to Save Blank Field and correct Camera image written by Greg Joss, 1999-01-25 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 The Blank Field is not inverted as in menu version. Note that there is also a margin for both flexibility and error in that If the current image is "Camera", [F4] save Blank Field will use it otherwise capture a new image. (same as per menu) In that this makes it easy to use an old captured camera image as "Blank Field" rather than the "current" or what would otherwise be a "live" image. } function findWindow(s:string):boolean; var i,j:integer; begin if nPics>1 then begin selectPic(picNumber);j:=picNumber; repeat begin showMessage(i,j,nPics); choosePic(i+j); if (i+j=npics) then j:=i-npics; i:=i+1; end until (windowTitle=s) or (i=nPics+1); end; if nPics>0 then selectPic(picNumber); findWindow:=(windowTitle=s); end procedure correctShadow(pid,bid);var n,mean,mode,min,max:integer;begin selectPic(bid); selectAll;measure;getResults(n,mean,mode,min,max);killroi; imageMath('divide',pid,bid,mean,0,pid); setPicName(windowTitle,'(Corrected)') end macro'[F1] Capture shadow corrected image';var pid,bid:integer;begin capture; pid:=pidNumber; if findWindow('Blank Field') then bid:=pidNumber else exit('save Blank Field first'); correctShadow(pid,bid); end macro '[F4] save Blank Field';begin if windowTitle='Camera' then stopCapturing; while findWindow('Blank Field') do dispose; if windowTitle<>'Camera' then capture; duplicate('Blank Field'); end __________________________cut________________________________________ 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 Jan 25 11:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA23856 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 11:52:45 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 11:52:45 -0500 (EST) X-Sender: merchant@mail.persci.com Message-Id: Mime-Version: 1.0 Date: Mon, 25 Jan 1999 10:19:54 -0600 To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU From: "Fatima A. Merchant" Subject: Position Available Cc: microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Resent-Message-ID: <"WTxsd.0.By4.td9hs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/877 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1950 Perceptive Scientific Instruments (PSI) currently has the following employment opportunity open in its Research Department: Software Engineer The position involves algorithm and software development for new products in automated light microscope instrumentation. Two to five years software development experience is required. Strong analytical skills and Macintosh C/C++ experience are essential. Experience with object oriented programming methodologies is a definite plus. Digital image processing experience is highly desirable. Biological experience is also desirable. PSI is a recognized leader in the development and supply of digital imaging systems for biological, clinical and research applications. Based in the Houston, Texas area, PSI develops state of the art digital imaging software for gray scale and color image processing and analysis on the Apple Power Macintosh platform. PSI is a division of IRIS, a publicly-held manufacturer of in-vitro diagnostic instruments based in Chatsworth, California. PSI's Research Department conducts advanced development projects and government sponsored research. For more information on the activities of the department, see IEEE Engineering in Medicine and Biology Magazine, 15(1):67-75, Jan/Feb 1996. Qualified candidates should send a resume to: Perceptive Scientific Instruments, Inc. Attention: Fatima Merchant 2525 South Shore Boulevard, Suite 100 League City, Texas 77573 Phone (281) 334-3027 Fax (281) 538-2222 E-Mail: merchant@persci.com Web: http://www.persci.com/ <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 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 Mon Jan 25 11:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA24277; Mon, 25 Jan 1999 11:56:16 -0500 (EST) Date: Mon, 25 Jan 1999 11:56:16 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901251656.LAA24277@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #22 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/22 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: 11329 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 22 Today's Topics: Re: Summer Biology Microscopy Techni [ ad1054@worldpath.net (Dr. Christoph ] Re: more save blank field macro [ GJOSS@rna.bio.mq.edu.au ] Position Available [ "Fatima A. Merchant" Content-Type: text/plain; charset="us-ascii" Dear Louie, I am interested in this position. My last position was running the image laboratory for the Los Alamos National Laboratory (LANL) Life Science Division's Human Genome Project. I ran the laser confocal microscope and the epifluorescence microscopes and got involved in automating image analysis. I have been a professional photographer and have extensive experience in darkroom work as well as image processing. Getting my Ph.D. caused LANL to terminate my position there, since they didn't have funds for the mandatory pay increase. Since that time I have discovered I am over-qualified for local positions and am forced to work as an apprentice electrician here in New Hampshire (I have been a master electrician elsewhere). I would love the opportunity to be your summer microscopy technician, and if you would consider hiring me, I will send my resume. Sincerely, Chris Coulon > SUMMER MICROSCOPY TECHNICIAN > POSITION AVAILABLE > >A three month (June, July, and August) position is open for a microscopy >oriented technician at the Marine Biological Laboratory, Woods Hole, MA. >We would like to attract someone with some knowledge of biological >preparative techniques and experience in laser scanning confocal >microscopy, TEM, SEM, and/or LM. > >The technician will assist in the Central Microscopy Facility. The >technician's duties will be to check out incoming investigators in the >usage of our equipment and then to supervise its continuing usage and to >perform contract work for investigators. This may include fixation, >embedding, sectioning, scope use, darkroom work, etc. The technician will >also provide routine maintenance. > >This is a short term and scientifically rewarding position. Salary will be >in the $7 to $10/hour range. Housing may be available to rent through MBL. > >For more information, including a more detailed position description, >please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. >Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. >Please apply to: Human Resources, MBL, 7 MBL Street, >Woods Hole, MA 02543. or resume@mbl.edu. > >An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. > >Louie Kerr >Research and Education Support Coordinator >Marine Biological Laboratory >7 MBL Street >Woods Hole, MA 02543 >508-289-7273 >508-540-6902 (FAX) > >VISIT OUR WEB SITE: >http://www.mbl.edu * * * * * * * * * * * * * * * * * * * Dr. Christopher Hunt Coulon * * The GAIA Group * * 40 Chick Road * * Wolfeboro, New Hampshire 03894 * * 603 569-0028 * * * * * * * * * * * * * * * * * * * ------------------------------ Date: Mon, 25 Jan 1999 15:50:15 +1100 From: GJOSS@rna.bio.mq.edu.au To: grawling@nmt.edu, nih-image@io.ece.drexel.edu Subject: Re: more save blank field macro Message-ID: <3E6BA01B86@rna.bio.mq.edu.au> >Date: Sat, 23 Jan 1999 22:46:07 -0700 >To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu >From: "Geoffrey C. Rawling" >Subject: Re: more save blank field macro > >Greg and the list, > > Here's an attempt at a macro to do the "save blank field" operation as >described below in the bit of source code. I don't claim to understand the >"fudge factor". It gives a result that looks very similar to the result >from the menu command but comparing the two results with image math shows >differences of +/- 20 pixel values. Is precision being lost somewhere? Of >course its real slow too! Geff, Doing macro operations on an image on a pixel by pixel basis IS VERY SLOW. Fortunately, many operations can be done via macro on an image (rather than pixel) basis. Your code doesn't show the capture/origin of the save'd blank field but note that when NIH-Image does "Save Blank Field", the Blank Field is in fact the Camera field inverted. This can be easlily seen by comparing Blank Field and Camera images and/or their histograms. I suspect that you would have stored the image as captured for Blank Field rather than an intensity inverted image and that this might be a source of difference in this version. With some reflection on the Pascal source code statement: value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; I realised that the + (BFLine^[i] div 2) term is simply a means of achieving rounding to the nearest integer in integer arithmetic. The fractions would otherwise be lost in the integer mode divison and adding 0.5 to the result is not effective in integer arithmetic. (note that all macro arithmetic is actually done as Pascal float). I now recall querying Wayne on a similar operation in the HSV coversion routine. A difference in the macro as you posted it originally and the operation via menu lies in the limits in Wayne's code: IF value>254 THEN value:=254; IF value<1 THEN value:=1; versus the real arithmetic in your macro ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); Your real image as displayed of as converted to integer will cause the real image pixel values to be scaled rather than limited to 1<>254. Your comment "Doing the imagemath without the 'real' changes the result, but it doesn't reproduce the menu command." is a little ambiguous in that there was also the ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); which would presumably overflow substancially without the "real". I dont know why Wayne would choose to store the Blank Field as inverted and then invert the camera values forward and back. However, I have convinced myself that the appended macro achieves the same result and the menu operation. If you would like to pursue further the problems your code or if you dispute that the following works correctly, it might be better to take our exchange offine rather than bore others and for you to email a sample image set to me as attachments. The whole function (ie division, scaleing by mean, and limiting by truncation to 8-bit integer) is effectively done in imageMath('divide',pid,bid,mean,0,pid); in the appended macro. __________________________cut________________________________________ { blankFieldMacro NIH-Image macro to Save Blank Field and correct Camera image written by Greg Joss, 1999-01-25 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 The Blank Field is not inverted as in menu version. Note that there is also a margin for both flexibility and error in that If the current image is "Camera", [F4] save Blank Field will use it otherwise capture a new image. (same as per menu) In that this makes it easy to use an old captured camera image as "Blank Field" rather than the "current" or what would otherwise be a "live" image. } function findWindow(s:string):boolean; var i,j:integer; begin if nPics>1 then begin selectPic(picNumber);j:=picNumber; repeat begin showMessage(i,j,nPics); choosePic(i+j); if (i+j=npics) then j:=i-npics; i:=i+1; end until (windowTitle=s) or (i=nPics+1); end; if nPics>0 then selectPic(picNumber); findWindow:=(windowTitle=s); end procedure correctShadow(pid,bid);var n,mean,mode,min,max:integer;begin selectPic(bid); selectAll;measure;getResults(n,mean,mode,min,max);killroi; imageMath('divide',pid,bid,mean,0,pid); setPicName(windowTitle,'(Corrected)') end macro'[F1] Capture shadow corrected image';var pid,bid:integer;begin capture; pid:=pidNumber; if findWindow('Blank Field') then bid:=pidNumber else exit('save Blank Field first'); correctShadow(pid,bid); end macro '[F4] save Blank Field';begin if windowTitle='Camera' then stopCapturing; while findWindow('Blank Field') do dispose; if windowTitle<>'Camera' then capture; duplicate('Blank Field'); end __________________________cut________________________________________ 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, 25 Jan 1999 10:19:54 -0600 From: "Fatima A. Merchant" To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU Cc: microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Subject: Position Available Message-Id: Content-Type: text/plain; charset="us-ascii" Perceptive Scientific Instruments (PSI) currently has the following employment opportunity open in its Research Department: Software Engineer The position involves algorithm and software development for new products in automated light microscope instrumentation. Two to five years software development experience is required. Strong analytical skills and Macintosh C/C++ experience are essential. Experience with object oriented programming methodologies is a definite plus. Digital image processing experience is highly desirable. Biological experience is also desirable. PSI is a recognized leader in the development and supply of digital imaging systems for biological, clinical and research applications. Based in the Houston, Texas area, PSI develops state of the art digital imaging software for gray scale and color image processing and analysis on the Apple Power Macintosh platform. PSI is a division of IRIS, a publicly-held manufacturer of in-vitro diagnostic instruments based in Chatsworth, California. PSI's Research Department conducts advanced development projects and government sponsored research. For more information on the activities of the department, see IEEE Engineering in Medicine and Biology Magazine, 15(1):67-75, Jan/Feb 1996. Qualified candidates should send a resume to: Perceptive Scientific Instruments, Inc. Attention: Fatima Merchant 2525 South Shore Boulevard, Suite 100 League City, Texas 77573 Phone (281) 334-3027 Fax (281) 538-2222 E-Mail: merchant@persci.com Web: http://www.persci.com/ <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 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 V99 Issue #22 *************************************** From nih-image-request@io.ece.drexel.edu Mon Jan 25 12:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA24906 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 12:01:31 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 12:01:31 -0500 (EST) X-Sender: bmenard@pop-server.unil.ch Message-Id: Mime-Version: 1.0 Content-Transfer-Encoding: 8bit Date: Mon, 25 Jan 1999 17:36:52 +0100 To: nih-image@io.ece.drexel.edu From: Bertrand Menard Subject: Re: Averaging video slices Resent-Message-ID: <"RQEBy.0.bO5.ys9hs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/878 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: 826 Hi Douge, Why don't you use the integrate on chip facilities ? Best regards. Bertrand ********************************************************** Bertrand MENARD University of Lausanne Université de Lausanne Institut of Ecology Institut d'écologie Plant Biology and Physiology Biologie et Physiologie Végétales 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 Jan 25 12:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA27739 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 12:28:14 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 12:28:14 -0500 (EST) Message-Id: <199901251702.MAA11839@red.seas.upenn.edu> Subject: Mouse x-y coordinates To: nih-image@io.ece.drexel.edu (NIH Image) Date: Mon, 25 Jan 1999 12:02:57 -0500 (EST) From: "DAVID W SCHMIDTKE" X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"jFxIz.0.586.8FAhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/879 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2969 I am a new user to NIH-Image, and I am trying to get a set of x-y points of a moving particle from a movie. I found a macro "Get x-y points" at ftp://zippy.nimh.nih.gov/pub/nih-image/user-macros/kinematics_macros.txt (see below) which essentially does what I want. However, when I run this macro and click on points to the left side of my image, I get negative values for my x-coordinates. In contrast, when I move the cursor around in the image window, the x-y coordinates in the info window are never negative, and the x coordinate ranges from 0 on the left side of the image to 640 on the right side of the screen. Similarly, if I use the show results command and click the cursor I get the same x-y values as the info window. For example if I click on 3 points going from the right to the left I get the following results from the macro and the info window. Results from Results from Macro "Get x-y points" Info Window point x-coord y-coord x-coord y-coord 1 411 354 591 347 2 176 357 356 350 3 -142 362 38 355 It appears that all of the x-coordinates are shifted by a value of 180 and the y-coordinates shifted by about 7. The question I have is how do I get the macro results to agree with the Info Window results? I know that the command GetMouse(x,y) returns the location of cursor in local pixel coordinates. Is this "local pixel coordinate" suppose to be different from the pixel coordinate in the info window, if so how do I change this. Does anybody have any ideas to solve this problem. Thanks for the help. David Schmidtke dws@seas.upenn.edu macro 'Get X-Y Points [F7]'; { This macro gets a set of x-y data points from a movie. The movie is rewound, and then each frame is displayed sequentially. The user picks a point with the mouse, and its coordinates are recorded in a data window. At the end, the data is saved. Copyright 1995, Theodore Hodapp, Jesse Smasal, Hamline University Physics Department. } var CountSlices,Counter, width, height:integer; x,y:integer; begin if (nPics > 1) then begin PutMessage('This macro will not work when more than one window is open.'); exit; end; GetPicSize(width,height); InvertY(true); { Open a window for the data. } NewTextWindow('Data',250,250); MoveWindow(250,320); Writeln('Frame, X, Y'); SetCursor('cross'); CountSlices:=nSlices; for Counter:=1 to CountSlices do begin ChooseSlice(Counter); NextWindow; ShowMessage('Select a point on your object with the cursor and then press the mouse button.'); Repeat Until Button; GetMouse(x,y); Wait(.1); SelectWindow('Data'); Writeln(Counter:5:0,',',x:5:0,',',(height-y):5:0,); end; ShowMessage(''); Save; end; {=================================================================} From nih-image-request@io.ece.drexel.edu Mon Jan 25 12:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA29408 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 12:44:24 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 12:44:24 -0500 (EST) X-Sender: merchant@mail.persci.com Message-Id: In-Reply-To: <199901251702.MAA11839@red.seas.upenn.edu> Mime-Version: 1.0 Date: Mon, 25 Jan 1999 11:19:04 -0600 To: nih-image@io.ece.drexel.edu From: "Fatima A. Merchant" Subject: Macro for Red/Green Stereo Resent-Message-ID: <"4gWXk2.0.NY6.kUAhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/880 X-Loop: nih-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 Hi: I was wondering if there is a macro that will build a Red/Green stereo image from a stack of confocal miccroscope images? TIA, Fatima Merchant PSI, Inc. League City, Texas From nih-image-request@io.ece.drexel.edu Mon Jan 25 13:43 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA05590 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 13:43:36 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 13:43:36 -0500 (EST) Message-Id: <199901251808.MAA19178@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, 25 Jan 1999 12:03:13 -0600 To: nih-image@io.ece.drexel.edu From: Kevin Vogt Subject: Re: nih-image-d Digest V99 #22 Resent-Message-ID: <"HlxSo3.0.4X.UDBhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/881 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 11600 I wish to unsubscribe to this mailing list. Please remove my name from the registry Thank you At 11:52 AM 1/25/99 -0500, you wrote: >nih-image-d Digest Volume 99 : Issue 22 > >Today's Topics: > Re: Summer Biology Microscopy Techni [ ad1054@worldpath.net (Dr. Christoph ] > Re: more save blank field macro [ GJOSS@rna.bio.mq.edu.au ] > Position Available [ "Fatima A. Merchant" Date: Sun, 24 Jan 1999 15:48:51 -0500 >From: ad1054@worldpath.net (Dr. Christopher Coulon) >To: nih-image@io.ece.drexel.edu >Subject: Re: Summer Biology Microscopy Technician Position >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >Dear Louie, > >I am interested in this position. My last position was running the image >laboratory for the Los Alamos National Laboratory (LANL) Life Science >Division's Human Genome Project. I ran the laser confocal microscope and >the epifluorescence microscopes and got involved in automating image >analysis. I have been a professional photographer and have extensive >experience in darkroom work as well as image processing. Getting my Ph.D. >caused LANL to terminate my position there, since they didn't have funds >for the mandatory pay increase. Since that time I have discovered I am >over-qualified for local positions and am forced to work as an apprentice >electrician here in New Hampshire (I have been a master electrician >elsewhere). I would love the opportunity to be your summer microscopy >technician, and if you would consider hiring me, I will send my resume. > >Sincerely, > >Chris Coulon > >> SUMMER MICROSCOPY TECHNICIAN >> POSITION AVAILABLE >> >>A three month (June, July, and August) position is open for a microscopy >>oriented technician at the Marine Biological Laboratory, Woods Hole, MA. >>We would like to attract someone with some knowledge of biological >>preparative techniques and experience in laser scanning confocal >>microscopy, TEM, SEM, and/or LM. >> >>The technician will assist in the Central Microscopy Facility. The >>technician's duties will be to check out incoming investigators in the >>usage of our equipment and then to supervise its continuing usage and to >>perform contract work for investigators. This may include fixation, >>embedding, sectioning, scope use, darkroom work, etc. The technician will >>also provide routine maintenance. >> >>This is a short term and scientifically rewarding position. Salary will be >>in the $7 to $10/hour range. Housing may be available to rent through MBL. >> >>For more information, including a more detailed position description, >>please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. >>Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. >>Please apply to: Human Resources, MBL, 7 MBL Street, >>Woods Hole, MA 02543. or resume@mbl.edu. >> >>An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. >> >>Louie Kerr >>Research and Education Support Coordinator >>Marine Biological Laboratory >>7 MBL Street >>Woods Hole, MA 02543 >>508-289-7273 >>508-540-6902 (FAX) >> >>VISIT OUR WEB SITE: >>http://www.mbl.edu > >* * * * * * * * * * * * * * * * * * >* Dr. Christopher Hunt Coulon * >* The GAIA Group * >* 40 Chick Road * >* Wolfeboro, New Hampshire 03894 * >* 603 569-0028 * >* * * * * * * * * * * * * * * * * * >Date: Mon, 25 Jan 1999 15:50:15 +1100 >From: GJOSS@rna.bio.mq.edu.au >To: grawling@nmt.edu, nih-image@io.ece.drexel.edu >Subject: Re: more save blank field macro >Message-ID: <3E6BA01B86@rna.bio.mq.edu.au> > >>Date: Sat, 23 Jan 1999 22:46:07 -0700 >>To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu >>From: "Geoffrey C. Rawling" >>Subject: Re: more save blank field macro >> >>Greg and the list, >> >> Here's an attempt at a macro to do the "save blank field" operation as >>described below in the bit of source code. I don't claim to understand the >>"fudge factor". It gives a result that looks very similar to the result >>from the menu command but comparing the two results with image math shows >>differences of +/- 20 pixel values. Is precision being lost somewhere? Of >>course its real slow too! > >Geff, > Doing macro operations on an image on a pixel by pixel basis IS VERY SLOW. >Fortunately, many operations can be done via macro on an image (rather than pixel) >basis. > >Your code doesn't show the capture/origin of the save'd blank field but note that >when NIH-Image does "Save Blank Field", the Blank Field is in fact the Camera field >inverted. This can be easlily seen by comparing Blank Field and Camera images >and/or their histograms. I suspect that you would have stored the image as captured >for Blank Field rather than an intensity inverted image and that this might be a >source of difference in this version. > >With some reflection on the Pascal source code statement: > value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; >I realised that the + (BFLine^[i] div 2) term is simply a means of achieving >rounding to the nearest integer in integer arithmetic. The fractions would >otherwise be lost in the integer mode divison and adding 0.5 to the result is not >effective in integer arithmetic. (note that all macro arithmetic is actually done >as Pascal float). I now recall querying Wayne on a similar operation in the HSV >coversion routine. > >A difference in the macro as you posted it originally and the operation via menu >lies in the limits in Wayne's code: > IF value>254 THEN value:=254; > IF value<1 THEN value:=1; >versus the real arithmetic in your macro > ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); > >Your real image as displayed of as converted to integer will cause the real image >pixel values to be scaled rather than limited to 1<>254. >Your comment "Doing the imagemath without the 'real' changes the result, but it >doesn't reproduce the menu command." is a little ambiguous in that there was also >the ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); >which would presumably overflow substancially without the "real". > >I dont know why Wayne would choose to store the Blank Field as inverted and then >invert the camera values forward and back. > >However, I have convinced myself that the appended macro achieves the same result >and the menu operation. If you would like to pursue further the problems your code >or if you dispute that the following works correctly, it might be better to take >our exchange offine rather than bore others and for you to email a sample image set >to me as attachments. >The whole function (ie division, scaleing by mean, and limiting by truncation to >8-bit integer) is effectively done in > imageMath('divide',pid,bid,mean,0,pid); >in the appended macro. >__________________________cut________________________________________ > >{ blankFieldMacro >NIH-Image macro to Save Blank Field and correct Camera image >written by >Greg Joss, 1999-01-25 >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 > >The Blank Field is not inverted as in menu version. >Note that there is also a margin for both flexibility and error in that >If the current image is "Camera", [F4] save Blank Field will use it otherwise >capture a new image. (same as per menu) >In that this makes it easy to use an old captured camera image as "Blank Field" >rather than the "current" or what would otherwise be a "live" image. >} > >function findWindow(s:string):boolean; > var i,j:integer; > begin > if nPics>1 then begin > selectPic(picNumber);j:=picNumber; > repeat begin > showMessage(i,j,nPics); > choosePic(i+j); > if (i+j=npics) then j:=i-npics; > i:=i+1; > end > until (windowTitle=s) or (i=nPics+1); > end; > if nPics>0 then selectPic(picNumber); > findWindow:=(windowTitle=s); > end > >procedure correctShadow(pid,bid);var n,mean,mode,min,max:integer;begin > selectPic(bid); > selectAll;measure;getResults(n,mean,mode,min,max);killroi; > imageMath('divide',pid,bid,mean,0,pid); > setPicName(windowTitle,'(Corrected)') > end > >macro'[F1] Capture shadow corrected image';var pid,bid:integer;begin > capture; > pid:=pidNumber; > if findWindow('Blank Field') > then bid:=pidNumber > else exit('save Blank Field first'); > correctShadow(pid,bid); > end > >macro '[F4] save Blank Field';begin > if windowTitle='Camera' then stopCapturing; > while findWindow('Blank Field') do dispose; > if windowTitle<>'Camera' then capture; > duplicate('Blank Field'); > end >__________________________cut________________________________________ > > > > > > >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, 25 Jan 1999 10:19:54 -0600 >From: "Fatima A. Merchant" >To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU >Cc: microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu >Subject: Position Available >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >Perceptive Scientific Instruments (PSI) currently has the following >employment opportunity open in its Research Department: > >Software Engineer > >The position involves algorithm and software development for new >products in automated light microscope instrumentation. Two to five >years software development experience is required. Strong analytical >skills and Macintosh C/C++ experience are essential. Experience with >object oriented programming methodologies is a definite plus. Digital >image processing experience is highly desirable. Biological experience >is also desirable. > >PSI is a recognized leader in the development and supply of digital >imaging systems for biological, clinical and research applications. >Based in the Houston, Texas area, PSI develops state of the art digital >imaging software for gray scale and color image processing and analysis >on the Apple Power Macintosh platform. PSI is a division of IRIS, a >publicly-held manufacturer of in-vitro diagnostic instruments based in >Chatsworth, California. > >PSI's Research Department conducts advanced development projects and >government sponsored research. For more information on the activities of >the department, see IEEE Engineering in Medicine and Biology Magazine, >15(1):67-75, Jan/Feb 1996. > >Qualified candidates should send a resume to: > >Perceptive Scientific Instruments, Inc. >Attention: Fatima Merchant >2525 South Shore Boulevard, Suite 100 >League City, Texas 77573 >Phone (281) 334-3027 >Fax (281) 538-2222 >E-Mail: merchant@persci.com >Web: http://www.persci.com/ > > > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> > > 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 > > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> > Kevin Vogt 262-1360 University of Wisconsin-Madison Dept. of Biomolecular Chemistry 580 MSC 1300 University Ave. Madison, WI 53706 From nih-image-request@io.ece.drexel.edu Mon Jan 25 15:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA17960 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 15:26:27 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 15:26:27 -0500 (EST) Date: Mon, 25 Jan 1999 20:00:18 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: case statements in macros Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"5y7TX2.0.bk3.8sChs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/882 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 338 Dear all, I want to use a Pascal case statement in a macro but Image complains about undefined identifier. Is it possible to use a case statement? 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 Mon Jan 25 18:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA05709 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 18:17:48 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 18:17:48 -0500 (EST) Message-Id: In-Reply-To: References: <199901251702.MAA11839@red.seas.upenn.edu> Mime-Version: 1.0 Date: Mon, 25 Jan 1999 23:45:32 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: Macro for Red/Green Stereo Resent-Message-ID: <"YBR-X3.0.MV.ZGFhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/883 X-Loop: nih-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 Look at the StackMacros 1.0 on: These macros let you create b/w stereo pairs and red/green or red/blue stereo impressions combined with animated rotation around a desired angle. The look-up tables are interlaced with continuously increasing darkness, so the images also make sense if you look at them in greyscale. To create an animated stereo image, issue these macros: - Project for stereo sequence ... then, using the projection stack, issue - "Red green stereo sequence" or "Greyscale stereo sequence" The macros also include a means to merge two stacks to one color stack in "replace mode", where one stack replaces the other at those spots where intensity is above a certain level, useful for marking FISH spots in a different color. N. Vischer From nih-image-request@io.ece.drexel.edu Mon Jan 25 21:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA27197 for cshtest@io.ece.drexel.edu; Mon, 25 Jan 1999 21:44:36 -0500 (EST) Resent-Date: Mon, 25 Jan 1999 21:44:36 -0500 (EST) Date: Mon, 25 Jan 1999 21:20:24 -0500 (EST) From: Cengizhan Ozturk X-Sender: cozturk@ariel To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Uf54p1.0.vw5.qPIhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/884 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 789 Hi, Couple of months ago when I was browsing matlab web side there were several public domain functions for creating stereo image, romdom dot stereograms.. etc If projection macros at NIH-image are not adequate I would try that route Good luck Cengizhan -------------------------------------------- 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 Mon, 25 Jan 1999, Fatima A. Merchant wrote: > Hi: > > I was wondering if there is a macro that will build a > Red/Green stereo image from a stack of confocal miccroscope images? > > TIA, > > Fatima Merchant > PSI, Inc. > League City, Texas > > > From nih-image-request@io.ece.drexel.edu Tue Jan 26 02:29 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA01623 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 02:29:39 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 02:29:39 -0500 (EST) Message-Id: <3.0.6.32.19990126080724.009fd210@pop3.demon.nl> X-Sender: ksalam@pop3.demon.nl X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 26 Jan 1999 08:07:24 +0100 To: nih-image@io.ece.drexel.edu From: K Salam Subject: unsubscribe In-Reply-To: <199812141339.HAA32972@mail5.doit.wisc.edu> References: <199812131111.GAA17419@io.ece.drexel.edu> Mime-Version: 1.0 Resent-Message-ID: <"5Z_D62.0.6r6.3YMhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/885 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 15 unsubscribe From nih-image-request@io.ece.drexel.edu Tue Jan 26 03:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09401 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 03:28:13 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 03:28:13 -0500 (EST) From: "Anatomia Patologica CF" To: Date: Tue, 26 Jan 1999 08:58:56 +0100 Message-ID: <01be4901$b93c8a20$71029a9a@cpana1.ulssasolo.ven.it> MIME-Version: 1.0 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"tQ1a02.0.fE1.7KNhs"@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/886 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: 13 unsubscribe From nih-image-d-request@io.ece.drexel.edu Tue Jan 26 03:37 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA10749; Tue, 26 Jan 1999 03:37:09 -0500 (EST) Date: Tue, 26 Jan 1999 03:37:09 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901260837.DAA10749@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #23 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/23 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: 21171 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 23 Today's Topics: Re: Averaging video slices [ Bertrand Menard ] Re: Macro for Red/Green Stereo [ Norbert Vischer ] Unidentified subject! [ "Anatomia Patologica CF" To: nih-image@io.ece.drexel.edu Subject: Re: Averaging video slices Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hi Douge, Why don't you use the integrate on chip facilities ? Best regards. Bertrand ********************************************************** Bertrand MENARD University of Lausanne Université de Lausanne Institut of Ecology Institut d'écologie Plant Biology and Physiology Biologie et Physiologie Végétales 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, 25 Jan 1999 12:02:57 -0500 (EST) From: "DAVID W SCHMIDTKE" To: nih-image@io.ece.drexel.edu (NIH Image) Subject: Mouse x-y coordinates Message-Id: <199901251702.MAA11839@red.seas.upenn.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I am a new user to NIH-Image, and I am trying to get a set of x-y points of a moving particle from a movie. I found a macro "Get x-y points" at ftp://zippy.nimh.nih.gov/pub/nih-image/user-macros/kinematics_macros.txt (see below) which essentially does what I want. However, when I run this macro and click on points to the left side of my image, I get negative values for my x-coordinates. In contrast, when I move the cursor around in the image window, the x-y coordinates in the info window are never negative, and the x coordinate ranges from 0 on the left side of the image to 640 on the right side of the screen. Similarly, if I use the show results command and click the cursor I get the same x-y values as the info window. For example if I click on 3 points going from the right to the left I get the following results from the macro and the info window. Results from Results from Macro "Get x-y points" Info Window point x-coord y-coord x-coord y-coord 1 411 354 591 347 2 176 357 356 350 3 -142 362 38 355 It appears that all of the x-coordinates are shifted by a value of 180 and the y-coordinates shifted by about 7. The question I have is how do I get the macro results to agree with the Info Window results? I know that the command GetMouse(x,y) returns the location of cursor in local pixel coordinates. Is this "local pixel coordinate" suppose to be different from the pixel coordinate in the info window, if so how do I change this. Does anybody have any ideas to solve this problem. Thanks for the help. David Schmidtke dws@seas.upenn.edu macro 'Get X-Y Points [F7]'; { This macro gets a set of x-y data points from a movie. The movie is rewound, and then each frame is displayed sequentially. The user picks a point with the mouse, and its coordinates are recorded in a data window. At the end, the data is saved. Copyright 1995, Theodore Hodapp, Jesse Smasal, Hamline University Physics Department. } var CountSlices,Counter, width, height:integer; x,y:integer; begin if (nPics > 1) then begin PutMessage('This macro will not work when more than one window is open.'); exit; end; GetPicSize(width,height); InvertY(true); { Open a window for the data. } NewTextWindow('Data',250,250); MoveWindow(250,320); Writeln('Frame, X, Y'); SetCursor('cross'); CountSlices:=nSlices; for Counter:=1 to CountSlices do begin ChooseSlice(Counter); NextWindow; ShowMessage('Select a point on your object with the cursor and then press the mouse button.'); Repeat Until Button; GetMouse(x,y); Wait(.1); SelectWindow('Data'); Writeln(Counter:5:0,',',x:5:0,',',(height-y):5:0,); end; ShowMessage(''); Save; end; {=================================================================} ------------------------------ Date: Mon, 25 Jan 1999 11:19:04 -0600 From: "Fatima A. Merchant" To: nih-image@io.ece.drexel.edu Subject: Macro for Red/Green Stereo Message-Id: Content-Type: text/plain; charset="us-ascii" Hi: I was wondering if there is a macro that will build a Red/Green stereo image from a stack of confocal miccroscope images? TIA, Fatima Merchant PSI, Inc. League City, Texas ------------------------------ Date: Mon, 25 Jan 1999 12:03:13 -0600 From: Kevin Vogt To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #22 Message-Id: <199901251808.MAA19178@mail1.doit.wisc.edu> Content-Type: text/plain; charset="us-ascii" I wish to unsubscribe to this mailing list. Please remove my name from the registry Thank you At 11:52 AM 1/25/99 -0500, you wrote: >nih-image-d Digest Volume 99 : Issue 22 > >Today's Topics: > Re: Summer Biology Microscopy Techni [ ad1054@worldpath.net (Dr. Christoph ] > Re: more save blank field macro [ GJOSS@rna.bio.mq.edu.au ] > Position Available [ "Fatima A. Merchant" Date: Sun, 24 Jan 1999 15:48:51 -0500 >From: ad1054@worldpath.net (Dr. Christopher Coulon) >To: nih-image@io.ece.drexel.edu >Subject: Re: Summer Biology Microscopy Technician Position >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >Dear Louie, > >I am interested in this position. My last position was running the image >laboratory for the Los Alamos National Laboratory (LANL) Life Science >Division's Human Genome Project. I ran the laser confocal microscope and >the epifluorescence microscopes and got involved in automating image >analysis. I have been a professional photographer and have extensive >experience in darkroom work as well as image processing. Getting my Ph.D. >caused LANL to terminate my position there, since they didn't have funds >for the mandatory pay increase. Since that time I have discovered I am >over-qualified for local positions and am forced to work as an apprentice >electrician here in New Hampshire (I have been a master electrician >elsewhere). I would love the opportunity to be your summer microscopy >technician, and if you would consider hiring me, I will send my resume. > >Sincerely, > >Chris Coulon > >> SUMMER MICROSCOPY TECHNICIAN >> POSITION AVAILABLE >> >>A three month (June, July, and August) position is open for a microscopy >>oriented technician at the Marine Biological Laboratory, Woods Hole, MA. >>We would like to attract someone with some knowledge of biological >>preparative techniques and experience in laser scanning confocal >>microscopy, TEM, SEM, and/or LM. >> >>The technician will assist in the Central Microscopy Facility. The >>technician's duties will be to check out incoming investigators in the >>usage of our equipment and then to supervise its continuing usage and to >>perform contract work for investigators. This may include fixation, >>embedding, sectioning, scope use, darkroom work, etc. The technician will >>also provide routine maintenance. >> >>This is a short term and scientifically rewarding position. Salary will be >>in the $7 to $10/hour range. Housing may be available to rent through MBL. >> >>For more information, including a more detailed position description, >>please contact Louis Kerr at: MBL, 7 MBL Street, Woods Hole, MA 02543. >>Telephone, 508-289-7273; or at Email: lkerr@mbl.edu. >>Please apply to: Human Resources, MBL, 7 MBL Street, >>Woods Hole, MA 02543. or resume@mbl.edu. >> >>An Equal Opportunity/Affirmative Action Employer/ Non-smoking workplace. >> >>Louie Kerr >>Research and Education Support Coordinator >>Marine Biological Laboratory >>7 MBL Street >>Woods Hole, MA 02543 >>508-289-7273 >>508-540-6902 (FAX) >> >>VISIT OUR WEB SITE: >>http://www.mbl.edu > >* * * * * * * * * * * * * * * * * * >* Dr. Christopher Hunt Coulon * >* The GAIA Group * >* 40 Chick Road * >* Wolfeboro, New Hampshire 03894 * >* 603 569-0028 * >* * * * * * * * * * * * * * * * * * >Date: Mon, 25 Jan 1999 15:50:15 +1100 >From: GJOSS@rna.bio.mq.edu.au >To: grawling@nmt.edu, nih-image@io.ece.drexel.edu >Subject: Re: more save blank field macro >Message-ID: <3E6BA01B86@rna.bio.mq.edu.au> > >>Date: Sat, 23 Jan 1999 22:46:07 -0700 >>To: GJOSS@rna.bio.mq.edu.au, nih-image@io.ece.drexel.edu >>From: "Geoffrey C. Rawling" >>Subject: Re: more save blank field macro >> >>Greg and the list, >> >> Here's an attempt at a macro to do the "save blank field" operation as >>described below in the bit of source code. I don't claim to understand the >>"fudge factor". It gives a result that looks very similar to the result >>from the menu command but comparing the two results with image math shows >>differences of +/- 20 pixel values. Is precision being lost somewhere? Of >>course its real slow too! > >Geff, > Doing macro operations on an image on a pixel by pixel basis IS VERY SLOW. >Fortunately, many operations can be done via macro on an image (rather than pixel) >basis. > >Your code doesn't show the capture/origin of the save'd blank field but note that >when NIH-Image does "Save Blank Field", the Blank Field is in fact the Camera field >inverted. This can be easlily seen by comparing Blank Field and Camera images >and/or their histograms. I suspect that you would have stored the image as captured >for Blank Field rather than an intensity inverted image and that this might be a >source of difference in this version. > >With some reflection on the Pascal source code statement: > value:=(value * BFMean + (BFLine^[i] div 2)) DIV BFLine^[i]; >I realised that the + (BFLine^[i] div 2) term is simply a means of achieving >rounding to the nearest integer in integer arithmetic. The fractions would >otherwise be lost in the integer mode divison and adding 0.5 to the result is not >effective in integer arithmetic. (note that all macro arithmetic is actually done >as Pascal float). I now recall querying Wayne on a similar operation in the HSV >coversion routine. > >A difference in the macro as you posted it originally and the operation via menu >lies in the limits in Wayne's code: > IF value>254 THEN value:=254; > IF value<1 THEN value:=1; >versus the real arithmetic in your macro > ImageMath('div real',t1,cfw2,1,0,'corrected t-sect image'); > >Your real image as displayed of as converted to integer will cause the real image >pixel values to be scaled rather than limited to 1<>254. >Your comment "Doing the imagemath without the 'real' changes the result, but it >doesn't reproduce the menu command." is a little ambiguous in that there was also >the ImageMath('mul real',b1,cfw1,invmean,0,'correction factor window 2'); >which would presumably overflow substancially without the "real". > >I dont know why Wayne would choose to store the Blank Field as inverted and then >invert the camera values forward and back. > >However, I have convinced myself that the appended macro achieves the same result >and the menu operation. If you would like to pursue further the problems your code >or if you dispute that the following works correctly, it might be better to take >our exchange offine rather than bore others and for you to email a sample image set >to me as attachments. >The whole function (ie division, scaleing by mean, and limiting by truncation to >8-bit integer) is effectively done in > imageMath('divide',pid,bid,mean,0,pid); >in the appended macro. >__________________________cut________________________________________ > >{ blankFieldMacro >NIH-Image macro to Save Blank Field and correct Camera image >written by >Greg Joss, 1999-01-25 >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 > >The Blank Field is not inverted as in menu version. >Note that there is also a margin for both flexibility and error in that >If the current image is "Camera", [F4] save Blank Field will use it otherwise >capture a new image. (same as per menu) >In that this makes it easy to use an old captured camera image as "Blank Field" >rather than the "current" or what would otherwise be a "live" image. >} > >function findWindow(s:string):boolean; > var i,j:integer; > begin > if nPics>1 then begin > selectPic(picNumber);j:=picNumber; > repeat begin > showMessage(i,j,nPics); > choosePic(i+j); > if (i+j=npics) then j:=i-npics; > i:=i+1; > end > until (windowTitle=s) or (i=nPics+1); > end; > if nPics>0 then selectPic(picNumber); > findWindow:=(windowTitle=s); > end > >procedure correctShadow(pid,bid);var n,mean,mode,min,max:integer;begin > selectPic(bid); > selectAll;measure;getResults(n,mean,mode,min,max);killroi; > imageMath('divide',pid,bid,mean,0,pid); > setPicName(windowTitle,'(Corrected)') > end > >macro'[F1] Capture shadow corrected image';var pid,bid:integer;begin > capture; > pid:=pidNumber; > if findWindow('Blank Field') > then bid:=pidNumber > else exit('save Blank Field first'); > correctShadow(pid,bid); > end > >macro '[F4] save Blank Field';begin > if windowTitle='Camera' then stopCapturing; > while findWindow('Blank Field') do dispose; > if windowTitle<>'Camera' then capture; > duplicate('Blank Field'); > end >__________________________cut________________________________________ > > > > > > >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, 25 Jan 1999 10:19:54 -0600 >From: "Fatima A. Merchant" >To: CONFOCAL@LISTSERV.ACSU.BUFFALO.EDU >Cc: microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu >Subject: Position Available >Message-Id: >Content-Type: text/plain; charset="us-ascii" > >Perceptive Scientific Instruments (PSI) currently has the following >employment opportunity open in its Research Department: > >Software Engineer > >The position involves algorithm and software development for new >products in automated light microscope instrumentation. Two to five >years software development experience is required. Strong analytical >skills and Macintosh C/C++ experience are essential. Experience with >object oriented programming methodologies is a definite plus. Digital >image processing experience is highly desirable. Biological experience >is also desirable. > >PSI is a recognized leader in the development and supply of digital >imaging systems for biological, clinical and research applications. >Based in the Houston, Texas area, PSI develops state of the art digital >imaging software for gray scale and color image processing and analysis >on the Apple Power Macintosh platform. PSI is a division of IRIS, a >publicly-held manufacturer of in-vitro diagnostic instruments based in >Chatsworth, California. > >PSI's Research Department conducts advanced development projects and >government sponsored research. For more information on the activities of >the department, see IEEE Engineering in Medicine and Biology Magazine, >15(1):67-75, Jan/Feb 1996. > >Qualified candidates should send a resume to: > >Perceptive Scientific Instruments, Inc. >Attention: Fatima Merchant >2525 South Shore Boulevard, Suite 100 >League City, Texas 77573 >Phone (281) 334-3027 >Fax (281) 538-2222 >E-Mail: merchant@persci.com >Web: http://www.persci.com/ > > > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> > > 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 > > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> > Kevin Vogt 262-1360 University of Wisconsin-Madison Dept. of Biomolecular Chemistry 580 MSC 1300 University Ave. Madison, WI 53706 ------------------------------ Date: Mon, 25 Jan 1999 20:00:18 +0000 (GMT) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: case statements in macros Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I want to use a Pascal case statement in a macro but Image complains about undefined identifier. Is it possible to use a case statement? 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: Mon, 25 Jan 1999 23:45:32 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: Content-Type: text/plain; charset="us-ascii" Look at the StackMacros 1.0 on: These macros let you create b/w stereo pairs and red/green or red/blue stereo impressions combined with animated rotation around a desired angle. The look-up tables are interlaced with continuously increasing darkness, so the images also make sense if you look at them in greyscale. To create an animated stereo image, issue these macros: - Project for stereo sequence ... then, using the projection stack, issue - "Red green stereo sequence" or "Greyscale stereo sequence" The macros also include a means to merge two stacks to one color stack in "replace mode", where one stack replaces the other at those spots where intensity is above a certain level, useful for marking FISH spots in a different color. N. Vischer ------------------------------ Date: Mon, 25 Jan 1999 21:20:24 -0500 (EST) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Couple of months ago when I was browsing matlab web side there were several public domain functions for creating stereo image, romdom dot stereograms.. etc If projection macros at NIH-image are not adequate I would try that route Good luck Cengizhan -------------------------------------------- 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 Mon, 25 Jan 1999, Fatima A. Merchant wrote: > Hi: > > I was wondering if there is a macro that will build a > Red/Green stereo image from a stack of confocal miccroscope images? > > TIA, > > Fatima Merchant > PSI, Inc. > League City, Texas > > > ------------------------------ Date: Tue, 26 Jan 1999 08:07:24 +0100 From: K Salam To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.6.32.19990126080724.009fd210@pop3.demon.nl> Content-Type: text/plain; charset="us-ascii" unsubscribe ------------------------------ Date: Tue, 26 Jan 1999 08:58:56 +0100 From: "Anatomia Patologica CF" To: Subject: Unidentified subject! Message-ID: <01be4901$b93c8a20$71029a9a@cpana1.ulssasolo.ven.it> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit unsubscribe -------------------------------- End of nih-image-d Digest V99 Issue #23 *************************************** From nih-image-request@io.ece.drexel.edu Tue Jan 26 04:49 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA20000 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 04:49:35 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 04:49:35 -0500 (EST) Message-ID: <36AD8862.44699979@starlab.net> Date: Tue, 26 Jan 1999 10:18:26 +0100 From: gregoire X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: find objects in an image References: <6FE6FE3338A@rna.bio.mq.edu.au> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"0aS3R2.0.at3.eWOhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/887 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 533 Hi, Would anybody know where I can find a code for routines to find objects in an image? Macros are a bit slow, so I'm now trying to program part of the processing in C. Thanks in advance Gregoire -- ========================================================= Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-51-13 http://www.starlab.org/ mailto:gregoire@starlab.net ========================================================= From nih-image-request@io.ece.drexel.edu Tue Jan 26 06:05 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29793 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 06:05:15 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 06:05:15 -0500 (EST) From: "Anatomia Patologica CF" To: Subject: Unsubscribe Date: Tue, 26 Jan 1999 11:48:55 +0100 Message-ID: <01be4919$7882ca40$71029a9a@cpana1.ulssasolo.ven.it> MIME-Version: 1.0 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"KYEYd1.0.2e6.hpPhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/888 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: 13 Unsubscribe From nih-image-request@io.ece.drexel.edu Tue Jan 26 15:11 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA07906 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 15:11:16 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 15:11:16 -0500 (EST) Message-ID: <36ADD1CE.14A711D4@maine.rr.com> Date: Tue, 26 Jan 1999 14:31:47 +0000 From: Marcia Goldfarb X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) MIME-Version: 1.0 To: Nih-image Subject: digital camera Content-Transfer-Encoding: 7bit Resent-Message-ID: <"DkOj91.0.zU.RUXhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/889 X-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: 1073 On 1/14/99 I asked for help understanding best procedure to use with images (2-D gels) from a digital camera Olympus D-620L. I thank those who answered. Now that I have had a chance to use the camera for awhile, I want to respond to John Russ's comment that a digital camera is not appropriate for scientific use. The digital images (using SHQ, super high quality setting) are more sensitive than the film images (S64 kodachrome). That is I am seeing more spots on the gel. The slides always had a blue cast. The digital camera sees the light box as white. I can measure 11 steps of a Kodak greyscale when calibrating in NIH-Image, whereas previously, I could only measure 6. There are differences in spot size measurement. Some of this is due to the fact that a greater area is being detected. However. the density means and intergrated density relationships are very close. If the color printer paper and cartridge weren't so expensive, I would consider this a 100% improvement. Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com From nih-image-request@io.ece.drexel.edu Tue Jan 26 16:22 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA18102 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 16:22:46 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 16:22:46 -0500 (EST) From: Lynn_N_Li@notes.seagate.com X-Lotus-FromDomain: SEAGATE@INTERNET To: nih-image@io.ece.drexel.edu Message-ID: <88256705.0071B5CB.00@sv-gw1.stsv.seagate.com> Date: Tue, 26 Jan 1999 14:42:00 -0600 Subject: unsubscribe Resent-Message-ID: <"yAStR3.0.gH3.ChYhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/890 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Tue Jan 26 16:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA18222 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 16:23:42 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 16:23:42 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Tue, 26 Jan 1999 15:51:29 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: digital camera Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"B_eUp2.0.PM3.6jYhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/891 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 610 In a message dated 1/26/99 7:55:38 PM, anatekep@maine.rr.com writes: >I want to respond to John Russ's comment that a digital camera is not >appropriate for scientific use. That is DEFINITELY NOT what I said, sorry. I strongly encourage the use of digital cameras, use them myself, and have many times on this list pointed out their numerous advantages. What I have said, that you may be referring to, is a warning not to use image compression on images that will be subjected to measurement. Some cameras do not let you turn off compression. Please, if you are going to quote me, get it right. John Russ From nih-image-request@io.ece.drexel.edu Tue Jan 26 18:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA28985 for cshtest@io.ece.drexel.edu; Tue, 26 Jan 1999 18:04:46 -0500 (EST) Resent-Date: Tue, 26 Jan 1999 18:04:46 -0500 (EST) X-Sender: amtha@mail.xs4all.nl Message-Id: In-Reply-To: <199901260759.CAA05542@io.ece.drexel.edu> Mime-Version: 1.0 Date: Tue, 26 Jan 1999 23:36:50 +0100 To: nih-image@io.ece.drexel.edu From: "Anneke M.Th. Harbers and Ard Jonker" Subject: DT 2250/Performa 630 Resent-Message-ID: <"vYYjP3.0._J6.EEahs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/892 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 87 Is anyone running this combination with recent drivers (ie. sys 8.1 compliant?) Ard From nih-image-d-request@io.ece.drexel.edu Wed Jan 27 02:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA01220; Wed, 27 Jan 1999 02:45:39 -0500 (EST) Date: Wed, 27 Jan 1999 02:45:39 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901270745.CAA01220@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #24 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/24 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: 6202 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 24 Today's Topics: find objects in an image [ gregoire ] Unsubscribe [ "Anatomia Patologica CF" To: nih-image@io.ece.drexel.edu Subject: find objects in an image Message-ID: <36AD8862.44699979@starlab.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Would anybody know where I can find a code for routines to find objects in an image? Macros are a bit slow, so I'm now trying to program part of the processing in C. Thanks in advance Gregoire -- ========================================================= Dr Gregoire R THOMAS (Research Scientist) Starlab nv, Excelsiorlaan 40-42, Zaventem 1930, Belgium Tel: +32 (0)2 721-54-54 Fax: +32(0)2 721-51-13 http://www.starlab.org/ mailto:gregoire@starlab.net ========================================================= ------------------------------ Date: Tue, 26 Jan 1999 11:48:55 +0100 From: "Anatomia Patologica CF" To: Subject: Unsubscribe Message-ID: <01be4919$7882ca40$71029a9a@cpana1.ulssasolo.ven.it> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Unsubscribe ------------------------------ Date: Tue, 26 Jan 1999 14:31:47 +0000 From: Marcia Goldfarb To: Nih-image Subject: digital camera Message-ID: <36ADD1CE.14A711D4@maine.rr.com> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit On 1/14/99 I asked for help understanding best procedure to use with images (2-D gels) from a digital camera Olympus D-620L. I thank those who answered. Now that I have had a chance to use the camera for awhile, I want to respond to John Russ's comment that a digital camera is not appropriate for scientific use. The digital images (using SHQ, super high quality setting) are more sensitive than the film images (S64 kodachrome). That is I am seeing more spots on the gel. The slides always had a blue cast. The digital camera sees the light box as white. I can measure 11 steps of a Kodak greyscale when calibrating in NIH-Image, whereas previously, I could only measure 6. There are differences in spot size measurement. Some of this is due to the fact that a greater area is being detected. However. the density means and intergrated density relationships are very close. If the color printer paper and cartridge weren't so expensive, I would consider this a 100% improvement. Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com ------------------------------ Date: Tue, 26 Jan 1999 14:42:00 -0600 From: Lynn_N_Li@notes.seagate.com To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: <88256705.0071B5CB.00@sv-gw1.stsv.seagate.com> ------------------------------ Date: Tue, 26 Jan 1999 15:51:29 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: digital camera Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 1/26/99 7:55:38 PM, anatekep@maine.rr.com writes: >I want to respond to John Russ's comment that a digital camera is not >appropriate for scientific use. That is DEFINITELY NOT what I said, sorry. I strongly encourage the use of digital cameras, use them myself, and have many times on this list pointed out their numerous advantages. What I have said, that you may be referring to, is a warning not to use image compression on images that will be subjected to measurement. Some cameras do not let you turn off compression. Please, if you are going to quote me, get it right. John Russ ------------------------------ Date: Tue, 26 Jan 1999 23:36:50 +0100 From: "Anneke M.Th. Harbers and Ard Jonker" To: nih-image@io.ece.drexel.edu Subject: DT 2250/Performa 630 Message-Id: Content-Type: text/plain; charset="us-ascii" Is anyone running this combination with recent drivers (ie. sys 8.1 compliant?) Ard ------------------------------ Date: Wed, 27 Jan 1999 18:23:14 +1100 From: GJOSS@rna.bio.mq.edu.au To: Kreft@cardiff.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: case statements in macros Message-ID: <169DE71B68@rna.bio.mq.edu.au> >Date: Mon, 25 Jan 1999 20:00:18 +0000 (GMT) >From: Jan Kreft >To: nih-image@io.ece.drexel.edu >Subject: case statements in macros > >Dear all, > >I want to use a Pascal case statement in a macro but Image complains about >undefined identifier. Is it possible to use a case statement? > >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 Image doesnt load the macro symbol table with 'case in Macros2.p so the parser doesn't look for it. I think you are stuck with an 'if then else' construct. var case:integer; begin if case=1 then begin... end else if case=2 then begin... end ,, ,, else if case=N then begin... end else begin... end; In any case :-), the interpreter reads though all intervening code during execution even if it doesn't execute it. 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 V99 Issue #24 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 27 02:48 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA01635 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 02:48:01 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 02:48:01 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: Kreft@cardiff.ac.uk, nih-image@io.ece.drexel.edu Date: Wed, 27 Jan 1999 18:23:14 +1100 Subject: Re: case statements in macros Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <169DE71B68@rna.bio.mq.edu.au> Resent-Message-ID: <"ykZrs2.0.Vv6.F-hhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/893 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1135 >Date: Mon, 25 Jan 1999 20:00:18 +0000 (GMT) >From: Jan Kreft >To: nih-image@io.ece.drexel.edu >Subject: case statements in macros > >Dear all, > >I want to use a Pascal case statement in a macro but Image complains about >undefined identifier. Is it possible to use a case statement? > >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 Image doesnt load the macro symbol table with 'case in Macros2.p so the parser doesn't look for it. I think you are stuck with an 'if then else' construct. var case:integer; begin if case=1 then begin... end else if case=2 then begin... end ,, ,, else if case=N then begin... end else begin... end; In any case :-), the interpreter reads though all intervening code during execution even if it doesn't execute it. 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 Jan 27 03:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA09936 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 03:52:38 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 03:52:38 -0500 (EST) Message-ID: <36AEDF10.53A5@wxs.nl> Date: Wed, 27 Jan 1999 09:40:43 +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: upgraded 7100/AV Content-Transfer-Encoding: 7bit Resent-Message-ID: <"03k791.0.Qz1.n2jhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/894 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 577 Dear all, About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 card . I am very happy with it because it works very fast now , a change from 66 MHz to 214 Mhz . Now only one problem left , it was told that the most stable OS for the 7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. Now I upgraded to G3 it made me wonder whether it has an advantage to change to OS 8 I asked Sonnet , the maker of the upgrade card , but they did not know the answer. Can anybody help me with the correct advice? Pieter Houpt BIOMET The Hague , The Netherlands. From nih-image-request@io.ece.drexel.edu Wed Jan 27 04:22 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA13906 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 04:22:23 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 04:22:23 -0500 (EST) Message-Id: <3.0.6.32.19990127101206.009e28f0@pop3.demon.nl> X-Sender: ksalam@pop3.demon.nl X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 27 Jan 1999 10:12:06 +0100 To: nih-image@io.ece.drexel.edu From: K Salam Subject: unsubscribe In-Reply-To: <01be4919$7882ca40$71029a9a@cpana1.ulssasolo.ven.it> Mime-Version: 1.0 Resent-Message-ID: <"r8n1s.0.Mz2.VVjhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/895 X-Loop: nih-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 Wed Jan 27 07:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA08606 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 07:39:35 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 07:39:35 -0500 (EST) Date: Wed, 27 Jan 1999 12:25:18 +0000 (BST) From: "A.B.D. Brown" Reply-To: "A.B.D. Brown" To: nih-image@io.ece.drexel.edu Subject: Scion image and my com (rs-232) port Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"ED_U03.0.xc1.xMmhs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/896 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 692 Hi! I'm wanting to capture images and drive some equipment using my PC. In order to drive the equipment I need to be able to send some simple commands, such as 'stop' and 'go' down my rs-232 line. Is it possible to send such commands using the macro language of Scion Image?? Thanks Ben Brown abdb1@cus.cam.ac.uk --------------------------------------------------------------------------- Andrew Benjamin David Brown Semiconductor Physics Cavendish Lab. Tel (01223) 337478 Madingley Rd. Fax (01223) 337271 Cambridge CB3 0HE --------------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Wed Jan 27 09:06 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA19191 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 09:06:41 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 09:06:41 -0500 (EST) From: "Anatomia Patologica CF" To: Subject: unsubscribe Date: Wed, 27 Jan 1999 14:52:40 +0100 Message-ID: <01be49fc$4ea56140$71029a9a@cpana1.ulssasolo.ven.it> MIME-Version: 1.0 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"40TXX3.0.w84.nbnhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/897 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: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Wed Jan 27 13:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA22365 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 13:46:08 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 13:46:08 -0500 (EST) Date: Wed, 27 Jan 1999 10:12:26 -0800 (PST) From: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"QISkq.0.bZ4.JSrhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/898 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 360 All you need is duct tape. (Well, the Canadians on the list will understand anyway.) Lesley Weston. On Mon, 25 Jan 1999, Fatima A. Merchant wrote: > Hi: > > I was wondering if there is a macro that will build a > Red/Green stereo image from a stack of confocal miccroscope images? > > TIA, > > Fatima Merchant > PSI, Inc. > League City, Texas > > > From nih-image-request@io.ece.drexel.edu Wed Jan 27 15:03 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA01250 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 15:03:42 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 15:03:42 -0500 (EST) Date: Wed, 27 Jan 1999 11:30:15 -0800 From: David Linker To: nih-image@io.ece.drexel.edu Subject: Serial control of VCR on new G3's? Message-ID: <130156.3126425415@huginn.medicine.washington.edu> Originator-Info: login-id=dtlinker; server=dtlinker.deskmail.washington.edu X-Mailer: Mulberry (MacOS) [1.4.0, s/n U-300938] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline Resent-Message-ID: <"muyiA1.0.RY6.Hbshs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/900 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 652 I was wondering if anyone on the list knows whether it is possible to use the serial control features of Image on a USB machine. We have a number of macros that control a VCR using RS422 on our current setup (7100AV). We would like to get a new G3, and run the same programs. I understand that there are no "printer" and "modem" ports, only a USB. Also, there are attachments for USB to serial devices. What is unclear to me is whether such a serial adaptor attached to the USB would work with existing software (NIH Image) written for the old ports. If not, howmuch re-writing of the code would be necessary. Any thought/comments out there? DTL From nih-image-request@io.ece.drexel.edu Wed Jan 27 15:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA01315 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 15:04:13 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 15:04:13 -0500 (EST) Subject: Re: Macro for Red/Green Stereo/DUCT TAPE Date: Wed, 27 Jan 99 14:29:14 -0500 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: Mime-Version: 1.0 Message-ID: <13BD94B230A@qc1.qc.edu> Resent-Message-ID: <"KLikR2.0.EX6.zashs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/899 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 43 but- what about all the other americans?? From nih-image-request@io.ece.drexel.edu Wed Jan 27 15:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA02498 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 15:13:35 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 15:13:35 -0500 (EST) X-Sender: jbrody@itsa.ucsf.edu (Unverified) Message-Id: In-Reply-To: <36AEDF10.53A5@wxs.nl> Mime-Version: 1.0 Date: Wed, 27 Jan 1999 11:42:05 -0800 To: nih-image@io.ece.drexel.edu From: Joel Brody Subject: Re: upgraded 7100/AV Resent-Message-ID: <"-8B4v1.0.cu6.umshs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/901 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 997 Sonnet told me that 8.5 is fine with the latest version of their software available on their Web site. Joel >Dear all, > >About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 >card . I am very happy with it because it works very fast now , a change >from 66 MHz to 214 Mhz . >Now only one problem left , it was told that the most stable OS for the >7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. >Now I upgraded to G3 it made me wonder whether it has an advantage to >change to OS 8 >I asked Sonnet , the maker of the upgrade card , but they did not know >the answer. >Can anybody help me with the correct advice? > >Pieter Houpt > > > >BIOMET > >The Hague , The Netherlands. **************************************************************************** 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 Wed Jan 27 16:32 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA12055 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 16:32:12 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 16:32:12 -0500 (EST) Message-ID: <36AF7E5A.253DCCE@nymc.edu> Date: Wed, 27 Jan 1999 16:00:20 -0500 From: Takafumi Inoue Reply-To: takafumi_inoue@nymc.edu X-Mailer: Mozilla 4.5 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Scion LG-3 and new Mac Content-Transfer-Encoding: 7bit Resent-Message-ID: <"_x19f1.0.L62.Xyths"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/902 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 184 Hello, Does somebody know whether Scion LG-3 works on the new G3 Mac with NIH-Image? Takafumi Inoue, MD., Ph.D. Research Fellow Department of Physiology New York Medical College From nih-image-request@io.ece.drexel.edu Wed Jan 27 18:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA24032 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 18:17:29 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 18:17:29 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: nih-image@io.ece.drexel.edu Date: Thu, 28 Jan 1999 9:49:33 +1100 Subject: Re: Macro for Red/Green Stereo/DUCT TAPE Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <260F616923@rna.bio.mq.edu.au> Resent-Message-ID: <"eER9B2.0.ex4.nSvhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/903 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 373 >Date: Wed, 27 Jan 99 14:29:14 -0500 >From: "Jared L. Rifkin" >To: > >but- what about all the other americans?? > and what about me :-( 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 Jan 27 18:38 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA26849 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 18:38:47 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 18:38:47 -0500 (EST) Message-ID: <36AF9D9F.91CEDA72@netmatters.co.uk> Date: Wed, 27 Jan 1999 23:13:39 +0000 From: Jeremy Brown Reply-To: brownj@netmatters.co.uk X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: upgraded 7100/AV References: <36AEDF10.53A5@wxs.nl> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"djO5v1.0.Sh5.Qrvhs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/904 X-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: 1307 "P.M. Houpt" wrote: > Dear all, > > About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 > card . I am very happy with it because it works very fast now , a change > from 66 MHz to 214 Mhz . > Now only one problem left , it was told that the most stable OS for the > 7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. > Now I upgraded to G3 it made me wonder whether it has an advantage to > change to OS 8 > I asked Sonnet , the maker of the upgrade card , but they did not know > the answer. > Can anybody help me with the correct advice? > > Pieter Houpt > > BIOMET > > The Hague , The Netherlands. I've been using a MAC 7100/80 AV (80 MB RAM) for almost a year now with OS 8.1. It has crasher twice, No Joke! Both times were due to Speed doubler 8's speed copy function. All the other machines I use crash a lot more frequently. I was considering upgrading it to a G3 and/or OS 8.5 but I'm loathed to do any thing to it that might tarnish this rather legendary record. Generally I find the more physical RAM a MAC has the less likely it is to crash 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 Jan 27 19:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA01682 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 19:09:58 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 19:09:58 -0500 (EST) Message-Id: <199901272340.SAA22738@codon.nih.gov> X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Date: Wed, 27 Jan 1999 18:49:40 -0500 To: nih-image@io.ece.drexel.edu From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) Subject: Re: Scion LG-3 and new Mac Resent-Message-ID: <"lyEtb1.0.sw6.dNwhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/905 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: 821 At 4:00 PM 01/27/99, Takafumi Inoue wrote: > Hello, > > > Does somebody know whether Scion LG-3 works on the new G3 Mac with NIH-Image? > > > Takafumi Inoue, MD., Ph.D. > > Research Fellow > Department of Physiology > New York Medical College Hi, So far, Scion LG-3 is working well on new G3 Mac with NIH Image in our lab. However, Iomega Buz is not working with the new G3 for unknown reason (the system freezes immediately after image capturing starts). ________________________________________ 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 Wed Jan 27 19:12 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA02019; Wed, 27 Jan 1999 19:12:20 -0500 (EST) Date: Wed, 27 Jan 1999 19:12:20 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901280012.TAA02019@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #25 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/25 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: 10812 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 25 Today's Topics: upgraded 7100/AV [ "P.M. Houpt" ] unsubscribe [ K Salam ] Scion image and my com (rs-232) port [ "A.B.D. Brown" ] Scion LG-3 and new Mac [ Takafumi Inoue To: "nih-image@io.ece.drexel.edu" Subject: upgraded 7100/AV Message-ID: <36AEDF10.53A5@wxs.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 card . I am very happy with it because it works very fast now , a change from 66 MHz to 214 Mhz . Now only one problem left , it was told that the most stable OS for the 7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. Now I upgraded to G3 it made me wonder whether it has an advantage to change to OS 8 I asked Sonnet , the maker of the upgrade card , but they did not know the answer. Can anybody help me with the correct advice? Pieter Houpt BIOMET The Hague , The Netherlands. ------------------------------ Date: Wed, 27 Jan 1999 10:12:06 +0100 From: K Salam To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: <3.0.6.32.19990127101206.009e28f0@pop3.demon.nl> Content-Type: text/plain; charset="us-ascii" unsubscribe ------------------------------ Date: Wed, 27 Jan 1999 12:25:18 +0000 (BST) From: "A.B.D. Brown" To: nih-image@io.ece.drexel.edu Subject: Scion image and my com (rs-232) port Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I'm wanting to capture images and drive some equipment using my PC. In order to drive the equipment I need to be able to send some simple commands, such as 'stop' and 'go' down my rs-232 line. Is it possible to send such commands using the macro language of Scion Image?? Thanks Ben Brown abdb1@cus.cam.ac.uk --------------------------------------------------------------------------- Andrew Benjamin David Brown Semiconductor Physics Cavendish Lab. Tel (01223) 337478 Madingley Rd. Fax (01223) 337271 Cambridge CB3 0HE --------------------------------------------------------------------------- ------------------------------ Date: Wed, 27 Jan 1999 14:52:40 +0100 From: "Anatomia Patologica CF" To: Subject: unsubscribe Message-ID: <01be49fc$4ea56140$71029a9a@cpana1.ulssasolo.ven.it> Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Wed, 27 Jan 1999 10:12:26 -0800 (PST) From: Lesley Weston To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII All you need is duct tape. (Well, the Canadians on the list will understand anyway.) Lesley Weston. On Mon, 25 Jan 1999, Fatima A. Merchant wrote: > Hi: > > I was wondering if there is a macro that will build a > Red/Green stereo image from a stack of confocal miccroscope images? > > TIA, > > Fatima Merchant > PSI, Inc. > League City, Texas > > > ------------------------------ Date: Wed, 27 Jan 99 14:29:14 -0500 From: "Jared L. Rifkin" To: Subject: Re: Macro for Red/Green Stereo/DUCT TAPE Message-ID: <13BD94B230A@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" but- what about all the other americans?? ------------------------------ Date: Wed, 27 Jan 1999 11:30:15 -0800 From: David Linker To: nih-image@io.ece.drexel.edu Subject: Serial control of VCR on new G3's? Message-ID: <130156.3126425415@huginn.medicine.washington.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline I was wondering if anyone on the list knows whether it is possible to use the serial control features of Image on a USB machine. We have a number of macros that control a VCR using RS422 on our current setup (7100AV). We would like to get a new G3, and run the same programs. I understand that there are no "printer" and "modem" ports, only a USB. Also, there are attachments for USB to serial devices. What is unclear to me is whether such a serial adaptor attached to the USB would work with existing software (NIH Image) written for the old ports. If not, howmuch re-writing of the code would be necessary. Any thought/comments out there? DTL ------------------------------ Date: Wed, 27 Jan 1999 11:42:05 -0800 From: Joel Brody To: nih-image@io.ece.drexel.edu Subject: Re: upgraded 7100/AV Message-Id: Content-Type: text/plain; charset="us-ascii" Sonnet told me that 8.5 is fine with the latest version of their software available on their Web site. Joel >Dear all, > >About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 >card . I am very happy with it because it works very fast now , a change >from 66 MHz to 214 Mhz . >Now only one problem left , it was told that the most stable OS for the >7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. >Now I upgraded to G3 it made me wonder whether it has an advantage to >change to OS 8 >I asked Sonnet , the maker of the upgrade card , but they did not know >the answer. >Can anybody help me with the correct advice? > >Pieter Houpt > > > >BIOMET > >The Hague , The Netherlands. **************************************************************************** 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: Wed, 27 Jan 1999 16:00:20 -0500 From: Takafumi Inoue To: nih-image@io.ece.drexel.edu Subject: Scion LG-3 and new Mac Message-ID: <36AF7E5A.253DCCE@nymc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Does somebody know whether Scion LG-3 works on the new G3 Mac with NIH-Image? Takafumi Inoue, MD., Ph.D. Research Fellow Department of Physiology New York Medical College ------------------------------ Date: Thu, 28 Jan 1999 9:49:33 +1100 From: GJOSS@rna.bio.mq.edu.au To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo/DUCT TAPE Message-ID: <260F616923@rna.bio.mq.edu.au> >Date: Wed, 27 Jan 99 14:29:14 -0500 >From: "Jared L. Rifkin" >To: > >but- what about all the other americans?? > and what about me :-( 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: Wed, 27 Jan 1999 23:13:39 +0000 From: Jeremy Brown To: nih-image@io.ece.drexel.edu Subject: Re: upgraded 7100/AV Message-ID: <36AF9D9F.91CEDA72@netmatters.co.uk> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit "P.M. Houpt" wrote: > Dear all, > > About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 > card . I am very happy with it because it works very fast now , a change > from 66 MHz to 214 Mhz . > Now only one problem left , it was told that the most stable OS for the > 7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. > Now I upgraded to G3 it made me wonder whether it has an advantage to > change to OS 8 > I asked Sonnet , the maker of the upgrade card , but they did not know > the answer. > Can anybody help me with the correct advice? > > Pieter Houpt > > BIOMET > > The Hague , The Netherlands. I've been using a MAC 7100/80 AV (80 MB RAM) for almost a year now with OS 8.1. It has crasher twice, No Joke! Both times were due to Speed doubler 8's speed copy function. All the other machines I use crash a lot more frequently. I was considering upgrading it to a G3 and/or OS 8.5 but I'm loathed to do any thing to it that might tarnish this rather legendary record. Generally I find the more physical RAM a MAC has the less likely it is to crash Jeremy ************************************************ Jeremy Brown Edinburgh University/Moredun Research Institute http://www.netmatters.co.uk/users/brownj/HomePage.html ************************************************ ------------------------------ Date: Wed, 27 Jan 1999 18:49:40 -0500 From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) To: nih-image@io.ece.drexel.edu Subject: Re: Scion LG-3 and new Mac Message-Id: <199901272340.SAA22738@codon.nih.gov> Content-Type: text/plain; charset="ISO-2022-JP" At 4:00 PM 01/27/99, Takafumi Inoue wrote: > Hello, > > > Does somebody know whether Scion LG-3 works on the new G3 Mac with NIH-Image? > > > Takafumi Inoue, MD., Ph.D. > > Research Fellow > Department of Physiology > New York Medical College Hi, So far, Scion LG-3 is working well on new G3 Mac with NIH Image in our lab. However, Iomega Buz is not working with the new G3 for unknown reason (the system freezes immediately after image capturing starts). ________________________________________ 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 V99 Issue #25 *************************************** From nih-image-request@io.ece.drexel.edu Wed Jan 27 22:57 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA02418 for cshtest@io.ece.drexel.edu; Wed, 27 Jan 1999 22:57:42 -0500 (EST) Resent-Date: Wed, 27 Jan 1999 22:57:42 -0500 (EST) Date: Wed, 27 Jan 1999 19:33:45 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: system 8.1 In-Reply-To: <199901280014.TAA02358@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"yWW1c3.0.o77.ggzhs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/906 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 678 For what it's worth, System 8.1 has proven to be very reliable here with all of our PowerPC Macs, provided... they have adequate RAM, get rid of anything-Doubler, and if you use Netscape then version 4.5 or better. Even our AV machines have been better behaved with 8.1 than with 8.0 or 7.5.5. A question related to using the Iomega Buz, has anyone tried the VillageTronic MacPablo board for monochrome and composite color capture? 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 Thu Jan 28 04:35 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA15631 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 04:35:38 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 04:35:38 -0500 (EST) Message-Id: <199901280919.UAA22827@redback.ne.com.au> Subject: Averaging Video Slices - It Works! Date: Thu, 28 Jan 99 20:15:13 +1100 x-mailer: Claris Emailer 1.1 From: gecko To: Mime-Version: 1.0 Resent-Message-ID: <"XAtXp.0.C83.Wh2is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/907 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 2354 Hello All, Thanks heaps to those that supplied suggestions in this regard. The camera that I'm using is a B/W Sony Board CCD video camera (Disk Smith Electronics L-5870 about AU$80). This camera doesn't do on-chip integration. It's really meant for cheap security applications. The macro merges the first and last slices of your video clip then asks you to choose reference points for the start and end of the motion trail of the object. Then choose a point for the background colour (needed for the copy-shift-paste part). Then it calculates the total shift of the object, divides it by the number of slices and shifts each slice by the correct amount. After the average (AverageSlices;) the results are quite pleasing. I've tried this macro on unguided short clips (30-100 slices) of the Moon and Jupiter and it works well. If you would like to see the results they are available at ... http://www.ne.com.au/~gecko/astro/moonbefore.jpg (single slice from 20 slice clip) http://www.ne.com.au/~gecko/astro/moonafter.jpg They're about 20kb each. Thanks again! Doug Rolfe Geelong, Australia gecko@ne.com.au ------------------- macro 'VideoTrackAverage'; var x1,y1, x2,y2,n,bg,xbg,ybg,numslice,width,height,s0,s1,s2,s3:integer; dx,dy:real begin RequiresVersion(1.53); s0:= PicNumber; numslice := nSlices; SelectSlice(1); SelectAll; Copy; GetPicSize(width,height); SetNewSize(width,height); MakeNewWindow('Slice1'); Paste; s1:= PicNumber; SelectPic(s0); SelectSlice(numslice); SelectAll; Copy; MakeNewWindow('Slice2'); Paste; s2:= PicNumber; ImageMath('add' ,s1 ,s2, 0.5, 0, 'Start2Finish'); s3:= PicNumber; PutMessage('Select centre of Slice1 object with a single mouse click.'); SelectPic(s3); Repeat Until Button; GetMouse(x1,y1); PutMessage('Select centre of Slice2 object with a single mouse click.'); SelectPic(s3); Repeat Until Button; GetMouse(x2,y2); SelectPic(s0); PutMessage('Select a point for the background colour.'); Repeat Until Button; GetMouse(xbg,ybg); bg:=GetPixel(xbg,ybg); dx:=(x2-x1)/numslice; dy:=(y2-y1)/numslice; n:=1; Repeat; SelectPic(s0); SelectSlice(n); SelectAll; Copy; SetBackgroundColor(bg); Clear; MoveROI(-dx*n,-dy*n); Paste; n:=n+1; Until n=numslice+1; AverageSlices; end; From nih-image-request@io.ece.drexel.edu Thu Jan 28 07:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA11159 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 07:45:36 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 07:45:36 -0500 (EST) Message-Id: <3.0.5.32.19990128071859.00935430@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: Thu, 28 Jan 1999 07:18:59 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Macro for Red/Green Stereo In-Reply-To: References: <199901251702.MAA11839@red.seas.upenn.edu> Mime-Version: 1.0 Resent-Message-ID: <"eiMBM.0.8n1.-N5is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/908 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1178 So, Duct Tape aside, back to this issue. The LUT Macro's with NIH Image (at least with 1.62) includes one called "combine color images" or some such that takes two greyscale images (left eye and right eye) and combines them to produce one red-green (3-D stereo) image. So that module exists. One could take the stack, make the last slice the same right and left, and take each earlier slice and just move it left and/right by some number of pixels proportional to distance from back of the stack, then recomine all those into one image. It wouldn't be perfect 3-D perspective translation, but it wouldn't be horrible either. Problem is, that will not hide any hidden surfaces or lines. Before toying with it, what are your images? Just a few bright objects, like neurons, and a dark background, or is there a lot of detail everywhere? Wade (and the duct tape gang). At 11:19 AM 1/25/99 -0600, you wrote: >Hi: > >I was wondering if there is a macro that will build a >Red/Green stereo image from a stack of confocal miccroscope images? > >TIA, > >Fatima Merchant >PSI, Inc. >League City, Texas > > Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Thu Jan 28 07:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA11340 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 07:46:35 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 07:46:35 -0500 (EST) Message-Id: <3.0.5.32.19990128072035.00992d50@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: Thu, 28 Jan 1999 07:20:35 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Macro for Red/Green Stereo In-Reply-To: References: <199901251702.MAA11839@red.seas.upenn.edu> Mime-Version: 1.0 Resent-Message-ID: <"LTaTo1.0.Ar1.TP5is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/909 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 434 >I was wondering if there is a macro that will build a >Red/Green stereo image from a stack of confocal miccroscope images? by the way, who actually uses red/GREEN stereo? I have about 10 pairs of red/blue glasses that came with various products in the US, but I've never even seen red/green glasses. Are these in wide use somewhere? Just curious. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Thu Jan 28 08:06 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA14401 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 08:06:57 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 08:06:57 -0500 (EST) X-Sender: jpbrion@pop.ulb.ac.be Message-Id: Mime-Version: 1.0 Date: Wed, 30 Dec 1998 13:45:17 +0100 To: nih-image@io.ece.drexel.edu From: jpbrion Subject: camera Resent-Message-ID: <"E_y0n3.0.Ia2.6j5is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/910 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1175 Hello imagers, We are using the wonderful NIH image program since some years to analyse biological images from various sources. We are now planning to buy a color camera for image acquisition integrated with a PowerMac 8500 (upgraded with a Newer G3 card). We thought that the Dage DC-330 camera and the Scion CG7 framegrabber would be a good general solution. We would like to acquire histological pictures (in brightfield, for that we suppose there would not be any problems) but also in more demanding experimental conditions, eg double immunofluorescence of cultured cells, and EGFP transfected cells. Does anybody have enough experience with this system? What about the integration in low-light fluorescence? Is the integration quick enough for video acquisition (eg live cells transfected with EGFP vectors)? Thanks for any comments. JP Brion Laboratory of Pathology Free University of Brussels, Belgium email: jpbrion@ulb.ac.be Jean-Pierre Brion Laboratory of Pathology and Electron Microscopy Free University of Brussels School of Medicine 808, route de Lennik Bldg C-10 1070 - Brussels, Belgium tel: 32 2 555 4126 Fax: 32 2 555 4121 email: jpbrion@ulb.ac.be From nih-image-request@io.ece.drexel.edu Thu Jan 28 10:36 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA04319 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 10:36:34 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 10:36:34 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk Reply-To: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo In-Reply-To: <3.0.5.32.19990128072035.00992d50@s.imap.itd.umich.edu> Message-ID: Date: Thu, 28 Jan 1999 15:13:12 -0600 (Central 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: <"OA6IN1.0.4L.Kw7is"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/911 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 987 Bio-Rad used to use the red green projections when I was using the MRC-600 confocal about 3 years ago, I think that they still do. On Thu, 28 Jan 1999 07:20:35 -0500 Wade & Cheryll Schuette wrote: > >I was wondering if there is a macro that will build a > >Red/Green stereo image from a stack of confocal miccroscope images? > > by the way, who actually uses red/GREEN stereo? I have about 10 pairs > of red/blue glasses that came with various products in the US, but I've > never even seen red/green glasses. Are these in wide use somewhere? > > Just curious. > > Wade > > > Cheryll & Wade Schuette > 2345 Stone Road > Ann Arbor MI 48105 > 734-763-8278 ---------------------- 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-request@io.ece.drexel.edu Thu Jan 28 11:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA08817 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 11:10:14 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 11:10:14 -0500 (EST) X-Sender: merchant@mail.persci.com Message-Id: Mime-Version: 1.0 Date: Thu, 28 Jan 1999 09:45:06 -0600 To: nih-image@io.ece.drexel.edu From: Fatima Merchant Subject: Re: Macro for Red/Green Stereo Resent-Message-ID: <"ODreP2.0.gK1.OO8is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/912 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1664 Thanks a lot for the help with the macros for R/G stereo (duct tape included!) Dr. Vischer has macros that work, i downloaded them and got some good stereos. You can do both R/G or R/B. He has a macro for swapping colors also!! I am attaching his response below for all interested A million thanx, Fatima. >To: nih-image@io.ece.drexel.edu >From: Norbert Vischer >Subject: Re: Macro for Red/Green Stereo >Look at the StackMacros 1.0 on: > > > >These macros let you create b/w stereo pairs and red/green or red/blue >stereo impressions combined with animated rotation around a desired angle. >The look-up tables are interlaced with continuously increasing darkness, so >the images also make sense if you look at them in greyscale. >To create an animated stereo image, issue these macros: > >- Project for stereo sequence > ... then, using the projection stack, issue >- "Red green stereo sequence" or "Greyscale stereo sequence" > >The macros also include a means to merge two stacks to one color stack in >"replace mode", where one stack replaces the other at those spots where >intensity is above a certain level, useful for marking FISH spots in a >different color. > >N. Vischer > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 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: 230 Toll Free: (800) 288-3027 Ext: 230 Facsimile: (281) 538-2222 Email: merchant@persci.com <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> From nih-image-request@io.ece.drexel.edu Thu Jan 28 11:53 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA14565 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 11:53:46 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 11:53:46 -0500 (EST) Mime-Version: 1.0 Message-Id: Date: Thu, 28 Jan 1999 11:24:50 -0500 To: nih-image@io.ece.drexel.edu From: Bill Christens-Barry Subject: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? Resent-Message-ID: <"zuECE.0.BU2.fx8is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/913 X-Loop: nih-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 Has anyone implemented a GIF output format for TIFF files in a macro or recompiliation of Image? Right now my solution entails saving a TIFF, and then running an AppleScript that invokes clip2gif to do the conversion. Direct output in GIF would sure save a lot of trouble. Obliquely related question: where stands Apple Event awareness of Image? I know that several people have made forays in the past but I have not seen much progress recently. I know Wayne is moving Image forward in other ways - are there any folks who would be interested in jointly trying to add this capability? I would volunteer my meager skills to help in this effort. 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 Jan 28 12:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA16781 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 12:09:23 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 12:09:23 -0500 (EST) Message-Id: <3.0.5.32.19990128114231.0094f250@mailserver.aecom.yu.edu> X-Sender: cammer@mailserver.aecom.yu.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Thu, 28 Jan 1999 11:42:31 -0800 To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu From: Michael Cammer Subject: Re: Macro for Red/Green Stereo In-Reply-To: <3.0.5.32.19990128072035.00992d50@s.imap.itd.umich.edu> References: <199901251702.MAA11839@red.seas.upenn.edu> Mime-Version: 1.0 Resent-Message-ID: <"zFVjH1.0._13.1B9is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/914 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1218 At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >of red/blue glasses that came with various products in the US, but I've >never even seen red/green glasses. Are these in wide use somewhere? Red/green stereo used be be in very high demand. 1991 to 1996 we made tons of stereo images. I have no idea why, but in the past two years or so we have used it very occassionally. However, I still give demos for high school students, with it. I start with half a potato or apple on a glass plate. I tell them that this is the cell on the coverslip. Then I cut it into slices, show individual slices, and reconstruct the potato. Then we do this with cells on the confocal. And this eventually brings us to 3D glasses and rotations on th Mac. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* From nih-image-request@io.ece.drexel.edu Thu Jan 28 12:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA18538 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 12:25:07 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 12:25:07 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk Reply-To: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? In-Reply-To: Message-ID: Date: Thu, 28 Jan 1999 16:55:33 +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: <"RrI-p.0.nd3.LQ9is"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/915 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 873 > Has anyone implemented a GIF output format for TIFF files in a macro or > recompiliation of Image? Right now my solution entails saving a TIFF, and > then running an AppleScript that invokes clip2gif to do the conversion. > Direct output in GIF would sure save a lot of trouble. I do not have a direct method but for a few images I use Powerpoint 97 which allows tif images to be saved in gif format. ImageTool which can be found as a link in the NIH site is also useful (among other things) for file conversion - it will not do gif but will do a bunch of different jpg types. ---------------------- 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-request@io.ece.drexel.edu Thu Jan 28 12:57 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA22559 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 12:57:39 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 12:57:39 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 28 Jan 1999 13:33:40 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? Resent-Message-ID: <"riwIi2.0.Gb4.at9is"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/916 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1001 >Has anyone implemented a GIF output format for TIFF files in a macro or >recompiliation of Image? Right now my solution entails saving a TIFF, and >then running an AppleScript that invokes clip2gif to do the conversion. >Direct output in GIF would sure save a lot of trouble. My new ImageJ program at http://rsb.info.nih.gov/ij/ reads tiffs and saves in gif and jpeg format. It would be possible, but not easy, for someone to convert ImageJ's GifEncoder class from Java to Pascal and add it to NIH Image. >Obliquely related question: where stands Apple Event awareness of Image? I >know that several people have made forays in the past but I have not seen >much progress recently. I know Wayne is moving Image forward in other ways >- are there any folks who would be interested in jointly trying to add this >capability? I would volunteer my meager skills to help in this effort. Norbert Vischer is adding AppleScript support to ObjectImage (http://simon.bio.uva.nl/object-image.html). -wayne From nih-image-request@io.ece.drexel.edu Thu Jan 28 16:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA10747 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 16:02:17 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 16:02:17 -0500 (EST) Date: Thu, 28 Jan 1999 15:34:39 -0500 (EST) From: Cengizhan Ozturk X-Sender: cozturk@henryv To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo In-Reply-To: <3.0.5.32.19990128114231.0094f250@mailserver.aecom.yu.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"apCkF3.0.pq1.cdCis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/918 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 990 On Thu, 28 Jan 1999, Michael Cammer wrote: > At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: > >by the way, who actually uses red/GREEN stereo? I have about 10 pairs > >of red/blue glasses that came with various products in the US, but I've > >never even seen red/green glasses. Are these in wide use somewhere? > > Red/green stereo used be be in very high demand. 1991 to 1996 we made tons > of stereo images. I have no idea why, but in the past two years or so we > have used it very occassionally. However, I still give demos for high > school students, with it. I start with half a potato or apple on a glass > plate. I tell them that this is the cell on the coverslip. Then I cut it > into slices, show individual slices, and reconstruct the potato. Then we > do this with cells on the confocal. And this eventually brings us to 3D > glasses and rotations on th Mac. Hi, Where do we get cheap red/blue glasses ? Cengizhan Ozturk JHU- Medical Imaging Lab From nih-image-request@io.ece.drexel.edu Thu Jan 28 16:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA11036 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 16:04:20 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 16:04:20 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Thu, 28 Jan 1999 15:26:57 -0500 From: "Wade Schuette" To: cammer@aecom.yu.edu, nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"62iol.0.Ge1.dWCis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/917 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2032 Thanks for the reply, Michael. I was wondering if it was just me, or if high-tech (high-cost) Virtual Reality goggles were short-circuiting all lower-tech versions of 3D. I wrote a macro/demo for NIH once (maybe even posted to zippy) for people to learn to see 3-D in side-by-side images, but never got much feedback. In 1990 or so, I built a unit that ran Sega Game Glasses from a Mac so one could do color 3-D on a Mac (Silicon graphics envy), but there didn't seem to be much low-end interest either, and I don't think one can even get Sega Game glasses any more. Curious. Wade R. Wade Schuette MCIT CDR Team phone: 734 763-4486 alpha pager: 734 797-6622 Arbor Lakes, Bldg 3, Suite 1300 4251 Plymouth Rd. Ann Arbor, MI 48105-2785 >>> Michael Cammer 01/28 12:08 PM >>> At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >of red/blue glasses that came with various products in the US, but I've >never even seen red/green glasses. Are these in wide use somewhere? Red/green stereo used be be in very high demand. 1991 to 1996 we made tons of stereo images. I have no idea why, but in the past two years or so we have used it very occassionally. However, I still give demos for high school students, with it. I start with half a potato or apple on a glass plate. I tell them that this is the cell on the coverslip. Then I cut it into slices, show individual slices, and reconstruct the potato. Then we do this with cells on the confocal. And this eventually brings us to 3D glasses and rotations on th Mac. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* From nih-image-d-request@io.ece.drexel.edu Thu Jan 28 16:11 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA11848; Thu, 28 Jan 1999 16:11:16 -0500 (EST) Date: Thu, 28 Jan 1999 16:11:16 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901282111.QAA11848@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #26 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/26 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: 19392 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 26 Today's Topics: Re: system 8.1 [ "G. Macdonald" ] Re: Macro for Red/Green Stereo [ Wade & Cheryll Schuette ] Re: Macro for Red/Green Stereo [ paul stoodley ] Re: Macro for Red/Green Stereo [ "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: system 8.1 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII For what it's worth, System 8.1 has proven to be very reliable here with all of our PowerPC Macs, provided... they have adequate RAM, get rid of anything-Doubler, and if you use Netscape then version 4.5 or better. Even our AV machines have been better behaved with 8.1 than with 8.0 or 7.5.5. A question related to using the Iomega Buz, has anyone tried the VillageTronic MacPablo board for monochrome and composite color capture? 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: Thu, 28 Jan 99 20:15:13 +1100 From: gecko To: Subject: Averaging Video Slices - It Works! Message-Id: <199901280919.UAA22827@redback.ne.com.au> Content-Type: text/plain; charset="US-ASCII" Hello All, Thanks heaps to those that supplied suggestions in this regard. The camera that I'm using is a B/W Sony Board CCD video camera (Disk Smith Electronics L-5870 about AU$80). This camera doesn't do on-chip integration. It's really meant for cheap security applications. The macro merges the first and last slices of your video clip then asks you to choose reference points for the start and end of the motion trail of the object. Then choose a point for the background colour (needed for the copy-shift-paste part). Then it calculates the total shift of the object, divides it by the number of slices and shifts each slice by the correct amount. After the average (AverageSlices;) the results are quite pleasing. I've tried this macro on unguided short clips (30-100 slices) of the Moon and Jupiter and it works well. If you would like to see the results they are available at ... http://www.ne.com.au/~gecko/astro/moonbefore.jpg (single slice from 20 slice clip) http://www.ne.com.au/~gecko/astro/moonafter.jpg They're about 20kb each. Thanks again! Doug Rolfe Geelong, Australia gecko@ne.com.au ------------------- macro 'VideoTrackAverage'; var x1,y1, x2,y2,n,bg,xbg,ybg,numslice,width,height,s0,s1,s2,s3:integer; dx,dy:real begin RequiresVersion(1.53); s0:= PicNumber; numslice := nSlices; SelectSlice(1); SelectAll; Copy; GetPicSize(width,height); SetNewSize(width,height); MakeNewWindow('Slice1'); Paste; s1:= PicNumber; SelectPic(s0); SelectSlice(numslice); SelectAll; Copy; MakeNewWindow('Slice2'); Paste; s2:= PicNumber; ImageMath('add' ,s1 ,s2, 0.5, 0, 'Start2Finish'); s3:= PicNumber; PutMessage('Select centre of Slice1 object with a single mouse click.'); SelectPic(s3); Repeat Until Button; GetMouse(x1,y1); PutMessage('Select centre of Slice2 object with a single mouse click.'); SelectPic(s3); Repeat Until Button; GetMouse(x2,y2); SelectPic(s0); PutMessage('Select a point for the background colour.'); Repeat Until Button; GetMouse(xbg,ybg); bg:=GetPixel(xbg,ybg); dx:=(x2-x1)/numslice; dy:=(y2-y1)/numslice; n:=1; Repeat; SelectPic(s0); SelectSlice(n); SelectAll; Copy; SetBackgroundColor(bg); Clear; MoveROI(-dx*n,-dy*n); Paste; n:=n+1; Until n=numslice+1; AverageSlices; end; ------------------------------ Date: Thu, 28 Jan 1999 07:18:59 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: <3.0.5.32.19990128071859.00935430@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" So, Duct Tape aside, back to this issue. The LUT Macro's with NIH Image (at least with 1.62) includes one called "combine color images" or some such that takes two greyscale images (left eye and right eye) and combines them to produce one red-green (3-D stereo) image. So that module exists. One could take the stack, make the last slice the same right and left, and take each earlier slice and just move it left and/right by some number of pixels proportional to distance from back of the stack, then recomine all those into one image. It wouldn't be perfect 3-D perspective translation, but it wouldn't be horrible either. Problem is, that will not hide any hidden surfaces or lines. Before toying with it, what are your images? Just a few bright objects, like neurons, and a dark background, or is there a lot of detail everywhere? Wade (and the duct tape gang). At 11:19 AM 1/25/99 -0600, you wrote: >Hi: > >I was wondering if there is a macro that will build a >Red/Green stereo image from a stack of confocal miccroscope images? > >TIA, > >Fatima Merchant >PSI, Inc. >League City, Texas > > Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Thu, 28 Jan 1999 07:20:35 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: <3.0.5.32.19990128072035.00992d50@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" >I was wondering if there is a macro that will build a >Red/Green stereo image from a stack of confocal miccroscope images? by the way, who actually uses red/GREEN stereo? I have about 10 pairs of red/blue glasses that came with various products in the US, but I've never even seen red/green glasses. Are these in wide use somewhere? Just curious. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Wed, 30 Dec 1998 13:45:17 +0100 From: jpbrion To: nih-image@io.ece.drexel.edu Subject: camera Message-Id: Content-Type: text/plain; charset="us-ascii" Hello imagers, We are using the wonderful NIH image program since some years to analyse biological images from various sources. We are now planning to buy a color camera for image acquisition integrated with a PowerMac 8500 (upgraded with a Newer G3 card). We thought that the Dage DC-330 camera and the Scion CG7 framegrabber would be a good general solution. We would like to acquire histological pictures (in brightfield, for that we suppose there would not be any problems) but also in more demanding experimental conditions, eg double immunofluorescence of cultured cells, and EGFP transfected cells. Does anybody have enough experience with this system? What about the integration in low-light fluorescence? Is the integration quick enough for video acquisition (eg live cells transfected with EGFP vectors)? Thanks for any comments. JP Brion Laboratory of Pathology Free University of Brussels, Belgium email: jpbrion@ulb.ac.be Jean-Pierre Brion Laboratory of Pathology and Electron Microscopy Free University of Brussels School of Medicine 808, route de Lennik Bldg C-10 1070 - Brussels, Belgium tel: 32 2 555 4126 Fax: 32 2 555 4121 email: jpbrion@ulb.ac.be ------------------------------ Date: Thu, 28 Jan 1999 15:13:12 -0600 (Central Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Bio-Rad used to use the red green projections when I was using the MRC-600 confocal about 3 years ago, I think that they still do. On Thu, 28 Jan 1999 07:20:35 -0500 Wade & Cheryll Schuette wrote: > >I was wondering if there is a macro that will build a > >Red/Green stereo image from a stack of confocal miccroscope images? > > by the way, who actually uses red/GREEN stereo? I have about 10 pairs > of red/blue glasses that came with various products in the US, but I've > never even seen red/green glasses. Are these in wide use somewhere? > > Just curious. > > Wade > > > Cheryll & Wade Schuette > 2345 Stone Road > Ann Arbor MI 48105 > 734-763-8278 ---------------------- 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. ------------------------------ Date: Thu, 28 Jan 1999 09:45:06 -0600 From: Fatima Merchant To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: Content-Type: text/plain; charset="us-ascii" Thanks a lot for the help with the macros for R/G stereo (duct tape included!) Dr. Vischer has macros that work, i downloaded them and got some good stereos. You can do both R/G or R/B. He has a macro for swapping colors also!! I am attaching his response below for all interested A million thanx, Fatima. >To: nih-image@io.ece.drexel.edu >From: Norbert Vischer >Subject: Re: Macro for Red/Green Stereo >Look at the StackMacros 1.0 on: > > > >These macros let you create b/w stereo pairs and red/green or red/blue >stereo impressions combined with animated rotation around a desired angle. >The look-up tables are interlaced with continuously increasing darkness, so >the images also make sense if you look at them in greyscale. >To create an animated stereo image, issue these macros: > >- Project for stereo sequence > ... then, using the projection stack, issue >- "Red green stereo sequence" or "Greyscale stereo sequence" > >The macros also include a means to merge two stacks to one color stack in >"replace mode", where one stack replaces the other at those spots where >intensity is above a certain level, useful for marking FISH spots in a >different color. > >N. Vischer > <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 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: 230 Toll Free: (800) 288-3027 Ext: 230 Facsimile: (281) 538-2222 Email: merchant@persci.com <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> ------------------------------ Date: Thu, 28 Jan 1999 11:24:50 -0500 From: Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? Message-Id: Content-Type: text/plain; charset="us-ascii" Has anyone implemented a GIF output format for TIFF files in a macro or recompiliation of Image? Right now my solution entails saving a TIFF, and then running an AppleScript that invokes clip2gif to do the conversion. Direct output in GIF would sure save a lot of trouble. Obliquely related question: where stands Apple Event awareness of Image? I know that several people have made forays in the past but I have not seen much progress recently. I know Wayne is moving Image forward in other ways - are there any folks who would be interested in jointly trying to add this capability? I would volunteer my meager skills to help in this effort. Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- ------------------------------ Date: Thu, 28 Jan 1999 11:42:31 -0800 From: Michael Cammer To: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: <3.0.5.32.19990128114231.0094f250@mailserver.aecom.yu.edu> Content-Type: text/plain; charset="us-ascii" At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >of red/blue glasses that came with various products in the US, but I've >never even seen red/green glasses. Are these in wide use somewhere? Red/green stereo used be be in very high demand. 1991 to 1996 we made tons of stereo images. I have no idea why, but in the past two years or so we have used it very occassionally. However, I still give demos for high school students, with it. I start with half a potato or apple on a glass plate. I tell them that this is the cell on the coverslip. Then I cut it into slices, show individual slices, and reconstruct the potato. Then we do this with cells on the confocal. And this eventually brings us to 3D glasses and rotations on th Mac. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* ------------------------------ Date: Thu, 28 Jan 1999 16:55:33 +0000 (GMT Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > Has anyone implemented a GIF output format for TIFF files in a macro or > recompiliation of Image? Right now my solution entails saving a TIFF, and > then running an AppleScript that invokes clip2gif to do the conversion. > Direct output in GIF would sure save a lot of trouble. I do not have a direct method but for a few images I use Powerpoint 97 which allows tif images to be saved in gif format. ImageTool which can be found as a link in the NIH site is also useful (among other things) for file conversion - it will not do gif but will do a bunch of different jpg types. ---------------------- 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. ------------------------------ Date: Thu, 28 Jan 1999 13:33:40 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: saving TIFFs as GIFs in NIH Image; group interest in adding AppleScriptability? Message-Id: Content-Type: text/plain; charset="us-ascii" >Has anyone implemented a GIF output format for TIFF files in a macro or >recompiliation of Image? Right now my solution entails saving a TIFF, and >then running an AppleScript that invokes clip2gif to do the conversion. >Direct output in GIF would sure save a lot of trouble. My new ImageJ program at http://rsb.info.nih.gov/ij/ reads tiffs and saves in gif and jpeg format. It would be possible, but not easy, for someone to convert ImageJ's GifEncoder class from Java to Pascal and add it to NIH Image. >Obliquely related question: where stands Apple Event awareness of Image? I >know that several people have made forays in the past but I have not seen >much progress recently. I know Wayne is moving Image forward in other ways >- are there any folks who would be interested in jointly trying to add this >capability? I would volunteer my meager skills to help in this effort. Norbert Vischer is adding AppleScript support to ObjectImage (http://simon.bio.uva.nl/object-image.html). -wayne ------------------------------ Date: Thu, 28 Jan 1999 15:26:57 -0500 From: "Wade Schuette" To: cammer@aecom.yu.edu, nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Thanks for the reply, Michael. I was wondering if it was just me, or if high-tech (high-cost) Virtual Reality goggles were short-circuiting all lower-tech versions of 3D. I wrote a macro/demo for NIH once (maybe even posted to zippy) for people to learn to see 3-D in side-by-side images, but never got much feedback. In 1990 or so, I built a unit that ran Sega Game Glasses from a Mac so one could do color 3-D on a Mac (Silicon graphics envy), but there didn't seem to be much low-end interest either, and I don't think one can even get Sega Game glasses any more. Curious. Wade R. Wade Schuette MCIT CDR Team phone: 734 763-4486 alpha pager: 734 797-6622 Arbor Lakes, Bldg 3, Suite 1300 4251 Plymouth Rd. Ann Arbor, MI 48105-2785 >>> Michael Cammer 01/28 12:08 PM >>> At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >of red/blue glasses that came with various products in the US, but I've >never even seen red/green glasses. Are these in wide use somewhere? Red/green stereo used be be in very high demand. 1991 to 1996 we made tons of stereo images. I have no idea why, but in the past two years or so we have used it very occassionally. However, I still give demos for high school students, with it. I start with half a potato or apple on a glass plate. I tell them that this is the cell on the coverslip. Then I cut it into slices, show individual slices, and reconstruct the potato. Then we do this with cells on the confocal. And this eventually brings us to 3D glasses and rotations on th Mac. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* -------------------------------- End of nih-image-d Digest V99 Issue #26 *************************************** From nih-image-request@io.ece.drexel.edu Thu Jan 28 18:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA23826 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 18:25:10 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 18:25:10 -0500 (EST) Message-Id: <199901282247.RAA27165@codon.nih.gov> X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Date: Thu, 28 Jan 1999 17:55:28 -0500 To: nih-image@io.ece.drexel.edu From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) Subject: Re: Scion LG-3 and new Mac Resent-Message-ID: <"wYY9Q.0.v75.ZhEis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/919 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: 1468 At 1:49 PM 01/28/99, David Linker wrote: > Is this on one of the new, blue and white G3's? I was planning to get one > of the G3's with AV card, but they have been discontinued. I was then > thinking of using one of the new G3's with the Buz for video capture from > VCR for our research. I would be very interested in your experience and > thoughts. > > Have you resolved the problem? Can you use NIH Image for capture with the > Buz? > > Thanks, > > David Linker > Yes, it is blue and white G3. I asked Iomega support staff, and there are known incompatibility between new G3 and Buz (though there are no descriptions in their web page). On the PCI board of Buz, there is a Phillips chip, and a kind of serial number on it. There are two kinds of Phillips chips, 'v1' and 'v2'. If you have one with 'v1' chip, it will NOT work with new G3, but If you have one with 'v2' chip, it will work with new G3. Unfortunately I have 'v1' one. However, be sure that the information above will not ensure that Buz with 'v2' chips work with NIH Image. They will send me new one and I will check it soon. 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 Thu Jan 28 20:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA09648 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 20:50:38 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 20:50:38 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Date: Fri, 29 Jan 1999 12:32:13 +1100 Subject: Re: Averaging Video Slices - It Works! Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <40C6F46653@rna.bio.mq.edu.au> Resent-Message-ID: <"tXQWi2.0.Kf1.8xGis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/920 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2145 >From: gecko >To: >Mime-Version: 1.0 >Content-Type: text/plain; charset="US-ASCII" > >Thanks heaps to those that supplied suggestions in this regard. The >camera that I'm using is a B/W Sony Board CCD video camera (Disk Smith >Electronics L-5870 about AU$80). This camera doesn't do on-chip >integration. It's really meant for cheap security applications. > Doug, You got fairly quick and useful responses to your original post. I had intended to respond earlier with a direct answer to your question re imageMath and "real" but AverageSlices is a better way to go with an existing video stack anyway. >Should I be using 'real' to fix the problem? Yes, that would allow you to accumualte a total image. >Can I just add them without div/numslice if I'm using 'real'? When you convert the final "real" to integer (you can not save the accumulated "real" :-( eg by duplicate, the accumulated "real" would be automatically scaled anyway so no need to div/numslice. However you could do that explicity by using 1/numslice as the scale in ImageMath('op',pic1,pic2,scale,offset,result); An advantage using the ImageMath is that you could accumulate online rather than store the video for post processing. You could calibrate your system for dx,dy tracking parameters and then do the MoveROI(-dx*n,-dy*n); process on a time basis rather than sliceNumber. I had wanted to ask you re "cheap CCD board video camera" so appreciated the above specifics in your thankyou post. However I have been unable to find Sony L-5870 on either Dick Smith ElectRonics: http://www.dse.com.au/ExternalWeb/Search/SearchMain.asp or Sony Computing: http://www.ita.sel.sony.com/ I was interested to know how you interfaced the camera to the computer. Do you need a framegrabber or is that included in the AU$80? Can you give me a URL reference to Sony L-5870? (I looked at your images and appreciated your pleasure :-) 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 Jan 28 21:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA12969 for cshtest@io.ece.drexel.edu; Thu, 28 Jan 1999 21:16:43 -0500 (EST) Resent-Date: Thu, 28 Jan 1999 21:16:43 -0500 (EST) Message-ID: <36B0B657.1CB9@earthlink.net> Date: Thu, 28 Jan 1999 19:11:19 +0000 From: Penelope Spheeris Reply-To: penelopex@earthlink.net X-Mailer: Mozilla 2.0 (Macintosh; I; 68K) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: unsubscribe References: <199901251702.MAA11839@red.seas.upenn.edu> <3.0.5.32.19990128071859.00935430@s.imap.itd.umich.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"onR212.0.4X2.hKHis"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/921 X-Loop: nih-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 Fri Jan 29 08:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA01907 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 08:09:17 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 08:09:17 -0500 (EST) Message-ID: <439B2C16404ED211907500805FBEDA19B9C47D@ffxx1.nima.mil> From: "Plylar, Tracy A. [C]" To: nih-image@io.ece.drexel.edu Subject: unsubscribe Date: Fri, 29 Jan 1999 07:31:57 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Resent-Message-ID: <"nBeR3.0.IY6.9hQis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/922 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 2 From nih-image-d-request@io.ece.drexel.edu Fri Jan 29 08:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA03294; Fri, 29 Jan 1999 08:18:04 -0500 (EST) Date: Fri, 29 Jan 1999 08:18:04 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901291318.IAA03294@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #27 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/27 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: 6694 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 27 Today's Topics: Re: Macro for Red/Green Stereo [ Cengizhan Ozturk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu, nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 28 Jan 1999, Michael Cammer wrote: > At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: > >by the way, who actually uses red/GREEN stereo? I have about 10 pairs > >of red/blue glasses that came with various products in the US, but I've > >never even seen red/green glasses. Are these in wide use somewhere? > > Red/green stereo used be be in very high demand. 1991 to 1996 we made tons > of stereo images. I have no idea why, but in the past two years or so we > have used it very occassionally. However, I still give demos for high > school students, with it. I start with half a potato or apple on a glass > plate. I tell them that this is the cell on the coverslip. Then I cut it > into slices, show individual slices, and reconstruct the potato. Then we > do this with cells on the confocal. And this eventually brings us to 3D > glasses and rotations on th Mac. Hi, Where do we get cheap red/blue glasses ? Cengizhan Ozturk JHU- Medical Imaging Lab ------------------------------ Date: Thu, 28 Jan 1999 17:55:28 -0500 From: tsuyoshi@codon.nih.gov (Tsuyoshi Miyakawa) To: nih-image@io.ece.drexel.edu Subject: Re: Scion LG-3 and new Mac Message-Id: <199901282247.RAA27165@codon.nih.gov> Content-Type: text/plain; charset="ISO-2022-JP" At 1:49 PM 01/28/99, David Linker wrote: > Is this on one of the new, blue and white G3's? I was planning to get one > of the G3's with AV card, but they have been discontinued. I was then > thinking of using one of the new G3's with the Buz for video capture from > VCR for our research. I would be very interested in your experience and > thoughts. > > Have you resolved the problem? Can you use NIH Image for capture with the > Buz? > > Thanks, > > David Linker > Yes, it is blue and white G3. I asked Iomega support staff, and there are known incompatibility between new G3 and Buz (though there are no descriptions in their web page). On the PCI board of Buz, there is a Phillips chip, and a kind of serial number on it. There are two kinds of Phillips chips, 'v1' and 'v2'. If you have one with 'v1' chip, it will NOT work with new G3, but If you have one with 'v2' chip, it will work with new G3. Unfortunately I have 'v1' one. However, be sure that the information above will not ensure that Buz with 'v2' chips work with NIH Image. They will send me new one and I will check it soon. 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: Fri, 29 Jan 1999 12:32:13 +1100 From: GJOSS@rna.bio.mq.edu.au To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Subject: Re: Averaging Video Slices - It Works! Message-ID: <40C6F46653@rna.bio.mq.edu.au> >From: gecko >To: >Mime-Version: 1.0 >Content-Type: text/plain; charset="US-ASCII" > >Thanks heaps to those that supplied suggestions in this regard. The >camera that I'm using is a B/W Sony Board CCD video camera (Disk Smith >Electronics L-5870 about AU$80). This camera doesn't do on-chip >integration. It's really meant for cheap security applications. > Doug, You got fairly quick and useful responses to your original post. I had intended to respond earlier with a direct answer to your question re imageMath and "real" but AverageSlices is a better way to go with an existing video stack anyway. >Should I be using 'real' to fix the problem? Yes, that would allow you to accumualte a total image. >Can I just add them without div/numslice if I'm using 'real'? When you convert the final "real" to integer (you can not save the accumulated "real" :-( eg by duplicate, the accumulated "real" would be automatically scaled anyway so no need to div/numslice. However you could do that explicity by using 1/numslice as the scale in ImageMath('op',pic1,pic2,scale,offset,result); An advantage using the ImageMath is that you could accumulate online rather than store the video for post processing. You could calibrate your system for dx,dy tracking parameters and then do the MoveROI(-dx*n,-dy*n); process on a time basis rather than sliceNumber. I had wanted to ask you re "cheap CCD board video camera" so appreciated the above specifics in your thankyou post. However I have been unable to find Sony L-5870 on either Dick Smith ElectRonics: http://www.dse.com.au/ExternalWeb/Search/SearchMain.asp or Sony Computing: http://www.ita.sel.sony.com/ I was interested to know how you interfaced the camera to the computer. Do you need a framegrabber or is that included in the AU$80? Can you give me a URL reference to Sony L-5870? (I looked at your images and appreciated your pleasure :-) 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, 28 Jan 1999 19:11:19 +0000 From: Penelope Spheeris To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: <36B0B657.1CB9@earthlink.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Fri, 29 Jan 1999 07:31:57 -0500 From: "Plylar, Tracy A. [C]" To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-ID: <439B2C16404ED211907500805FBEDA19B9C47D@ffxx1.nima.mil> Content-Type: text/plain -------------------------------- End of nih-image-d Digest V99 Issue #27 *************************************** From nih-image-request@io.ece.drexel.edu Fri Jan 29 09:32 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA13535 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 09:32:10 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 09:32:10 -0500 (EST) Date: Fri, 29 Jan 1999 09:14:19 -0500 From: Michael Klug Subject: Dage camera and CG-7 To: nih-image@io.ece.drexel.edu Cc: jpbrion@ulb.ac.be Message-id: <05256708.004E3740.00@aammta1.d51.lilly.com> MIME-version: 1.0 Content-disposition: inline X-Lotus-FromDomain: LILLY Resent-Message-ID: <"6wPAu3.0.yi2.p9Sis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/923 X-Loop: nih-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 Jean-Pierre, I have the Dage camera and CG-7 card in a Power Mac. I use it for histology, immunohistology, and imaging of living, spontaneously contracting cardiomyocytes (by phase and fluorescence). It is reasonably sensitive, and I can image living, Calcein AM stained cells with a 1.6X objective (yes 1.6 X) without integration. Of course the signal from Calcien AM is brighter than for GFP and most immunofluorescence. Overall I am happy with the system, except for the following: 1. Vignetting--the field of view through the eyepieces is much greater than through the camera. 2. Card failure--I have sent the card back twice for the same repair (loss of one of the 3 color channels). Scion did fix it free and promptly though. 3. Speed--even slowly contracting cardiomyocytes will blur (even without integration). But the system is still faster than digital cameras. Regarding the integration speed, it would depend on what you are imaging. If your cells aren't moving, you will probably be fine. Integration is slow; however, I can integrate a field of contracting cardiomyocytes and some of them will not be blurred. Of course that depends on how many frames I integrate and how fast they are contracting. I would advise buying the card, cable and camera from Scion. The fact that I did so made it easier to get service from Scion when the card broke (Is it the card, cable or CAMERA?) Feel free to contact me for more information. -Michael G. Klug, Ph.D. Postdoctoral Fellow Eli Lilly and Company Indianapolis, IN 317-276-6951 klug_michael@lilly.com From nih-image-request@io.ece.drexel.edu Fri Jan 29 10:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA20068 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 10:18:03 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 10:18:03 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk Reply-To: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: Slowing down rotating movies on PC-Image In-Reply-To: <05256708.004E3740.00@aammta1.d51.lilly.com> Message-ID: Date: Fri, 29 Jan 1999 15:00:13 +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: <"m-ZG5.0.2I4.9qSis"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/924 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 522 I am using PC-Image to present 3D rotations and find that since I upgraded my computer they go so fast they are just a blur. Does anybody know how I can control the speed of the movies? Thanks for your help, Paul Stoodley, Exeter. ---------------------- 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-request@io.ece.drexel.edu Fri Jan 29 10:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA25107 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 10:56:51 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 10:56:51 -0500 (EST) Message-Id: <199901291532.KAA01068@red.seas.upenn.edu> Subject: Edge Finding in DIC To: nih-image@io.ece.drexel.edu (NIH Image) Date: Fri, 29 Jan 1999 10:32:55 -0500 (EST) From: "DAVID W SCHMIDTKE" X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"fi5Ei2.0.vM5.vITis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/925 X-Loop: nih-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 Does anyone have experience or a macro which will automatically find the edges of objects in images captured in differential interference contrast (DIC) ? I have captured DIC images of Neutrophils and would like to be able to outline the edge of the cells automatically. Thanks for the help. David Schmidtke dws@seas.upenn.edu From nih-image-request@io.ece.drexel.edu Fri Jan 29 12:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA09020 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 12:45:32 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 12:45:32 -0500 (EST) Date: Fri, 29 Jan 1999 18:18:17 +0100 Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Mark Wunsch Subject: IR camera for field observation Resent-Message-ID: <"Ql-dL2.0.qO1.ftUis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/926 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 633 Dear imagers! Does anyone of you have experience with an infrared red CCD camera and can recommend one? We need it for field and lab observations at night. Interchangeable lenses are a plus and good resolution would be important, small size prefered. Thanx for any hints! Mark ******************************** NEW TELEPHONE NEW TELEPHONE Mark Wunsch, Dipl.-Biologist Centre for Tropical Marine Ecology Fahrenheitstr. 1 28359 Bremen Phone ++49-421-23800-45 Phone Secretary ++49-421-23800-21 Fax ++49-421-2208330 mwunsch@uni-bremen.de http://www.zmt.uni-bremen.de/>http://www.zmt.uni-bremen.de ******************************** From nih-image-request@io.ece.drexel.edu Fri Jan 29 20:31 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA29621 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 20:31:49 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 20:31:49 -0500 (EST) Message-ID: <001901be4bed$7ae1bfe0$8e86e6d2@oemcomputer> From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" To: Subject: unsubscribe Date: Sat, 30 Jan 1999 10:11:30 +0900 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 Resent-Message-ID: <"6n_PF.0.ek6.uobis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/927 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: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Fri Jan 29 23:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA18674 for cshtest@io.ece.drexel.edu; Fri, 29 Jan 1999 23:18:02 -0500 (EST) Resent-Date: Fri, 29 Jan 1999 23:18:02 -0500 (EST) Message-Id: <199901300407.PAA25787@redback.ne.com.au> Subject: Re: Averaging video slices Sony L-5870 Date: Sat, 30 Jan 99 15:03:36 +1100 x-mailer: Claris Emailer 1.1 From: gecko To: Mime-Version: 1.0 Resent-Message-ID: <"Gr7jd1.0.K84.eIeis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/928 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 2141 Hello Greg, I've noticed some of you're postings on the list - you seem to be quite adept at this stuff. The 'L-5870' is the Disk Smith catalogue number for the Sony camera. It doesn't appear in the 98/99 retail catalogue, but is listed in the wholesale pricelist (secondary schools get great deals from Disk Smith - perhaps a Uni could too?). DSE Wholesale TEL 1300 366 644 FAX 02 9395 1155 I just plug the camera video output into the video-in on my mac. The mac came with Avid Cinema software so I use that to capture the clips. I like the idea of capturing within NIH image, but unfortunately the Avid video card is VERY unfriendly to other software. I'm thinking of a USB capture solution for the iMac that we're about to buy. The example video frame of the moon was actually from on older 'ELMO' camera and the resolution of the Sony far better. Unfortunately I have dumped my store of video clips from the sony camera to save space. I solved the averaging problem and then only had low quality ELMO clips to work with. Now I'm waiting for clear skys to really try it out. Here are some specs from the camera 'instructions' sheet. (the camera doesn't specify the model number - I can't remember what CCIR and EIA mean in the real world - If you plug it in to a normal VCR - it works, does that help? I think that it's CCIR) Model CS-350S/CS-360S Video system: CCIR/EIA Number of effective pixels: 290K/250K Number of total pixels: 320K/270K Scanning system: 2:1 Sync: Internal Resolution (TV lines): 400TV lines S/N ratio: 46dB Min illumination: 0.2 Lux Electronic shutter: 1/50 ~ 1/100000 Size: 38x38x24mm Horiz. sync. freq: 15625Hz/15750Hz Vert. sync. freq: 50Hz/60Hz Gamma correction: 0.5 Video output: 1V p-p 75ohm Built-in lens: 3.6mm Lens angle: 92 deg Storage temp: -20 ~ 80 deg C Working temp: -10 ~ 60 deg C Power source: DC 12V Supply Current: 95mA Hope that helps. Doug Rolfe Christian College, Highton. gecko@ne.com.au (PS. Radio Parts have a very good range of CCD board cameras including high image quality colour ones and also LCD vewing screens (around $250-400 and $200 respectively I think) From nih-image-d-request@io.ece.drexel.edu Sat Jan 30 06:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA03814; Sat, 30 Jan 1999 06:07:33 -0500 (EST) Date: Sat, 30 Jan 1999 06:07:33 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901301107.GAA03814@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #28 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/28 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: 7782 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 28 Today's Topics: Dage camera and CG-7 [ Michael Klug ] unsubscribe [ "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?= ] Re: Averaging video slices Sony L-58 [ gecko ] ------------------------------ Date: Fri, 29 Jan 1999 09:14:19 -0500 From: Michael Klug To: nih-image@io.ece.drexel.edu Cc: jpbrion@ulb.ac.be Subject: Dage camera and CG-7 Message-id: <05256708.004E3740.00@aammta1.d51.lilly.com> Content-type: text/plain; charset=us-ascii Content-disposition: inline Jean-Pierre, I have the Dage camera and CG-7 card in a Power Mac. I use it for histology, immunohistology, and imaging of living, spontaneously contracting cardiomyocytes (by phase and fluorescence). It is reasonably sensitive, and I can image living, Calcein AM stained cells with a 1.6X objective (yes 1.6 X) without integration. Of course the signal from Calcien AM is brighter than for GFP and most immunofluorescence. Overall I am happy with the system, except for the following: 1. Vignetting--the field of view through the eyepieces is much greater than through the camera. 2. Card failure--I have sent the card back twice for the same repair (loss of one of the 3 color channels). Scion did fix it free and promptly though. 3. Speed--even slowly contracting cardiomyocytes will blur (even without integration). But the system is still faster than digital cameras. Regarding the integration speed, it would depend on what you are imaging. If your cells aren't moving, you will probably be fine. Integration is slow; however, I can integrate a field of contracting cardiomyocytes and some of them will not be blurred. Of course that depends on how many frames I integrate and how fast they are contracting. I would advise buying the card, cable and camera from Scion. The fact that I did so made it easier to get service from Scion when the card broke (Is it the card, cable or CAMERA?) Feel free to contact me for more information. -Michael G. Klug, Ph.D. Postdoctoral Fellow Eli Lilly and Company Indianapolis, IN 317-276-6951 klug_michael@lilly.com ------------------------------ Date: Fri, 29 Jan 1999 15:00:13 +0000 (GMT Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu Subject: Re: Slowing down rotating movies on PC-Image Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I am using PC-Image to present 3D rotations and find that since I upgraded my computer they go so fast they are just a blur. Does anybody know how I can control the speed of the movies? Thanks for your help, Paul Stoodley, Exeter. ---------------------- 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. ------------------------------ Date: Fri, 29 Jan 1999 10:32:55 -0500 (EST) From: "DAVID W SCHMIDTKE" To: nih-image@io.ece.drexel.edu (NIH Image) Subject: Edge Finding in DIC Message-Id: <199901291532.KAA01068@red.seas.upenn.edu> Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Does anyone have experience or a macro which will automatically find the edges of objects in images captured in differential interference contrast (DIC) ? I have captured DIC images of Neutrophils and would like to be able to outline the edge of the cells automatically. Thanks for the help. David Schmidtke dws@seas.upenn.edu ------------------------------ Date: Fri, 29 Jan 1999 18:18:17 +0100 From: Mark Wunsch To: nih-image@io.ece.drexel.edu Subject: IR camera for field observation Message-Id: Content-Type: text/plain; charset="us-ascii" Dear imagers! Does anyone of you have experience with an infrared red CCD camera and can recommend one? We need it for field and lab observations at night. Interchangeable lenses are a plus and good resolution would be important, small size prefered. Thanx for any hints! Mark ******************************** NEW TELEPHONE NEW TELEPHONE Mark Wunsch, Dipl.-Biologist Centre for Tropical Marine Ecology Fahrenheitstr. 1 28359 Bremen Phone ++49-421-23800-45 Phone Secretary ++49-421-23800-21 Fax ++49-421-2208330 mwunsch@uni-bremen.de http://www.zmt.uni-bremen.de/>http://www.zmt.uni-bremen.de ******************************** ------------------------------ Date: Sat, 30 Jan 1999 10:11:30 +0900 From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" To: Subject: unsubscribe Message-ID: <001901be4bed$7ae1bfe0$8e86e6d2@oemcomputer> Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Sat, 30 Jan 99 15:03:36 +1100 From: gecko To: Subject: Re: Averaging video slices Sony L-5870 Message-Id: <199901300407.PAA25787@redback.ne.com.au> Content-Type: text/plain; charset="US-ASCII" Hello Greg, I've noticed some of you're postings on the list - you seem to be quite adept at this stuff. The 'L-5870' is the Disk Smith catalogue number for the Sony camera. It doesn't appear in the 98/99 retail catalogue, but is listed in the wholesale pricelist (secondary schools get great deals from Disk Smith - perhaps a Uni could too?). DSE Wholesale TEL 1300 366 644 FAX 02 9395 1155 I just plug the camera video output into the video-in on my mac. The mac came with Avid Cinema software so I use that to capture the clips. I like the idea of capturing within NIH image, but unfortunately the Avid video card is VERY unfriendly to other software. I'm thinking of a USB capture solution for the iMac that we're about to buy. The example video frame of the moon was actually from on older 'ELMO' camera and the resolution of the Sony far better. Unfortunately I have dumped my store of video clips from the sony camera to save space. I solved the averaging problem and then only had low quality ELMO clips to work with. Now I'm waiting for clear skys to really try it out. Here are some specs from the camera 'instructions' sheet. (the camera doesn't specify the model number - I can't remember what CCIR and EIA mean in the real world - If you plug it in to a normal VCR - it works, does that help? I think that it's CCIR) Model CS-350S/CS-360S Video system: CCIR/EIA Number of effective pixels: 290K/250K Number of total pixels: 320K/270K Scanning system: 2:1 Sync: Internal Resolution (TV lines): 400TV lines S/N ratio: 46dB Min illumination: 0.2 Lux Electronic shutter: 1/50 ~ 1/100000 Size: 38x38x24mm Horiz. sync. freq: 15625Hz/15750Hz Vert. sync. freq: 50Hz/60Hz Gamma correction: 0.5 Video output: 1V p-p 75ohm Built-in lens: 3.6mm Lens angle: 92 deg Storage temp: -20 ~ 80 deg C Working temp: -10 ~ 60 deg C Power source: DC 12V Supply Current: 95mA Hope that helps. Doug Rolfe Christian College, Highton. gecko@ne.com.au (PS. Radio Parts have a very good range of CCD board cameras including high image quality colour ones and also LCD vewing screens (around $250-400 and $200 respectively I think) -------------------------------- End of nih-image-d Digest V99 Issue #28 *************************************** From nih-image-request@io.ece.drexel.edu Sat Jan 30 12:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA14979 for cshtest@io.ece.drexel.edu; Sat, 30 Jan 1999 12:04:22 -0500 (EST) Resent-Date: Sat, 30 Jan 1999 12:04:22 -0500 (EST) X-Comment: UCONNVM.UConn.Edu: Mail was sent by d71h142.public.uconn.edu Message-Id: In-Reply-To: References: <3.0.5.32.19990128114231.0094f250@mailserver.aecom.yu.edu> Mime-Version: 1.0 Date: Sat, 30 Jan 1999 11:58:19 -0500 To: nih-image@io.ece.drexel.edu From: David Knecht Subject: Re: Macro for Red/Green Stereo Resent-Message-ID: <"88tZ71.0.yI3.jZpis"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/929 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1377 I get mine from: Rainbow Symphony INc. 6860 Canby Ave. #120 Reseda CA 91335 800-821-5122. These cost about $0.35 each but they are much more durable than some cheaper ones. Dave >On Thu, 28 Jan 1999, Michael Cammer wrote: > >> At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >> >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >> >of red/blue glasses that came with various products in the US, but I've >> >never even seen red/green glasses. Are these in wide use somewhere? >> >> Red/green stereo used be be in very high demand. 1991 to 1996 we made tons >> of stereo images. I have no idea why, but in the past two years or so we >> have used it very occassionally. However, I still give demos for high >> school students, with it. I start with half a potato or apple on a glass >> plate. I tell them that this is the cell on the coverslip. Then I cut it >> into slices, show individual slices, and reconstruct the potato. Then we >> do this with cells on the confocal. And this eventually brings us to 3D >> glasses and rotations on th Mac. > >Hi, > >Where do we get cheap red/blue glasses ? > >Cengizhan Ozturk >JHU- Medical Imaging Lab 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-d-request@io.ece.drexel.edu Sun Jan 31 06:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA10435; Sun, 31 Jan 1999 06:14:23 -0500 (EST) Date: Sun, 31 Jan 1999 06:14:23 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199901311114.GAA10435@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #29 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/29 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: 1974 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 29 Today's Topics: Re: Macro for Red/Green Stereo [ David Knecht To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-Id: Content-Type: text/plain; charset="us-ascii" I get mine from: Rainbow Symphony INc. 6860 Canby Ave. #120 Reseda CA 91335 800-821-5122. These cost about $0.35 each but they are much more durable than some cheaper ones. Dave >On Thu, 28 Jan 1999, Michael Cammer wrote: > >> At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: >> >by the way, who actually uses red/GREEN stereo? I have about 10 pairs >> >of red/blue glasses that came with various products in the US, but I've >> >never even seen red/green glasses. Are these in wide use somewhere? >> >> Red/green stereo used be be in very high demand. 1991 to 1996 we made tons >> of stereo images. I have no idea why, but in the past two years or so we >> have used it very occassionally. However, I still give demos for high >> school students, with it. I start with half a potato or apple on a glass >> plate. I tell them that this is the cell on the coverslip. Then I cut it >> into slices, show individual slices, and reconstruct the potato. Then we >> do this with cells on the confocal. And this eventually brings us to 3D >> glasses and rotations on th Mac. > >Hi, > >Where do we get cheap red/blue glasses ? > >Cengizhan Ozturk >JHU- Medical Imaging Lab 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) -------------------------------- End of nih-image-d Digest V99 Issue #29 *************************************** From nih-image-request@io.ece.drexel.edu Sun Jan 31 16:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA15733 for cshtest@io.ece.drexel.edu; Sun, 31 Jan 1999 16:14:36 -0500 (EST) Resent-Date: Sun, 31 Jan 1999 16:14:36 -0500 (EST) Date: Sun, 31 Jan 1999 15:58:39 -0500 X-Sender: gxt5@mail.psu.edu Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: gxt5@psu.edu (Graham Thomas) Subject: How to find center of outlines? Resent-Message-ID: <"IimO43.0.QO3.AGCjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/930 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1459 We are trying to obtain the area occupied by each cell in an epithelium from confocal images. The cells have been fixed and stained for a marker that nicely outlines each cell. I understand how to apply a threshold and use the appropriate wand to select, measure and label each cell. However, there is some variation in staining intensity across the images, which means that the threshold leads to big fat outlines in some areas of the image and consequently and underestimate of the true area occupied by those cells. What I would like to know is whether there is a macro that can take a thresholded image and find the center of all the outlines to generate an infinitely thin outline or at least one of a consistent pixel width. Any other suggestions are of course welcome. Cheers! Graham Thomas FliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFlies We have a new graduate program in Cell and Developmental Biology. Please PASS ON THIS URL to any aspiring graduate students: http://www.bmb.psu.edu/thomas/cdb/cdbhome.htm Graham Thomas, Departments of Biology and Biochemisty/Molecular Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802 Email GXT5@PSU.EDU Telephone (814)-863-0716 Fax (814)-865-9131 WWW http://www.bmb.psu.edu/thomas Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin From nih-image-request@io.ece.drexel.edu Sun Jan 31 16:42 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA19003 for cshtest@io.ece.drexel.edu; Sun, 31 Jan 1999 16:42:07 -0500 (EST) Resent-Date: Sun, 31 Jan 1999 16:42:07 -0500 (EST) Message-Id: <36B4CBC7.3CBE744C@maroon.tc.umn.edu> Date: Sun, 31 Jan 1999 15:31:52 -0600 From: "Michael J. Herron" Reply-To: Michael J Herron Organization: University of Minnesota X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: How to find center of outlines? References: Content-Transfer-Encoding: 7bit Resent-Message-ID: <"GF0zk1.0.QI4.nkCjs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/931 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1963 Graham, Threshold then Skeletonize the outlines. That should do it.......if I am understanding the question! Mike Graham Thomas wrote: > > We are trying to obtain the area occupied by each cell in an epithelium > from confocal images. The cells have been fixed and stained for a marker > that nicely outlines each cell. I understand how to apply a threshold and > use the appropriate wand to select, measure and label each cell. However, > there is some variation in staining intensity across the images, which > means that the threshold leads to big fat outlines in some areas of the > image and consequently and underestimate of the true area occupied by those > cells. What I would like to know is whether there is a macro that can take > a thresholded image and find the center of all the outlines to generate an > infinitely thin outline or at least one of a consistent pixel width. Any > other suggestions are of course welcome. > > Cheers! > Graham Thomas > > FliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFlies > > We have a new graduate program in Cell and Developmental > Biology. Please PASS ON THIS URL to any aspiring graduate students: > http://www.bmb.psu.edu/thomas/cdb/cdbhome.htm > > Graham Thomas, > Departments of Biology and Biochemisty/Molecular Biology, > The Pennsylvania State University, > 208 Mueller Laboratory, > University Park, PA, 16802 > > Email GXT5@PSU.EDU > Telephone (814)-863-0716 > Fax (814)-865-9131 > WWW http://www.bmb.psu.edu/thomas > > Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin -- _______________________________________________ / 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 Sun Jan 31 17:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA25534 for cshtest@io.ece.drexel.edu; Sun, 31 Jan 1999 17:46:07 -0500 (EST) Resent-Date: Sun, 31 Jan 1999 17:46:07 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gxt5@psu.edu, nih-image@io.ece.drexel.edu Date: Mon, 1 Feb 1999 9:37:25 +1100 Subject: Re: How to find center of outlines? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <85E24836A3@rna.bio.mq.edu.au> Resent-Message-ID: <"lkd152.0.Ju5.CfDjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/932 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2377 >Date: Sun, 31 Jan 1999 15:58:39 -0500 >To: nih-image@io.ece.drexel.edu >From: gxt5@psu.edu (Graham Thomas) >Subject: How to find center of outlines? > >We are trying to obtain the area occupied by each cell in an epithelium >from confocal images. The cells have been fixed and stained for a marker >that nicely outlines each cell. I understand how to apply a threshold and >use the appropriate wand to select, measure and label each cell. However, >there is some variation in staining intensity across the images, which >means that the threshold leads to big fat outlines in some areas of the >image and consequently and underestimate of the true area occupied by those >cells. What I would like to know is whether there is a macro that can take >a thresholded image and find the center of all the outlines to generate an >infinitely thin outline or at least one of a consistent pixel width. Any >other suggestions are of course welcome. > >Cheers! >Graham Thomas Graham, Mike herron has already given you the direct answer to your question. Skeletonise(Binary(Process will give you the geometric centre of the wide outlines obtained from thresholding. The outsides of the cell outlines will have intensities at the threshold so you will find the middle distance between two equal intensities. Possibly, a more consistant boundary can be drawn by looking for the inflexion in the intensity rather that the midpoint between two equal values. Try 'Find Edges'(Process on your image before you threshold. >From manual:" Find Edges - Performs a Sobel edge detection operation. Two convolutions are done using the kernels shown below, generating vertical and horizontal derivatives. The results are then combined by using the square root of the sum of the squares of the two derivatives. 1 2 1 1 0 -1 0 0 0 2 0 -2 -1 -2 -1 1 0 -1 " If staining level varies across field, then SubtractBackground( '2D Rolling Ball',radius); {where radius is commensurate with the scale of the largest feature you wish to retain (cell?)} can be very useful prior to thresholding. Essentially, this will convert image intensites to be relative to the local (radius) region. 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 Sun Jan 31 18:42 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA01700 for cshtest@io.ece.drexel.edu; Sun, 31 Jan 1999 18:42:31 -0500 (EST) Resent-Date: Sun, 31 Jan 1999 18:42:31 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Date: Mon, 1 Feb 1999 10:37:35 +1100 Subject: Re: Averaging video slices Sony L-5870 Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <86E2A70DE9@rna.bio.mq.edu.au> Resent-Message-ID: <"Q2M913.0.X6.iXEjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/933 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1614 >Subject: Re: Averaging video slices Sony L-5870 >Date: Sat, 30 Jan 99 15:03:36 +1100 >From: gecko >To: >............... >The 'L-5870' is the Disk Smith catalogue number for the Sony camera. >............... Doug, Thanks for the info on the camera. >The example video frame of the moon was actually from on older 'ELMO' >camera and the resolution of the Sony far better. Unfortunately I have >dumped my store of video clips from the sony camera to save space. I >solved the averaging problem and then only had low quality ELMO clips to >work with. Now I'm waiting for clear skys to really try it out. > I noted that the even/odd pairs of lines in http://www.ne.com.au/~gecko/astro/moonbefore.jpg are more or less duplicated (JPEG compression interferes with this a little) giving jagged edges. The 'ELMO' may be 1/2 resolution in the vertical direction? You didn't state the frame rate that the Avid video card captures your video sequence frames at but if it is anything like video rate 25 frames/sec, then I suspect that your averageing enhancement would also benefit from a separate 1/2 shift of alternate interlaced fields. You can generate a grid of alternate lines to be AND'ed with each frame to separate the fields and use moveRoi(x,0);setOption,doReplace; to account for horizontal movement between scans. If you would like help with this, please come back. 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 Feb 1 14:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA06614 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 14:07:43 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 14:07:43 -0500 (EST) Date: Mon, 1 Feb 1999 10:42:25 -0800 (PST) From: Lesley Weston To: Cengizhan Ozturk cc: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"_yztS2.0.hy.mMVjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/934 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1626 A few years ago, when we needed 16 pairs of red/blue glasses to send off with a grant application, I got them by buying 16 copies of a 3-D comic from the local comic-shop. The glasses that came with them worked fine, and we got the grant. By the way, for non-Canadians on the list, Red Green is the alter ego of Steve Smith. He's the ultimate handyman in his own unique way, and relies extensively on duct tape. He can be seen on Canada's CBC and some PBS stations, but I don't know if he's left North America yet. Lesley Weston. On Thu, 28 Jan 1999, Cengizhan Ozturk wrote: > > On Thu, 28 Jan 1999, Michael Cammer wrote: > > > At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: > > >by the way, who actually uses red/GREEN stereo? I have about 10 pairs > > >of red/blue glasses that came with various products in the US, but I've > > >never even seen red/green glasses. Are these in wide use somewhere? > > > > Red/green stereo used be be in very high demand. 1991 to 1996 we made tons > > of stereo images. I have no idea why, but in the past two years or so we > > have used it very occassionally. However, I still give demos for high > > school students, with it. I start with half a potato or apple on a glass > > plate. I tell them that this is the cell on the coverslip. Then I cut it > > into slices, show individual slices, and reconstruct the potato. Then we > > do this with cells on the confocal. And this eventually brings us to 3D > > glasses and rotations on th Mac. > > Hi, > > Where do we get cheap red/blue glasses ? > > Cengizhan Ozturk > JHU- Medical Imaging Lab > > > > From nih-image-d-request@io.ece.drexel.edu Mon Feb 1 14:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA07398; Mon, 1 Feb 1999 14:14:29 -0500 (EST) Date: Mon, 1 Feb 1999 14:14:29 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902011914.OAA07398@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #30 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/30 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: 11103 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 30 Today's Topics: How to find center of outlines? [ gxt5@psu.edu (Graham Thomas) ] Re: How to find center of outlines? [ "Michael J. Herron" Content-Type: text/plain; charset="us-ascii" We are trying to obtain the area occupied by each cell in an epithelium from confocal images. The cells have been fixed and stained for a marker that nicely outlines each cell. I understand how to apply a threshold and use the appropriate wand to select, measure and label each cell. However, there is some variation in staining intensity across the images, which means that the threshold leads to big fat outlines in some areas of the image and consequently and underestimate of the true area occupied by those cells. What I would like to know is whether there is a macro that can take a thresholded image and find the center of all the outlines to generate an infinitely thin outline or at least one of a consistent pixel width. Any other suggestions are of course welcome. Cheers! Graham Thomas FliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFlies We have a new graduate program in Cell and Developmental Biology. Please PASS ON THIS URL to any aspiring graduate students: http://www.bmb.psu.edu/thomas/cdb/cdbhome.htm Graham Thomas, Departments of Biology and Biochemisty/Molecular Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802 Email GXT5@PSU.EDU Telephone (814)-863-0716 Fax (814)-865-9131 WWW http://www.bmb.psu.edu/thomas Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin ------------------------------ Date: Sun, 31 Jan 1999 15:31:52 -0600 From: "Michael J. Herron" To: nih-image@io.ece.drexel.edu Subject: Re: How to find center of outlines? Message-Id: <36B4CBC7.3CBE744C@maroon.tc.umn.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Graham, Threshold then Skeletonize the outlines. That should do it.......if I am understanding the question! Mike Graham Thomas wrote: > > We are trying to obtain the area occupied by each cell in an epithelium > from confocal images. The cells have been fixed and stained for a marker > that nicely outlines each cell. I understand how to apply a threshold and > use the appropriate wand to select, measure and label each cell. However, > there is some variation in staining intensity across the images, which > means that the threshold leads to big fat outlines in some areas of the > image and consequently and underestimate of the true area occupied by those > cells. What I would like to know is whether there is a macro that can take > a thresholded image and find the center of all the outlines to generate an > infinitely thin outline or at least one of a consistent pixel width. Any > other suggestions are of course welcome. > > Cheers! > Graham Thomas > > FliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFliesFlies > > We have a new graduate program in Cell and Developmental > Biology. Please PASS ON THIS URL to any aspiring graduate students: > http://www.bmb.psu.edu/thomas/cdb/cdbhome.htm > > Graham Thomas, > Departments of Biology and Biochemisty/Molecular Biology, > The Pennsylvania State University, > 208 Mueller Laboratory, > University Park, PA, 16802 > > Email GXT5@PSU.EDU > Telephone (814)-863-0716 > Fax (814)-865-9131 > WWW http://www.bmb.psu.edu/thomas > > Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin Spectrin -- _______________________________________________ / Michael J. Herron / / U of MN,Medicine/Infectious Diseases / / herro001@maroon.tc.umn.edu / / http://128.101.243.213 / /__________________________________________/ ------------------------------ Date: Mon, 1 Feb 1999 9:37:25 +1100 From: GJOSS@rna.bio.mq.edu.au To: gxt5@psu.edu, nih-image@io.ece.drexel.edu Subject: Re: How to find center of outlines? Message-ID: <85E24836A3@rna.bio.mq.edu.au> >Date: Sun, 31 Jan 1999 15:58:39 -0500 >To: nih-image@io.ece.drexel.edu >From: gxt5@psu.edu (Graham Thomas) >Subject: How to find center of outlines? > >We are trying to obtain the area occupied by each cell in an epithelium >from confocal images. The cells have been fixed and stained for a marker >that nicely outlines each cell. I understand how to apply a threshold and >use the appropriate wand to select, measure and label each cell. However, >there is some variation in staining intensity across the images, which >means that the threshold leads to big fat outlines in some areas of the >image and consequently and underestimate of the true area occupied by those >cells. What I would like to know is whether there is a macro that can take >a thresholded image and find the center of all the outlines to generate an >infinitely thin outline or at least one of a consistent pixel width. Any >other suggestions are of course welcome. > >Cheers! >Graham Thomas Graham, Mike herron has already given you the direct answer to your question. Skeletonise(Binary(Process will give you the geometric centre of the wide outlines obtained from thresholding. The outsides of the cell outlines will have intensities at the threshold so you will find the middle distance between two equal intensities. Possibly, a more consistant boundary can be drawn by looking for the inflexion in the intensity rather that the midpoint between two equal values. Try 'Find Edges'(Process on your image before you threshold. >From manual:" Find Edges - Performs a Sobel edge detection operation. Two convolutions are done using the kernels shown below, generating vertical and horizontal derivatives. The results are then combined by using the square root of the sum of the squares of the two derivatives. 1 2 1 1 0 -1 0 0 0 2 0 -2 -1 -2 -1 1 0 -1 " If staining level varies across field, then SubtractBackground( '2D Rolling Ball',radius); {where radius is commensurate with the scale of the largest feature you wish to retain (cell?)} can be very useful prior to thresholding. Essentially, this will convert image intensites to be relative to the local (radius) region. 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, 1 Feb 1999 10:37:35 +1100 From: GJOSS@rna.bio.mq.edu.au To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Subject: Re: Averaging video slices Sony L-5870 Message-ID: <86E2A70DE9@rna.bio.mq.edu.au> >Subject: Re: Averaging video slices Sony L-5870 >Date: Sat, 30 Jan 99 15:03:36 +1100 >From: gecko >To: >............... >The 'L-5870' is the Disk Smith catalogue number for the Sony camera. >............... Doug, Thanks for the info on the camera. >The example video frame of the moon was actually from on older 'ELMO' >camera and the resolution of the Sony far better. Unfortunately I have >dumped my store of video clips from the sony camera to save space. I >solved the averaging problem and then only had low quality ELMO clips to >work with. Now I'm waiting for clear skys to really try it out. > I noted that the even/odd pairs of lines in http://www.ne.com.au/~gecko/astro/moonbefore.jpg are more or less duplicated (JPEG compression interferes with this a little) giving jagged edges. The 'ELMO' may be 1/2 resolution in the vertical direction? You didn't state the frame rate that the Avid video card captures your video sequence frames at but if it is anything like video rate 25 frames/sec, then I suspect that your averageing enhancement would also benefit from a separate 1/2 shift of alternate interlaced fields. You can generate a grid of alternate lines to be AND'ed with each frame to separate the fields and use moveRoi(x,0);setOption,doReplace; to account for horizontal movement between scans. If you would like help with this, please come back. 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, 1 Feb 1999 10:42:25 -0800 (PST) From: Lesley Weston To: Cengizhan Ozturk cc: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII A few years ago, when we needed 16 pairs of red/blue glasses to send off with a grant application, I got them by buying 16 copies of a 3-D comic from the local comic-shop. The glasses that came with them worked fine, and we got the grant. By the way, for non-Canadians on the list, Red Green is the alter ego of Steve Smith. He's the ultimate handyman in his own unique way, and relies extensively on duct tape. He can be seen on Canada's CBC and some PBS stations, but I don't know if he's left North America yet. Lesley Weston. On Thu, 28 Jan 1999, Cengizhan Ozturk wrote: > > On Thu, 28 Jan 1999, Michael Cammer wrote: > > > At 07:20 AM 1/28/99 -0500, Wade & Cheryll Schuette wrote: > > >by the way, who actually uses red/GREEN stereo? I have about 10 pairs > > >of red/blue glasses that came with various products in the US, but I've > > >never even seen red/green glasses. Are these in wide use somewhere? > > > > Red/green stereo used be be in very high demand. 1991 to 1996 we made tons > > of stereo images. I have no idea why, but in the past two years or so we > > have used it very occassionally. However, I still give demos for high > > school students, with it. I start with half a potato or apple on a glass > > plate. I tell them that this is the cell on the coverslip. Then I cut it > > into slices, show individual slices, and reconstruct the potato. Then we > > do this with cells on the confocal. And this eventually brings us to 3D > > glasses and rotations on th Mac. > > Hi, > > Where do we get cheap red/blue glasses ? > > Cengizhan Ozturk > JHU- Medical Imaging Lab > > > > -------------------------------- End of nih-image-d Digest V99 Issue #30 *************************************** From nih-image-request@io.ece.drexel.edu Mon Feb 1 14:42 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA10928 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 14:42:36 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 14:42:36 -0500 (EST) Mime-Version: 1.0 Message-Id: In-Reply-To: <36AEDF10.53A5@wxs.nl> Date: Mon, 1 Feb 1999 14:24:23 -0500 To: nih-image@io.ece.drexel.edu From: Gloria Hoffman Subject: Re: upgraded 7100/AV Resent-Message-ID: <"w3Rsf.0.442.O-Vjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/935 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 851 System 8.5 is definitely worth getting... 8.1 is also quite stable. >Dear all, > >About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 >card . I am very happy with it because it works very fast now , a change >from 66 MHz to 214 Mhz . >Now only one problem left , it was told that the most stable OS for the >7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. >Now I upgraded to G3 it made me wonder whether it has an advantage to >change to OS 8 >I asked Sonnet , the maker of the upgrade card , but they did not know >the answer. >Can anybody help me with the correct advice? > >Pieter Houpt > > > >BIOMET > >The Hague , The Netherlands. 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 Mon Feb 1 15:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA16839 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 15:39:59 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 15:39:59 -0500 (EST) X-Sender: sjm8@pop.cwru.edu Message-Id: Mime-Version: 1.0 Date: Mon, 1 Feb 1999 15:22:01 -0500 To: nih-image@io.ece.drexel.edu From: "Stephen J. Moorman" Resent-Message-ID: <"EQPGC1.0.Fb3.upWjs"@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/936 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 303 I have had consistent problems with OS 8.5 printing to any laser printer connected to a network. I am running OS 8.1 until this problem is resolved. Our local computer people clued me in to this problem before I upgraded to 8.5. I downgraded to 8.1 and have had no problem since. Regards, Stephen From nih-image-request@io.ece.drexel.edu Mon Feb 1 15:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA16866 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 15:40:08 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 15:40:08 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Mon, 1 Feb 1999 15:17:50 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Macro for Red/Green Stereo Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"PRoQa2.0.Pc3.8qWjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/937 X-Loop: nih-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 In a message dated 2/1/99 6:55:19 PM, lesley@interchange.ubc.ca writes: >By the way, for non-Canadians on the list, Red Green is the alter ego of >Steve >Smith. He's the ultimate handyman in his own unique way, and relies extensively >on duct tape. He can be seen on Canada's CBC and some PBS stations, but >I don't >know if he's left North America yet. Yes. I found Red on Channel 4 in the UK when I was living there. But unfortunately he doesn't seem to be on our local cable provider here in North Carolina. From nih-image-request@io.ece.drexel.edu Mon Feb 1 16:06 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA20013 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 16:06:19 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 16:06:19 -0500 (EST) Message-Id: <199902012049.HAA19938@redback.ne.com.au> Subject: Re: Averaging video slices Sony L-5870 Date: Tue, 2 Feb 99 07:44:55 +1100 x-mailer: Claris Emailer 1.1 From: gecko To: Mime-Version: 1.0 Resent-Message-ID: <"dEB973.0._G4.P9Xjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/938 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 776 Greg, >The 'ELMO' may be 1/2 resolution in the vertical direction? Thanks for the ideas. I think that the Sony camera doesn't have the 1/2 vertical resolution of the old ELMO camera. I'll have to wait until I capture some more video - which depends upon the weather. I'll leave the problem until then. >your averageing enhancement would also benefit from a separate 1/2 >shift of alternate interlaced fields You lost me there! After I have some more clips and have trialed them I'll follow this up. Does anyone have a quick opinion of the 'unsharp mask' filter in Adobe PhotoShop? It worked visual wonders for me on a trial and error approach. I was hoping for a more technical approach. Thanks Doug Rolfe Christian College, Highton, Australia gecko@ne.com.au From nih-image-request@io.ece.drexel.edu Mon Feb 1 17:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA00554 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 17:50:14 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 17:50:14 -0500 (EST) Mime-Version: 1.0 X-Sender: scm@128.250.6.196 Message-Id: In-Reply-To: Date: Tue, 2 Feb 1999 09:28:17 +1100 To: nih-image@io.ece.drexel.edu From: Steve Martin Subject: Re: Unidentified subject! Resent-Message-ID: <"LooVd1.0.Yu6.HgYjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/939 X-Loop: nih-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 I believe there is a problem with printing in OS 8.5 if Adobe Acrobat reader is installed in the default way - something to do with the location of the ATM control panel. Make sure it is in the Control Panels folder (?) good luck, Steve At 7:22 AM +1100 on 2/2/99, Stephen J. Moorman wrote: > I have had consistent problems with OS 8.5 printing to any laser printer > connected to a network. I am running OS 8.1 until this problem is > resolved. Our local computer people clued me in to this problem before I > upgraded to 8.5. I downgraded to 8.1 and have had no problem since. > > Regards, > Stephen From nih-image-request@io.ece.drexel.edu Mon Feb 1 21:06 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA22057 for cshtest@io.ece.drexel.edu; Mon, 1 Feb 1999 21:06:51 -0500 (EST) Resent-Date: Mon, 1 Feb 1999 21:06:51 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Date: Tue, 2 Feb 1999 12:54:23 +1100 Subject: Re: Averaging video slices (vs integration) Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"NQ2cq3.0.Wt4.Kebjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/940 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 5725 >Subject: Re: Averaging video slices Sony L-5870 >Date: Tue, 2 Feb 99 07:44:55 +1100 >From: gecko >To: >............. >I'll leave the problem until then. > >>your averageing enhancement would also benefit from a separate 1/2 >>shift of alternate interlaced fields > >You lost me there! After I have some more clips and have trialed them >I'll follow this up. > >.......... standard video uses 'interlaced' fields. ie a frame image is made in two scans of the field 2 lines apart ie a pass of odd lines followed by a pass of even lines which are presented as a frame. CCIR video (PAL) European standard which we (Aus) use is 25 frames/sec but fields are captured 50/sec. If you deinterlace frames you can double the time resolution. In your case where the image is constant but translating across the field of view, then (provided you are capturing at the video rate of 25 frames/sec) the fields are offset by 1/2 your calculated dx,dy. You could correct for this if you arrange for translation across field to be horizontal lines (by rotating camera?). Email me another URL ref to a sample stack when you and the weather are in conjunction. >Does anyone have a quick opinion of the 'unsharp mask' filter in Adobe >PhotoShop? It worked visual wonders for me on a trial and error approach. >I was hoping for a more technical approach. >From Photoshop Help: " Unsharp masking, or USM, is a traditional film compositing technique used to sharpen edges in an image. The Unsharp Mask filter corrects blurring introduced during photographing, scanning, resampling, or printing..... Numbers represent Unsharp Mask amount, Radius, and Threshold. The Unsharp Mask filter locates pixels that differ from surrounding pixels by the threshold you specify and increases the pixels' contrast by the amount you specify. In addition, you specify the radius of the region to which each pixel is compared. ......The default Threshold value(0) sharpens all pixels in the image. If applying the Unsharp Mask filter makes already bright colors appear overly saturated, convert the image to Lab mode and apply the filter to the L channel only. This technique sharpens the image without affecting the color components. " As I only have the JPEG versions from the URL you posted, it is difficult to be confident about original images but, as I retrieve them, they are 368 pixels wide not 366 as caption states. There is a 2 pixel wide white strip down the RHS. This could be a result of your capture or postprocessing. I suspect the major advantage you get from Photoshop's Unsharp filter is contrast enhancement on a localised basis. The contrast range in your 'moonbefore' image is 9<>252 which is pretty reasonable. With the Scion framegrabber, I would up the gain and offset to push the histogram towards the black 255 end until the peak of the bell distribution of the moon shadow was near 255. There seems little point in getting shades of black when presumablely the info is in the grays. I dont know if you can do this with your Avid video card? The averageSlices technique will force the contrast range of the resultant image to shrink (moonafter 15<>243) simply as a result of averaging. If you used imagemath('add real') to accumulate the aggregate and then convert to integer (by duplicate) (you cant save the real's) then the real's would be scaled to fill the range 0<>255 before integerisation; leaving you with more info (better contrast). As NIH-Image does enhanceContrast on a ROI basis, then the white stripe down the RHS of your image will prevent the white end from shifting and the few outliers also have a limiting effect. Until you correct the source of the white stripe, You can bypass it by makeing a selection. You can also examine the histogram; set contrast range in the Map window (only to the nearest 4) manually and then applyLut(Process. It would be better to do: imagemath('add real') to accumulate the aggregate convert to integer (by duplicate) scan the histogram from left and right to find outlier values convert this first pass integer image into masks of high end and low end outliers. use the masks to fold the outliers on the real image into new min/max values convert the limited real image to integer. The histogram of the result would now be full 0<>255 (of REAL information) without the gaps which would be introduced by a post enhanceContrast;applyLut; It is amazing the real contrast range you can get from a CCD when you use integration (note the distinction from averageing) to reduce/remove noise. The same technique will allow the contrast range to be expanded. ie even where the camera/framegrabber are at the maximum contrast range where further amplification would be unstable; real integration can be used to expand that part of the 0<>255 range which is of interest. Results can be reliable well beyond the intensity resolution of the integerised electronics as the statistical variation will result in 'fractional' results being accumulated. This is analogous to the determination of the bias on a loaded dice. The bias can be measured with the average of a large number of trials. The quality should improve in proportion to the square root of the number of frames integrated. For Scion/NIH-Image users who have read this far: checking Integrate(average frames..(Special menu will give much better results than just average frames... You dont need on-frameGrabber-board memory for this option. 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 Feb 2 06:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA22986; Tue, 2 Feb 1999 06:16:16 -0500 (EST) Date: Tue, 2 Feb 1999 06:16:16 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902021116.GAA22986@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #31 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/31 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: 11107 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 31 Today's Topics: Re: upgraded 7100/AV [ Gloria Hoffman ] Re: Unidentified subject! [ Steve Martin To: nih-image@io.ece.drexel.edu Subject: Re: upgraded 7100/AV Message-Id: Content-Type: text/plain; charset="us-ascii" System 8.5 is definitely worth getting... 8.1 is also quite stable. >Dear all, > >About 6 months ago I upgraded my Mac. 7100/66-AV with a crescendo G3 >card . I am very happy with it because it works very fast now , a change >from 66 MHz to 214 Mhz . >Now only one problem left , it was told that the most stable OS for the >7100 PPC is 7.5.5 , so I use tat OS for the last 2 years. >Now I upgraded to G3 it made me wonder whether it has an advantage to >change to OS 8 >I asked Sonnet , the maker of the upgrade card , but they did not know >the answer. >Can anybody help me with the correct advice? > >Pieter Houpt > > > >BIOMET > >The Hague , The Netherlands. 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: Mon, 1 Feb 1999 15:22:01 -0500 From: "Stephen J. Moorman" To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" I have had consistent problems with OS 8.5 printing to any laser printer connected to a network. I am running OS 8.1 until this problem is resolved. Our local computer people clued me in to this problem before I upgraded to 8.5. I downgraded to 8.1 and have had no problem since. Regards, Stephen ------------------------------ Date: Mon, 1 Feb 1999 15:17:50 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Macro for Red/Green Stereo Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 2/1/99 6:55:19 PM, lesley@interchange.ubc.ca writes: >By the way, for non-Canadians on the list, Red Green is the alter ego of >Steve >Smith. He's the ultimate handyman in his own unique way, and relies extensively >on duct tape. He can be seen on Canada's CBC and some PBS stations, but >I don't >know if he's left North America yet. Yes. I found Red on Channel 4 in the UK when I was living there. But unfortunately he doesn't seem to be on our local cable provider here in North Carolina. ------------------------------ Date: Tue, 2 Feb 99 07:44:55 +1100 From: gecko To: Subject: Re: Averaging video slices Sony L-5870 Message-Id: <199902012049.HAA19938@redback.ne.com.au> Content-Type: text/plain; charset="US-ASCII" Greg, >The 'ELMO' may be 1/2 resolution in the vertical direction? Thanks for the ideas. I think that the Sony camera doesn't have the 1/2 vertical resolution of the old ELMO camera. I'll have to wait until I capture some more video - which depends upon the weather. I'll leave the problem until then. >your averageing enhancement would also benefit from a separate 1/2 >shift of alternate interlaced fields You lost me there! After I have some more clips and have trialed them I'll follow this up. Does anyone have a quick opinion of the 'unsharp mask' filter in Adobe PhotoShop? It worked visual wonders for me on a trial and error approach. I was hoping for a more technical approach. Thanks Doug Rolfe Christian College, Highton, Australia gecko@ne.com.au ------------------------------ Date: Tue, 2 Feb 1999 09:28:17 +1100 From: Steve Martin To: nih-image@io.ece.drexel.edu Subject: Re: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" I believe there is a problem with printing in OS 8.5 if Adobe Acrobat reader is installed in the default way - something to do with the location of the ATM control panel. Make sure it is in the Control Panels folder (?) good luck, Steve At 7:22 AM +1100 on 2/2/99, Stephen J. Moorman wrote: > I have had consistent problems with OS 8.5 printing to any laser printer > connected to a network. I am running OS 8.1 until this problem is > resolved. Our local computer people clued me in to this problem before I > upgraded to 8.5. I downgraded to 8.1 and have had no problem since. > > Regards, > Stephen ------------------------------ Date: Tue, 2 Feb 1999 12:54:23 +1100 From: GJOSS@rna.bio.mq.edu.au To: gecko@ne.com.au, nih-image@io.ece.drexel.edu Subject: Re: Averaging video slices (vs integration) Message-ID: >Subject: Re: Averaging video slices Sony L-5870 >Date: Tue, 2 Feb 99 07:44:55 +1100 >From: gecko >To: >............. >I'll leave the problem until then. > >>your averageing enhancement would also benefit from a separate 1/2 >>shift of alternate interlaced fields > >You lost me there! After I have some more clips and have trialed them >I'll follow this up. > >.......... standard video uses 'interlaced' fields. ie a frame image is made in two scans of the field 2 lines apart ie a pass of odd lines followed by a pass of even lines which are presented as a frame. CCIR video (PAL) European standard which we (Aus) use is 25 frames/sec but fields are captured 50/sec. If you deinterlace frames you can double the time resolution. In your case where the image is constant but translating across the field of view, then (provided you are capturing at the video rate of 25 frames/sec) the fields are offset by 1/2 your calculated dx,dy. You could correct for this if you arrange for translation across field to be horizontal lines (by rotating camera?). Email me another URL ref to a sample stack when you and the weather are in conjunction. >Does anyone have a quick opinion of the 'unsharp mask' filter in Adobe >PhotoShop? It worked visual wonders for me on a trial and error approach. >I was hoping for a more technical approach. >From Photoshop Help: " Unsharp masking, or USM, is a traditional film compositing technique used to sharpen edges in an image. The Unsharp Mask filter corrects blurring introduced during photographing, scanning, resampling, or printing..... Numbers represent Unsharp Mask amount, Radius, and Threshold. The Unsharp Mask filter locates pixels that differ from surrounding pixels by the threshold you specify and increases the pixels' contrast by the amount you specify. In addition, you specify the radius of the region to which each pixel is compared. ......The default Threshold value(0) sharpens all pixels in the image. If applying the Unsharp Mask filter makes already bright colors appear overly saturated, convert the image to Lab mode and apply the filter to the L channel only. This technique sharpens the image without affecting the color components. " As I only have the JPEG versions from the URL you posted, it is difficult to be confident about original images but, as I retrieve them, they are 368 pixels wide not 366 as caption states. There is a 2 pixel wide white strip down the RHS. This could be a result of your capture or postprocessing. I suspect the major advantage you get from Photoshop's Unsharp filter is contrast enhancement on a localised basis. The contrast range in your 'moonbefore' image is 9<>252 which is pretty reasonable. With the Scion framegrabber, I would up the gain and offset to push the histogram towards the black 255 end until the peak of the bell distribution of the moon shadow was near 255. There seems little point in getting shades of black when presumablely the info is in the grays. I dont know if you can do this with your Avid video card? The averageSlices technique will force the contrast range of the resultant image to shrink (moonafter 15<>243) simply as a result of averaging. If you used imagemath('add real') to accumulate the aggregate and then convert to integer (by duplicate) (you cant save the real's) then the real's would be scaled to fill the range 0<>255 before integerisation; leaving you with more info (better contrast). As NIH-Image does enhanceContrast on a ROI basis, then the white stripe down the RHS of your image will prevent the white end from shifting and the few outliers also have a limiting effect. Until you correct the source of the white stripe, You can bypass it by makeing a selection. You can also examine the histogram; set contrast range in the Map window (only to the nearest 4) manually and then applyLut(Process. It would be better to do: imagemath('add real') to accumulate the aggregate convert to integer (by duplicate) scan the histogram from left and right to find outlier values convert this first pass integer image into masks of high end and low end outliers. use the masks to fold the outliers on the real image into new min/max values convert the limited real image to integer. The histogram of the result would now be full 0<>255 (of REAL information) without the gaps which would be introduced by a post enhanceContrast;applyLut; It is amazing the real contrast range you can get from a CCD when you use integration (note the distinction from averageing) to reduce/remove noise. The same technique will allow the contrast range to be expanded. ie even where the camera/framegrabber are at the maximum contrast range where further amplification would be unstable; real integration can be used to expand that part of the 0<>255 range which is of interest. Results can be reliable well beyond the intensity resolution of the integerised electronics as the statistical variation will result in 'fractional' results being accumulated. This is analogous to the determination of the bias on a loaded dice. The bias can be measured with the average of a large number of trials. The quality should improve in proportion to the square root of the number of frames integrated. For Scion/NIH-Image users who have read this far: checking Integrate(average frames..(Special menu will give much better results than just average frames... You dont need on-frameGrabber-board memory for this option. 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 V99 Issue #31 *************************************** From nih-image-request@io.ece.drexel.edu Tue Feb 2 09:57 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA17219 for cshtest@io.ece.drexel.edu; Tue, 2 Feb 1999 09:57:25 -0500 (EST) Resent-Date: Tue, 2 Feb 1999 09:57:25 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Tue, 2 Feb 1999 16:34:28 +0200 To: nih-image From: Matti Haveri Subject: Re: Importing DICOM with fixed windows Resent-Message-ID: <"9jc0u1.0.Aa3.Cqmjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/941 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2194 Recently I asked: > Let's say I want to open multiple DICOM CT-slices to 1029-1099 > densities (i.e. Hounsfield units W/L 70/40) to get a standard viewing > window and finer plots for a given density range in a 12-bit image > data. > > I can, with much work, DICOM import all the slices with Shift down > (fixed 16-bit to 8-bit scaling for all images), then > brightness/contrast one image with the mouse, choose > Options/Propagate/LUT and Rescale each image separately. > > However, the problem with NIH Image is that it is impossible to adjust > an image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via > the mouse. Furthermore, after Rescaling the HU-correction is lost and > the scale begings from 0 instead of -1024. The ability to adjust > brightness/contrast numerically would be nice but also this approach > would be clumsy. > > I guess the best solution would be to add the possibility to > DICOM-import a selected density range just like it is possible via > Custom import/Fixed Scale. > > Why don't I then just use the existing Custom import? Well, the > problem with DICOM files is that the Offset may be different for each > CT slice. I can calculate the Offset provided I know the matrix > (Offset = file size - (x * y * 2)) but this isn't practical if there > are many images. Custom import also doesn't automatically calibrate > densities to Hounfield units like DICOM import does (although now this > HU-info gets lost when Rescaling). I got an answer how to try it with image macros (thanks, Greg) but I guess an easier work-around is to first strip the headers off with Dr Razz: 1. Open the images as series with Dr Razz and then Save all as 16-bit raster files which saves only the pixel data and strips the headers off. 2. Import the raster files into NIH Image via 16-bit Custom import with zero Offset and 1029-1099 densities Fixed Scale (W/L 70/40). BTW, is there a simpler Mac utility which strips off headers like this, i.e. leaving a given amount of bytes to the _end_ of the file (524288 bytes for a 512 matrix CT-image, for example)? -- Matti Haveri From nih-image-request@io.ece.drexel.edu Tue Feb 2 12:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA29925 for cshtest@io.ece.drexel.edu; Tue, 2 Feb 1999 12:13:05 -0500 (EST) Resent-Date: Tue, 2 Feb 1999 12:13:05 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 2 Feb 1999 12:56:10 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Importing DICOM with fixed windows Resent-Message-ID: <"_CSyD3.0.2l6.Joojs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/942 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 486 >BTW, is there a simpler Mac utility which strips off headers like this, >i.e. leaving a given amount of bytes to the _end_ of the file (524288 bytes >for a 512 matrix CT-image, for example)? ImageJ (V0.98t or later) can open a folder of DICOM files as a 16-bit stack and save the stack as a raw data file that can easily be imported into NIH Image. For this to work, the DICOM files must have a ".dcm" extension. The ImageJ web page is at http://rsb.info.nih.gov/ij/ -wayne From nih-image-request@io.ece.drexel.edu Tue Feb 2 15:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15550 for cshtest@io.ece.drexel.edu; Tue, 2 Feb 1999 15:16:35 -0500 (EST) Resent-Date: Tue, 2 Feb 1999 15:16:35 -0500 (EST) X-Sender: bhopkins@mail-bh.acpub.duke.edu (Unverified) Message-Id: Mime-Version: 1.0 Date: Tue, 2 Feb 1999 14:54:21 -0400 To: nih-image@io.ece.drexel.edu From: Michael Benjamin Hopkins Subject: Opening Adobe Premiere docs Resent-Message-ID: <"7fEdI.0.Z73.UWrjs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/943 X-Loop: nih-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 Hello, I am trying to use Image 1.61 to open image stacks taken with Adobe Premiere 4.0. The computer we capture the images on is a PowerMac running system 7.5.3. Image 1.61 on this machine pulls up the picture without a problem. However, when I bring the file to other computers I cannot see an image for the file I just opened; all I get is a title bar and a blank field. The machines I have problems with are running system 8.1; one is a G3 and the other is a 7200. I tried copying the preferences from the Mac that works to those that don't, but this did not change anything. Any suggestions? Thanks a lot for your help. Ben Hopkins From nih-image-request@io.ece.drexel.edu Wed Feb 3 05:19 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA11060 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 05:19:52 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 05:19:52 -0500 (EST) Date: Wed, 3 Feb 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199902031005.FAA08888@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"0Xn2j.0.AB2.Fz1ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/944 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2239 NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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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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-d-request@io.ece.drexel.edu Wed Feb 3 05:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA11373; Wed, 3 Feb 1999 05:21:40 -0500 (EST) Date: Wed, 3 Feb 1999 05:21:40 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902031021.FAA11373@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #32 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/32 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: 7230 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 32 Today's Topics: Re: Importing DICOM with fixed windo [ Matti Haveri ] Opening Adobe Premiere docs [ Michael Benjamin Hopkins To: nih-image Subject: Re: Importing DICOM with fixed windows Message-Id: Content-Type: text/plain; charset="us-ascii" Recently I asked: > Let's say I want to open multiple DICOM CT-slices to 1029-1099 > densities (i.e. Hounsfield units W/L 70/40) to get a standard viewing > window and finer plots for a given density range in a 12-bit image > data. > > I can, with much work, DICOM import all the slices with Shift down > (fixed 16-bit to 8-bit scaling for all images), then > brightness/contrast one image with the mouse, choose > Options/Propagate/LUT and Rescale each image separately. > > However, the problem with NIH Image is that it is impossible to adjust > an image to exactly 1029-1099 (or in HU-scale W/L 70/40) densities via > the mouse. Furthermore, after Rescaling the HU-correction is lost and > the scale begings from 0 instead of -1024. The ability to adjust > brightness/contrast numerically would be nice but also this approach > would be clumsy. > > I guess the best solution would be to add the possibility to > DICOM-import a selected density range just like it is possible via > Custom import/Fixed Scale. > > Why don't I then just use the existing Custom import? Well, the > problem with DICOM files is that the Offset may be different for each > CT slice. I can calculate the Offset provided I know the matrix > (Offset = file size - (x * y * 2)) but this isn't practical if there > are many images. Custom import also doesn't automatically calibrate > densities to Hounfield units like DICOM import does (although now this > HU-info gets lost when Rescaling). I got an answer how to try it with image macros (thanks, Greg) but I guess an easier work-around is to first strip the headers off with Dr Razz: 1. Open the images as series with Dr Razz and then Save all as 16-bit raster files which saves only the pixel data and strips the headers off. 2. Import the raster files into NIH Image via 16-bit Custom import with zero Offset and 1029-1099 densities Fixed Scale (W/L 70/40). BTW, is there a simpler Mac utility which strips off headers like this, i.e. leaving a given amount of bytes to the _end_ of the file (524288 bytes for a 512 matrix CT-image, for example)? -- Matti Haveri ------------------------------ Date: Tue, 2 Feb 1999 12:56:10 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Importing DICOM with fixed windows Message-Id: Content-Type: text/plain; charset="us-ascii" >BTW, is there a simpler Mac utility which strips off headers like this, >i.e. leaving a given amount of bytes to the _end_ of the file (524288 bytes >for a 512 matrix CT-image, for example)? ImageJ (V0.98t or later) can open a folder of DICOM files as a 16-bit stack and save the stack as a raw data file that can easily be imported into NIH Image. For this to work, the DICOM files must have a ".dcm" extension. The ImageJ web page is at http://rsb.info.nih.gov/ij/ -wayne ------------------------------ Date: Tue, 2 Feb 1999 14:54:21 -0400 From: Michael Benjamin Hopkins To: nih-image@io.ece.drexel.edu Subject: Opening Adobe Premiere docs Message-Id: Content-Type: text/plain; charset="us-ascii" Hello, I am trying to use Image 1.61 to open image stacks taken with Adobe Premiere 4.0. The computer we capture the images on is a PowerMac running system 7.5.3. Image 1.61 on this machine pulls up the picture without a problem. However, when I bring the file to other computers I cannot see an image for the file I just opened; all I get is a title bar and a blank field. The machines I have problems with are running system 8.1; one is a G3 and the other is a 7200. I tried copying the preferences from the Mac that works to those that don't, but this did not change anything. Any suggestions? Thanks a lot for your help. Ben Hopkins ------------------------------ Date: Wed, 3 Feb 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: <199902031005.FAA08888@io.ece.drexel.edu> NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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 V99 Issue #32 *************************************** From nih-image-request@io.ece.drexel.edu Wed Feb 3 10:19 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15305 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 10:19:41 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 10:19:41 -0500 (EST) Date: Wed, 03 Feb 1999 14:59:21 +0000 (GMT) From: Stamatis Pagakis Subject: Job opening in Digital Microscopy In-reply-to: X-Sender: spagaki@membo2.nimr.mrc.ac.uk 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 JAA12907 Resent-Message-ID: <"HG-kf2.0.BA3.dH6ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/945 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 2184 NATIONAL INSTITUTE FOR MEDICAL RESEARCH PERMANENT RESEARCH MICROSCOPIST POSITION (Ref: GMB/SP/RT) Available immediately at the Confocal Microscopy and Image Analysis Laboratory (CIAL) which specialises in digital imaging in microscopy and provides a focus for interaction with many laboratories at NIMR. (http//www.nimr.mrc.ac.uk/~cial.) The successful candidate will assist in the day-to-day running of the lab. Main duties are maintenance and operation of confocal and deconvolution microscopes and associated computers, teaching and technical support of users and analysis of image data. Applicants should possess a Degree in an appropriate scientific discipline and significant experience in digital microscopy. The post requires excellent problem solving and interpersonal skills. Must be able to work with minimal supervision and have some experience with the use of networked computers (Unix, MacOS and Windows NT) for digital image processing and analysis. Hands-on experience with 3D imaging is highly desirable. Administration of Unix computers would be an advantage. Starting salary is up to £18,000 per annum (including Location allowance) depending on experience and, rising to £25,800 per annum (MRC band 5 post). MRC Pension Scheme option. Please telephone for an application form and job description, quoting the appropriate reference number on 0181-913 8544, or write to Personnel Manager, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA. The closing date for completed applications is 5th February 1999. The MRC is an Equal Opportunities employer - smoking is actively discouraged *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Membrane Biology Mobile: 0370 654288 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < From nih-image-request@io.ece.drexel.edu Wed Feb 3 11:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26092 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 11:50:43 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 11:50:43 -0500 (EST) X-Sender: bruckner@bruckner.deskmail.washington.edu Message-Id: In-Reply-To: <199902011916.OAA07579@io.ece.drexel.edu> Mime-Version: 1.0 X-Face: ,5-1`[.GWu}Gki.@O4TcoJhGF6#|nery_y7r1rD2hcNr&wc=q(lM_x Y$66Oe)MYC*)Mar76RpUIgnbJn!<[ Subject: Skeletonizing images Resent-Message-ID: <"Pd7dT3.0.mm5.tZ7ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/946 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 345 I want to reduce fibrous objects to simple lines. However, Skeleton creates small side dendrites whose length varies with the width of the fibers. What alternate techniques could I use? ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- From nih-image-request@io.ece.drexel.edu Wed Feb 3 12:36 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00961 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 12:36:49 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 12:36:49 -0500 (EST) Date: Wed, 3 Feb 1999 11:10:37 -0600 (CST) Message-Id: Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: "Malinda E.C. Fitzgerald" Subject: recovery of data Resent-Message-ID: <"mNYZt1.0.Ev6.kD8ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/947 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 730 HI I thought I would send out a general plea for help. We use a syquest drive to store our images. We have a disc that has a lot of data on it and we can't get the drive to mount with this disc. It doesn't appear to be a drive problem because other discs work. Has anyone had any experience recovering files from damaged discs? Does anyone know of a company that does this at a resonable cost? The only quote I have gotten is $1,000 for recovery of any data. That could be one file or 20. Any suggestions would be welcome. Thanks. Malinda Malinda E.C. Fitzgerald, Ph.D. Associate Professor Department of Biology 650 E Parkway So. Christian Brothers University Memphis, TN 38104 901-321-3262 office 901-321-4433 fax From nih-image-request@io.ece.drexel.edu Wed Feb 3 13:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA06341 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 13:25:24 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 13:25:24 -0500 (EST) Message-Id: <3.0.5.32.19990203130628.0093fe30@mailserver.aecom.yu.edu> X-Sender: cammer@mailserver.aecom.yu.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 03 Feb 1999 13:06:28 -0800 To: nih-image@io.ece.drexel.edu From: Michael Cammer Subject: Re: recovery of data In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"1k-QD2.0.ut.mz8ks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/948 X-Loop: nih-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 At the risk of causing a technology stock market crash, I will say the following regarding Syquest disks: they crash. They do so frequently. And the drives break too. But to make the market recover, I will say that their convenience is such that by popular demand we continue to make Syquest available. As for recovery, Drivesavers at www.drivesavers.com and Advanced Data Solutions at www.adv-data.com both recovered disks for us. Yes, the going rate is more than $1,000. But one of the disks had data from one full day of imaging. We knew that the experiment worked. And it cost one day of preparation, more than $500 in reagents, one full day of imaging on a machine that cost $20/hr. Based on the Postdoc's time and the money involved, recovery was well worth it. At 11:10 AM 2/3/99 -0600, you wrote: >HI I thought I would send out a general plea for help. We use a syquest >drive to store our images. We have a disc that has a lot of data on it and >we can't get the drive to mount with this disc. It doesn't appear to be a ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* From nih-image-request@io.ece.drexel.edu Wed Feb 3 14:47 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA15710 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 14:47:11 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 14:47:11 -0500 (EST) Subject: Re: recovery of data & syquest Date: Wed, 3 Feb 99 14:22:56 -0500 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: Mime-Version: 1.0 Message-ID: <1E3C5B85F34@qc1.qc.edu> Resent-Message-ID: <"bqZT_3.0.m03.t8Aks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/949 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 274 have you tried putting the 'disk' into another drive that is known to work? have you tried using "canopener" or the pc-equivalent? i've used canopener on a variety of media and drives- it is fantastic and will recover files of all kinds [however, it is a mac utility]. From nih-image-request@io.ece.drexel.edu Wed Feb 3 14:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA16419 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 14:52:38 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 14:52:38 -0500 (EST) X-Sender: d306604@nobel.si.uqam.ca Message-Id: In-Reply-To: <3.0.5.32.19990203130628.0093fe30@mailserver.aecom.yu.edu> References: Mime-Version: 1.0 Date: Wed, 3 Feb 1999 14:29:54 -0500 To: nih-image@io.ece.drexel.edu From: Dominique Berube Subject: Re: recovery of data Resent-Message-ID: <"Nbjgf2.0.RL3.KIAks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/950 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 720 >At the risk of causing a technology stock market crash, I will say the >following regarding Syquest disks: they crash. They do so frequently. >And the drives break too. But to make the market recover, I will say that >their convenience is such that by popular demand we continue to make >Syquest available. To my knowledge, Syquest are not available anymore, at least in Canada. Our retailers do not sell neither drive nor cartidges. They said they are out of business. Dominique Berube, Tel: 987 3000 (3986) Doctorat Sciences de l'environnement Fax: 987 7749 Universite du Quebec a Montreal E-mail:Berube.Dominique@uqam.ca CP 8888, Succ. Centre-Ville Montreal, (Quebec), Canada, H3C 3P8 From nih-image-request@io.ece.drexel.edu Wed Feb 3 16:37 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA28426 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 16:37:43 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 16:37:43 -0500 (EST) Date: Wed, 3 Feb 1999 16:10:30 -0500 (EST) From: Cengizhan Ozturk X-Sender: cozturk@ariel To: nih-image@io.ece.drexel.edu Subject: Re: Skeletonizing images In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"OiTBM2.0.m96.JjBks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/951 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1223 Hi, If you don't mind cutting the same amount at the edges of the main skeleton as the length of side dendrites, there is a little trick that you can use: After skeletonization, SetNeighborhoodCount to 7. Erode the binary image (as many times as the maximum length of the dendrites, or stop when the change of the total number of black pixels equals to 2 times the number of objects --this will add some time !!) Bring back the neighborhoodcount to default; You can all do this in the macro language. Good luck Cengizhan -------------------------------------------- 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, 3 Feb 1999, bruckner wrote: > I want to reduce fibrous objects to simple lines. However, Skeleton > creates small side dendrites whose length varies with the width of the > fibers. What alternate techniques could I use? > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- > > > From nih-image-request@io.ece.drexel.edu Wed Feb 3 17:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA03180 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 17:21:57 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 17:21:57 -0500 (EST) Date: Wed, 3 Feb 1999 13:55:34 -0800 (PST) From: Chris Poklemba Reply-To: Chris Poklemba To: nih-image@io.ece.drexel.edu Subject: Re: recovery of data & syquest In-Reply-To: <1E3C5B85F34@qc1.qc.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"1hFv51.0.s5.yNCks"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/952 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 375 Where can canopener be found? Thanks On Wed, 3 Feb 1999, Jared L. Rifkin wrote: > have you tried putting the 'disk' into another drive that is known to > work? > have you tried using "canopener" or the pc-equivalent? i've used > canopener on a variety of media and drives- it is fantastic and will > recover files of all kinds [however, it is a mac utility]. > > From nih-image-request@io.ece.drexel.edu Wed Feb 3 21:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA29814 for cshtest@io.ece.drexel.edu; Wed, 3 Feb 1999 21:13:15 -0500 (EST) Resent-Date: Wed, 3 Feb 1999 21:13:15 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: cozturk@mri.jhu.edu, bruckner@mailer03.u.washington.edu, nih-image@io.ece.drexel.edu Date: Thu, 4 Feb 1999 12:57:46 +1100 Subject: Re: Skeletonizing images Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <19FDCF64F5@rna.bio.mq.edu.au> Resent-Message-ID: <"nBj9S.0.vj6.AtFks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/953 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2817 I liked Cengizhan's suggestion and experimented with it. Skeletonizing of thick ring shaped segments obtained by densitysliceing had produced lots of 'wiskers' on the central core loop. As they were closed loops I had been able to automate droping of the wiskers by successive autoOutline from outside and inside with clearing and drawboundary but this relies on the closed loop. My implementation of Cengizhan's suggestion worked well except that the were a number of Y shaped wiskers and the procedure would not erode past the V of the Y shaped wiskers. Investigating the cause of the Y shaped wiskers led me to the realisation/discovery that a simple binary "open" ie erode;dilate; PRIOR to Skeletonize'ing results in a 'clean' skeleton without ANY problematic wiskers to be removed. If your objects are fibrous rather than closed rings you should also get the same clean result (unless of course your fibres have split or obtusely? blunt ends) by a simple erode;dilate; PRIOR to Skeletonize'ing. Greg Joss PS your particles must not have interior holes for clean Skeletonize'ing. You can achieve this with analyzeParticles('include') and a changeValues to reBinarise the result image. >Date: Wed, 3 Feb 1999 16:10:30 -0500 (EST) >From: Cengizhan Ozturk >To: nih-image@io.ece.drexel.edu >Subject: Re: Skeletonizing images > >If you don't mind cutting the same amount at the edges of the main skeleton >as the length of side dendrites, there is a little trick that you can >use: > >After skeletonization, > >SetNeighborhoodCount to 7. Erode the binary image (as many times as the >maximum length of the dendrites, or stop when the change of the total number >of black pixels equals to 2 times the number of objects --this will add some >time !!) > >Bring back the neighborhoodcount to default; > >You can all do this in the macro language. > >Good luck > >Cengizhan > >-------------------------------------------- >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, 3 Feb 1999, bruckner wrote: > >> I want to reduce fibrous objects to simple lines. However, Skeleton >> creates small side dendrites whose length varies with the width of the >> fibers. What alternate techniques could I use? >> >> ----------------------- >> Carsten Bruckner >> U. of Washington >> Dept. of Chemistry >> Box 351700 >> Seattle, WA 98195-1700 >> >> Tel. 206-543-6144 >> ----------------------- >> >> >> > > 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 Feb 4 06:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02629; Thu, 4 Feb 1999 06:15:36 -0500 (EST) Date: Thu, 4 Feb 1999 06:15:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902041115.GAA02629@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #33 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/33 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: 13670 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 33 Today's Topics: Job opening in Digital Microscopy [ Stamatis Pagakis To: nih-image@io.ece.drexel.edu Subject: Job opening in Digital Microscopy Message-id: Content-type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit NATIONAL INSTITUTE FOR MEDICAL RESEARCH PERMANENT RESEARCH MICROSCOPIST POSITION (Ref: GMB/SP/RT) Available immediately at the Confocal Microscopy and Image Analysis Laboratory (CIAL) which specialises in digital imaging in microscopy and provides a focus for interaction with many laboratories at NIMR. (http//www.nimr.mrc.ac.uk/~cial.) The successful candidate will assist in the day-to-day running of the lab. Main duties are maintenance and operation of confocal and deconvolution microscopes and associated computers, teaching and technical support of users and analysis of image data. Applicants should possess a Degree in an appropriate scientific discipline and significant experience in digital microscopy. The post requires excellent problem solving and interpersonal skills. Must be able to work with minimal supervision and have some experience with the use of networked computers (Unix, MacOS and Windows NT) for digital image processing and analysis. Hands-on experience with 3D imaging is highly desirable. Administration of Unix computers would be an advantage. Starting salary is up to £18,000 per annum (including Location allowance) depending on experience and, rising to £25,800 per annum (MRC band 5 post). MRC Pension Scheme option. Please telephone for an application form and job description, quoting the appropriate reference number on 0181-913 8544, or write to Personnel Manager, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA. The closing date for completed applications is 5th February 1999. The MRC is an Equal Opportunities employer - smoking is actively discouraged *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Membrane Biology Mobile: 0370 654288 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < ------------------------------ Date: Wed, 3 Feb 1999 08:26:28 -0800 From: bruckner To: nih-image@io.ece.drexel.edu Subject: Skeletonizing images Message-Id: Content-Type: text/plain; charset="us-ascii" I want to reduce fibrous objects to simple lines. However, Skeleton creates small side dendrites whose length varies with the width of the fibers. What alternate techniques could I use? ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- ------------------------------ Date: Wed, 3 Feb 1999 11:10:37 -0600 (CST) From: "Malinda E.C. Fitzgerald" To: nih-image@io.ece.drexel.edu Subject: recovery of data Message-Id: Content-Type: text/plain; charset="us-ascii" HI I thought I would send out a general plea for help. We use a syquest drive to store our images. We have a disc that has a lot of data on it and we can't get the drive to mount with this disc. It doesn't appear to be a drive problem because other discs work. Has anyone had any experience recovering files from damaged discs? Does anyone know of a company that does this at a resonable cost? The only quote I have gotten is $1,000 for recovery of any data. That could be one file or 20. Any suggestions would be welcome. Thanks. Malinda Malinda E.C. Fitzgerald, Ph.D. Associate Professor Department of Biology 650 E Parkway So. Christian Brothers University Memphis, TN 38104 901-321-3262 office 901-321-4433 fax ------------------------------ Date: Wed, 03 Feb 1999 13:06:28 -0800 From: Michael Cammer To: nih-image@io.ece.drexel.edu Subject: Re: recovery of data Message-Id: <3.0.5.32.19990203130628.0093fe30@mailserver.aecom.yu.edu> Content-Type: text/plain; charset="us-ascii" At the risk of causing a technology stock market crash, I will say the following regarding Syquest disks: they crash. They do so frequently. And the drives break too. But to make the market recover, I will say that their convenience is such that by popular demand we continue to make Syquest available. As for recovery, Drivesavers at www.drivesavers.com and Advanced Data Solutions at www.adv-data.com both recovered disks for us. Yes, the going rate is more than $1,000. But one of the disks had data from one full day of imaging. We knew that the experiment worked. And it cost one day of preparation, more than $500 in reagents, one full day of imaging on a machine that cost $20/hr. Based on the Postdoc's time and the money involved, recovery was well worth it. At 11:10 AM 2/3/99 -0600, you wrote: >HI I thought I would send out a general plea for help. We use a syquest >drive to store our images. We have a disc that has a lot of data on it and >we can't get the drive to mount with this disc. It doesn't appear to be a ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* ------------------------------ Date: Wed, 3 Feb 99 14:22:56 -0500 From: "Jared L. Rifkin" To: Subject: Re: recovery of data & syquest Message-ID: <1E3C5B85F34@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" have you tried putting the 'disk' into another drive that is known to work? have you tried using "canopener" or the pc-equivalent? i've used canopener on a variety of media and drives- it is fantastic and will recover files of all kinds [however, it is a mac utility]. ------------------------------ Date: Wed, 3 Feb 1999 14:29:54 -0500 From: Dominique Berube To: nih-image@io.ece.drexel.edu Subject: Re: recovery of data Message-Id: Content-Type: text/plain; charset="us-ascii" >At the risk of causing a technology stock market crash, I will say the >following regarding Syquest disks: they crash. They do so frequently. >And the drives break too. But to make the market recover, I will say that >their convenience is such that by popular demand we continue to make >Syquest available. To my knowledge, Syquest are not available anymore, at least in Canada. Our retailers do not sell neither drive nor cartidges. They said they are out of business. Dominique Berube, Tel: 987 3000 (3986) Doctorat Sciences de l'environnement Fax: 987 7749 Universite du Quebec a Montreal E-mail:Berube.Dominique@uqam.ca CP 8888, Succ. Centre-Ville Montreal, (Quebec), Canada, H3C 3P8 ------------------------------ Date: Wed, 3 Feb 1999 16:10:30 -0500 (EST) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: Skeletonizing images Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, If you don't mind cutting the same amount at the edges of the main skeleton as the length of side dendrites, there is a little trick that you can use: After skeletonization, SetNeighborhoodCount to 7. Erode the binary image (as many times as the maximum length of the dendrites, or stop when the change of the total number of black pixels equals to 2 times the number of objects --this will add some time !!) Bring back the neighborhoodcount to default; You can all do this in the macro language. Good luck Cengizhan -------------------------------------------- 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, 3 Feb 1999, bruckner wrote: > I want to reduce fibrous objects to simple lines. However, Skeleton > creates small side dendrites whose length varies with the width of the > fibers. What alternate techniques could I use? > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- > > > ------------------------------ Date: Wed, 3 Feb 1999 13:55:34 -0800 (PST) From: Chris Poklemba To: nih-image@io.ece.drexel.edu Subject: Re: recovery of data & syquest Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Where can canopener be found? Thanks On Wed, 3 Feb 1999, Jared L. Rifkin wrote: > have you tried putting the 'disk' into another drive that is known to > work? > have you tried using "canopener" or the pc-equivalent? i've used > canopener on a variety of media and drives- it is fantastic and will > recover files of all kinds [however, it is a mac utility]. > > ------------------------------ Date: Thu, 4 Feb 1999 12:57:46 +1100 From: GJOSS@rna.bio.mq.edu.au To: cozturk@mri.jhu.edu, bruckner@mailer03.u.washington.edu, nih-image@io.ece.drexel.edu Subject: Re: Skeletonizing images Message-ID: <19FDCF64F5@rna.bio.mq.edu.au> I liked Cengizhan's suggestion and experimented with it. Skeletonizing of thick ring shaped segments obtained by densitysliceing had produced lots of 'wiskers' on the central core loop. As they were closed loops I had been able to automate droping of the wiskers by successive autoOutline from outside and inside with clearing and drawboundary but this relies on the closed loop. My implementation of Cengizhan's suggestion worked well except that the were a number of Y shaped wiskers and the procedure would not erode past the V of the Y shaped wiskers. Investigating the cause of the Y shaped wiskers led me to the realisation/discovery that a simple binary "open" ie erode;dilate; PRIOR to Skeletonize'ing results in a 'clean' skeleton without ANY problematic wiskers to be removed. If your objects are fibrous rather than closed rings you should also get the same clean result (unless of course your fibres have split or obtusely? blunt ends) by a simple erode;dilate; PRIOR to Skeletonize'ing. Greg Joss PS your particles must not have interior holes for clean Skeletonize'ing. You can achieve this with analyzeParticles('include') and a changeValues to reBinarise the result image. >Date: Wed, 3 Feb 1999 16:10:30 -0500 (EST) >From: Cengizhan Ozturk >To: nih-image@io.ece.drexel.edu >Subject: Re: Skeletonizing images > >If you don't mind cutting the same amount at the edges of the main skeleton >as the length of side dendrites, there is a little trick that you can >use: > >After skeletonization, > >SetNeighborhoodCount to 7. Erode the binary image (as many times as the >maximum length of the dendrites, or stop when the change of the total number >of black pixels equals to 2 times the number of objects --this will add some >time !!) > >Bring back the neighborhoodcount to default; > >You can all do this in the macro language. > >Good luck > >Cengizhan > >-------------------------------------------- >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, 3 Feb 1999, bruckner wrote: > >> I want to reduce fibrous objects to simple lines. However, Skeleton >> creates small side dendrites whose length varies with the width of the >> fibers. What alternate techniques could I use? >> >> ----------------------- >> Carsten Bruckner >> U. of Washington >> Dept. of Chemistry >> Box 351700 >> Seattle, WA 98195-1700 >> >> Tel. 206-543-6144 >> ----------------------- >> >> >> > > 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 V99 Issue #33 *************************************** From nih-image-request@io.ece.drexel.edu Fri Feb 5 05:35 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA19073 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 05:35:57 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 05:35:57 -0500 (EST) Message-Id: <4.0.2-J.19990205191251.00e87c60@kuniric.kuni.co.jp> X-Sender: fwix7566@mb.infoweb.ne.jp (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.2-J Date: Fri, 05 Feb 1999 19:20:13 +0900 To: nih-image@io.ece.drexel.edu From: Ishikawa Subject: Motion analysis Mime-Version: 1.0 Resent-Message-ID: <"YuL4R1.0.D84.YNiks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/954 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 297 I am looking for below software system. If somebody get the information Please let me know. I have one question. Can you analyze following? Baseball Pitcher's form would like to compare 2 different forms. Is this possible we can do above by using the software? regards, Tatsumasa Ishikawa From nih-image-request@io.ece.drexel.edu Fri Feb 5 09:05 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA14787 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 09:05:51 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 09:05:51 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Fri, 05 Feb 1999 08:45:17 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu, fwix7566@mb.infoweb.ne.jp Subject: Re: Motion analysis Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"7xFtR3.0.zy2.3Olks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/955 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2592 Ishikawa-san, NIH-Image software has basic tools, but does not understand high-level concepts like motion or acceleration, or baseball. It has no understanding of image CONTENT (MEANING) If baseball were a written novel, NIH-Image could recognize letters and some words, but would have no idea of sentences or meaning, let alone how to write a paragraph. With the right computer and digitizer, you could read in a video of a pitcher and create a "stack" of 200 images at 0.016 second intervals. You would have to click on various parts of the pitcher's body (left knee, left arm, left wrist, right wrist) for the computer to know where they were. You would have to write a program that asked for these and stored the values. You would have to write a program that could take two views of the same pitcher from two positions to compute what is going on in 3-D space. You would have to make a model of a pitcher and assign mass to various parts, such as left-forearm. You would have to write a program to convert all the X-Y-Z coordinates over time into motions and accelerations. It could be done using NIH-Image by someone willing to put the time into learning NIH-Image's programming language, similar to Pascal. It would be a great deal of work, but I can't think of any OTHER software that would be much easier to use, and I can think of several that would be a lot harder to learn and program (eg, Khoros, IP-Lab). In 1965 I did this sort of thing by hand, using strobe photos of people walking, to help design artificial hip-joints. Best advantage of NIH-Image is this group, which has always been quite fast and helpful in answering questions and helping people get started and solve problems. It will still not be an easy thing to do in any software. Still, if I had to do it today, I'd use NIH-Image for the front-end work. The really nice thing is FEEDBACK - as you program in NIH-IMAGE, you can also display easily back on the image what you are doing (such as a motion vector you compute) and that way you can catch errors and fix them as you code, which makes debugging 1000% easier than it would be writing C code directly. regards, Wade Schuette University of Michigan Ann Arbor, MI USA >>> Ishikawa 02/05 5:35 AM >>> I am looking for below software system. If somebody get the information Please let me know. I have one question. Can you analyze following? Baseball Pitcher's form would like to compare 2 different forms. Is this possible we can do above by using the software? regards, Tatsumasa Ishikawa From nih-image-request@io.ece.drexel.edu Fri Feb 5 16:55 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA15121 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 16:55:19 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 16:55:19 -0500 (EST) Date: Fri, 5 Feb 1999 11:40:37 -1000 From: Maaya A Yasuda X-Sender: maaya@uhunix1 To: nih-image Subject: Mean density VS integrated density Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"M6jmZ1.0.CM3.-Lsks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/956 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 366 I am a new user of nihimage and have a question. From the ANALYZE menu I select OPTIONS and get a window with a bunch of differnt boxes to check off, two of which are mean density and integrated density. WHAT IS THE DIFFERENCE BETWEEN MEAN DENSITY AND INTEGRATED DENSITY? Any input is greatly appreciated and I can provide more details if needed. Thanks, Maaya From nih-image-request@io.ece.drexel.edu Fri Feb 5 17:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA20154 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 17:45:52 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 17:45:52 -0500 (EST) Message-Id: <199902052234.RAA18857@io.ece.drexel.edu> Date: Thu, 04 Feb 1999 09:53:41 -0500 From: "McCoy, Carol" Subject: RE: Opening Adobe Premiere docs To: nih-image@io.ece.drexel.edu MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"Xh65.0.tc4.C8tks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/957 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: 1065 I do not think this message was intended for me. I am a Merck Urology Specialty representative in California. There is another Carol L. McCoy listed in our Global Address book. -----Original Message----- From: Michael Benjamin Hopkins [mailto:bhopkins@acpub.duke.edu] Sent: Tuesday, February 02, 1999 10:54 AM To: nih-image@io.ece.drexel.edu Subject: Opening Adobe Premiere docs Hello, I am trying to use Image 1.61 to open image stacks taken with Adobe Premiere 4.0. The computer we capture the images on is a PowerMac running system 7.5.3. Image 1.61 on this machine pulls up the picture without a problem. However, when I bring the file to other computers I cannot see an image for the file I just opened; all I get is a title bar and a blank field. The machines I have problems with are running system 8.1; one is a G3 and the other is a 7200. I tried copying the preferences from the Mac that works to those that don't, but this did not change anything. Any suggestions? Thanks a lot for your help. Ben Hopkins From nih-image-request@io.ece.drexel.edu Fri Feb 5 20:32 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA10706 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 20:32:39 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 20:32:39 -0500 (EST) Date: Fri, 5 Feb 1999 15:17:36 -1000 From: Maaya A Yasuda X-Sender: maaya@uhunix2 To: nih-image listserve Subject: Quantitative Immunocytochemistry Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"h86xU1.0.J62.IXvks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/958 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 117 Has anyone done - or heard of - doing quantitative immunocytochemistry with NIH Image software? Thanks, Maaya From nih-image-d-request@io.ece.drexel.edu Fri Feb 5 23:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04491; Fri, 5 Feb 1999 23:39:43 -0500 (EST) Date: Fri, 5 Feb 1999 23:39:43 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902060439.XAA04491@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #34 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/34 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: 6892 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 34 Today's Topics: Motion analysis [ Ishikawa ] RE: Opening Adobe Premiere docs [ "McCoy, Carol" ] unsubscribe [ Heidi Guetschow To: nih-image@io.ece.drexel.edu Subject: Motion analysis Message-Id: <4.0.2-J.19990205191251.00e87c60@kuniric.kuni.co.jp> Content-Type: text/plain; charset="us-ascii" I am looking for below software system. If somebody get the information Please let me know. I have one question. Can you analyze following? Baseball Pitcher's form would like to compare 2 different forms. Is this possible we can do above by using the software? regards, Tatsumasa Ishikawa ------------------------------ Date: Fri, 05 Feb 1999 08:45:17 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu, fwix7566@mb.infoweb.ne.jp Subject: Re: Motion analysis Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Ishikawa-san, NIH-Image software has basic tools, but does not understand high-level concepts like motion or acceleration, or baseball. It has no understanding of image CONTENT (MEANING) If baseball were a written novel, NIH-Image could recognize letters and some words, but would have no idea of sentences or meaning, let alone how to write a paragraph. With the right computer and digitizer, you could read in a video of a pitcher and create a "stack" of 200 images at 0.016 second intervals. You would have to click on various parts of the pitcher's body (left knee, left arm, left wrist, right wrist) for the computer to know where they were. You would have to write a program that asked for these and stored the values. You would have to write a program that could take two views of the same pitcher from two positions to compute what is going on in 3-D space. You would have to make a model of a pitcher and assign mass to various parts, such as left-forearm. You would have to write a program to convert all the X-Y-Z coordinates over time into motions and accelerations. It could be done using NIH-Image by someone willing to put the time into learning NIH-Image's programming language, similar to Pascal. It would be a great deal of work, but I can't think of any OTHER software that would be much easier to use, and I can think of several that would be a lot harder to learn and program (eg, Khoros, IP-Lab). In 1965 I did this sort of thing by hand, using strobe photos of people walking, to help design artificial hip-joints. Best advantage of NIH-Image is this group, which has always been quite fast and helpful in answering questions and helping people get started and solve problems. It will still not be an easy thing to do in any software. Still, if I had to do it today, I'd use NIH-Image for the front-end work. The really nice thing is FEEDBACK - as you program in NIH-IMAGE, you can also display easily back on the image what you are doing (such as a motion vector you compute) and that way you can catch errors and fix them as you code, which makes debugging 1000% easier than it would be writing C code directly. regards, Wade Schuette University of Michigan Ann Arbor, MI USA >>> Ishikawa 02/05 5:35 AM >>> I am looking for below software system. If somebody get the information Please let me know. I have one question. Can you analyze following? Baseball Pitcher's form would like to compare 2 different forms. Is this possible we can do above by using the software? regards, Tatsumasa Ishikawa ------------------------------ Date: Fri, 5 Feb 1999 11:40:37 -1000 From: Maaya A Yasuda To: nih-image Subject: Mean density VS integrated density Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am a new user of nihimage and have a question. From the ANALYZE menu I select OPTIONS and get a window with a bunch of differnt boxes to check off, two of which are mean density and integrated density. WHAT IS THE DIFFERENCE BETWEEN MEAN DENSITY AND INTEGRATED DENSITY? Any input is greatly appreciated and I can provide more details if needed. Thanks, Maaya ------------------------------ Date: Thu, 04 Feb 1999 09:53:41 -0500 From: "McCoy, Carol" To: nih-image@io.ece.drexel.edu Subject: RE: Opening Adobe Premiere docs Message-Id: <199902052234.RAA18857@io.ece.drexel.edu> Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT I do not think this message was intended for me. I am a Merck Urology Specialty representative in California. There is another Carol L. McCoy listed in our Global Address book. -----Original Message----- From: Michael Benjamin Hopkins [mailto:bhopkins@acpub.duke.edu] Sent: Tuesday, February 02, 1999 10:54 AM To: nih-image@io.ece.drexel.edu Subject: Opening Adobe Premiere docs Hello, I am trying to use Image 1.61 to open image stacks taken with Adobe Premiere 4.0. The computer we capture the images on is a PowerMac running system 7.5.3. Image 1.61 on this machine pulls up the picture without a problem. However, when I bring the file to other computers I cannot see an image for the file I just opened; all I get is a title bar and a blank field. The machines I have problems with are running system 8.1; one is a G3 and the other is a 7200. I tried copying the preferences from the Mac that works to those that don't, but this did not change anything. Any suggestions? Thanks a lot for your help. Ben Hopkins ------------------------------ Date: Fri, 5 Feb 1999 15:17:36 -1000 From: Maaya A Yasuda To: nih-image listserve Subject: Quantitative Immunocytochemistry Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone done - or heard of - doing quantitative immunocytochemistry with NIH Image software? Thanks, Maaya ------------------------------ Date: Fri, 05 Feb 1999 22:30:37 -0600 (CST) From: Heidi Guetschow To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: <01J7EFVGHMTU8Y5K5S@carleton.edu> -------------------------------- End of nih-image-d Digest V99 Issue #34 *************************************** From nih-image-request@io.ece.drexel.edu Fri Feb 5 23:42 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA04979 for cshtest@io.ece.drexel.edu; Fri, 5 Feb 1999 23:42:15 -0500 (EST) Resent-Date: Fri, 5 Feb 1999 23:42:15 -0500 (EST) Date: Fri, 05 Feb 1999 22:30:37 -0600 (CST) From: Heidi Guetschow Subject: unsubscribe To: nih-image@io.ece.drexel.edu Message-id: <01J7EFVGHMTU8Y5K5S@carleton.edu> X-VMS-To: IN::"nih-image@io.ece.drexel.edu" MIME-version: 1.0 Resent-Message-ID: <"Vfjur.0.Kl.GMyks"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/959 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Sun Feb 7 20:29 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA14849 for cshtest@io.ece.drexel.edu; Sun, 7 Feb 1999 20:29:56 -0500 (EST) Resent-Date: Sun, 7 Feb 1999 20:29:56 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: maaya@hawaii.edu, nih-image@io.ece.drexel.edu Date: Mon, 8 Feb 1999 12:16:38 +1100 Subject: Re: Mean density VS integrated density Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <7955050712@rna.bio.mq.edu.au> Resent-Message-ID: <"LNTJ41.0.gB3.GfZls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/960 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1249 >Date: Fri, 5 Feb 1999 11:40:37 -1000 >From: Maaya A Yasuda >X-Sender: maaya@uhunix1 >To: nih-image >Subject: Mean density VS integrated density > >I am a new user of nihimage and have a question. From the ANALYZE menu I >select OPTIONS and get a window with a bunch of differnt boxes to check >off, two of which are mean density and integrated density. > >WHAT IS THE DIFFERENCE BETWEEN MEAN DENSITY AND INTEGRATED DENSITY? > >Any input is greatly appreciated and I can provide more details if needed. > >Thanks, >Maaya > A search using gopher://gopher.soils.umn.edu:7151/77/wais-sources/nih-image-archive?'integrated density' (see NIH-Image Home Page) yields a list of posts on this subject. Unfortuneately, it is NOT SO EASY TO SEARCH RECENT POSTINGS. Basically: Integrated density = mean * area but the result has the background subtracted. Evaluation of background is a bit of a long story :-) so I have forwarded a previous post on this subject directly to you rather than repeat on the maillist. 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 Feb 8 09:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA06624 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 09:26:12 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 09:26:12 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 8 Feb 1999 09:05:25 -0500 To: nih-image@io.ece.drexel.edu From: Richard Kollmar Subject: Set Count (?) macro command Resent-Message-ID: <"AIS4g2.0.__.oykls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/961 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 645 Dear Fellow Imagers, How does one set in a macro the number of iterations for the rank filters, such as "Opening" and "Closing"? The NIH image documentation mentions the command "Set Count", but only under the "SetBinaryCount(n)" command and nowhere else. I have tried, e.g., "Set Count(5)" and "SetCount(5)", but in both cases received errro messages. Am I missing something obvious here? Thank you for any help, Richard Richard Kollmar, Ph.D. Laboratory of Sensory Neuroscience The Rockefeller University 1230 York Ave., Box 314 New York, NY 10021-6399 Tel. (212) 327 7353 FAX (212) 327 7352 e-mail kollmar@rockvax.rockefeller.edu From nih-image-request@io.ece.drexel.edu Mon Feb 8 09:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA06645 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 09:26:19 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 09:26:19 -0500 (EST) X-Sender: elb@marlin.bio.umass.edu Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 8 Feb 1999 09:07:50 -0500 To: nih-image@io.ece.drexel.edu From: Eric Bittman Subject: Re: Quantitative Immunocytochemistry Resent-Message-ID: <"9wxtk1.0.Z41.x-kls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/962 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 218 We have used NIH image for this purpose, as have many others. Check out Amer J Physiol 271:R64-72, 1996. Eric L. Bittman Professor of Biology University of Massachusetts Amherst, MA 01003 (413)545-4344 (FAX: -3243) From nih-image-request@io.ece.drexel.edu Mon Feb 8 10:07 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA11329 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 10:07:41 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 10:07:41 -0500 (EST) Message-ID: <6A2A9250C347D111AF9B00805F1951173A4492@EPITAXX_XCHANGE> From: DAVID MARCELLUS To: "'nih-image@io.ece.drexel.edu'" Subject: unsubscribe Date: Mon, 8 Feb 1999 09:48:14 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Resent-Message-ID: <"IHzcT3.0.dE2.kblls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/963 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01BE5372.0E6DCB6A" Content-Length: 626 This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01BE5372.0E6DCB6A Content-Type: text/plain; charset="iso-8859-1" ------_=_NextPart_001_01BE5372.0E6DCB6A Content-Type: text/html; charset="iso-8859-1" unsubscribe ------_=_NextPart_001_01BE5372.0E6DCB6A-- From nih-image-request@io.ece.drexel.edu Mon Feb 8 12:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA00709 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 12:59:29 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 12:59:29 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Mon, 08 Feb 1999 12:38:45 -0500 From: "Wade Schuette" To: maaya@hawaii.edu, nih-image@io.ece.drexel.edu Subject: Re: Quantitative Immunocytochemistry Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"IBKoZ.0.kv6.k5ols"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/964 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1464 I'd say this is a good list for questions related to quantitative Immunocytochemistry. Seconding Eric Bittman's reply, I got 150 or so hits on my web site re "Quantitative Biomedical Imaging" in January, primarily from NIH-Image users. Some list-members use other software (eg, IPLab) for color-intensive work, although I'd expect Image/J to become much more important for color-based work, as Java 1.2 is loaded with wonderful new image-handling tools just waiting for someone to implement them in Image/J. The archives can be searched for specific topics,eg, "quantitative immuno" put into the gopher search of the NIH Image archives at URL = gopher://gopher.soils.umn.edu:7151/77/wais-sources/nih-image-archive My own web site is at URL = http://www-personal.umich.edu/~schuette/imaging/ and has some working papers on quantitation of dual-stained regions (eg immunoperoxidase counterstained with hematoxylin) and ideas about precisely what regions to measure. I'd personally love to see more active discussion of the issues and topics here and think they'd be in place on this list, or in side discussions sparked by a posting on the list, although those would not get archived and the archives are valuable. Wade Schuette University of Michigan Medical Center Ann Arbor, MI >>> Maaya A Yasuda 02/05 8:32 PM >>> Has anyone done - or heard of - doing quantitative immunocytochemistry with NIH Image software? Thanks, Maaya From nih-image-d-request@io.ece.drexel.edu Mon Feb 8 13:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA01784; Mon, 8 Feb 1999 13:08:58 -0500 (EST) Date: Mon, 8 Feb 1999 13:08:58 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902081808.NAA01784@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #35 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/35 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: 6325 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 35 Today's Topics: Re: Mean density VS integrated densi [ GJOSS@rna.bio.mq.edu.au ] Set Count (?) macro command [ Richard Kollmar ] unsubscribe [ DAVID MARCELLUS >Date: Fri, 5 Feb 1999 11:40:37 -1000 >From: Maaya A Yasuda >X-Sender: maaya@uhunix1 >To: nih-image >Subject: Mean density VS integrated density > >I am a new user of nihimage and have a question. From the ANALYZE menu I >select OPTIONS and get a window with a bunch of differnt boxes to check >off, two of which are mean density and integrated density. > >WHAT IS THE DIFFERENCE BETWEEN MEAN DENSITY AND INTEGRATED DENSITY? > >Any input is greatly appreciated and I can provide more details if needed. > >Thanks, >Maaya > A search using gopher://gopher.soils.umn.edu:7151/77/wais-sources/nih-image-archive?'integrated density' (see NIH-Image Home Page) yields a list of posts on this subject. Unfortuneately, it is NOT SO EASY TO SEARCH RECENT POSTINGS. Basically: Integrated density = mean * area but the result has the background subtracted. Evaluation of background is a bit of a long story :-) so I have forwarded a previous post on this subject directly to you rather than repeat on the maillist. 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, 8 Feb 1999 09:05:25 -0500 From: Richard Kollmar To: nih-image@io.ece.drexel.edu Subject: Set Count (?) macro command Message-Id: Content-Type: text/plain; charset="us-ascii" Dear Fellow Imagers, How does one set in a macro the number of iterations for the rank filters, such as "Opening" and "Closing"? The NIH image documentation mentions the command "Set Count", but only under the "SetBinaryCount(n)" command and nowhere else. I have tried, e.g., "Set Count(5)" and "SetCount(5)", but in both cases received errro messages. Am I missing something obvious here? Thank you for any help, Richard Richard Kollmar, Ph.D. Laboratory of Sensory Neuroscience The Rockefeller University 1230 York Ave., Box 314 New York, NY 10021-6399 Tel. (212) 327 7353 FAX (212) 327 7352 e-mail kollmar@rockvax.rockefeller.edu ------------------------------ Date: Mon, 8 Feb 1999 09:07:50 -0500 From: Eric Bittman To: nih-image@io.ece.drexel.edu Subject: Re: Quantitative Immunocytochemistry Message-Id: Content-Type: text/plain; charset="us-ascii" We have used NIH image for this purpose, as have many others. Check out Amer J Physiol 271:R64-72, 1996. Eric L. Bittman Professor of Biology University of Massachusetts Amherst, MA 01003 (413)545-4344 (FAX: -3243) ------------------------------ Date: Mon, 8 Feb 1999 09:48:14 -0500 From: DAVID MARCELLUS To: "'nih-image@io.ece.drexel.edu'" Subject: unsubscribe Message-ID: <6A2A9250C347D111AF9B00805F1951173A4492@EPITAXX_XCHANGE> Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01BE5372.0E6DCB6A" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01BE5372.0E6DCB6A Content-Type: text/plain; charset="iso-8859-1" ------_=_NextPart_001_01BE5372.0E6DCB6A Content-Type: text/html; charset="iso-8859-1" unsubscribe ------_=_NextPart_001_01BE5372.0E6DCB6A-- ------------------------------ Date: Mon, 08 Feb 1999 12:38:45 -0500 From: "Wade Schuette" To: maaya@hawaii.edu, nih-image@io.ece.drexel.edu Subject: Re: Quantitative Immunocytochemistry Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline I'd say this is a good list for questions related to quantitative Immunocytochemistry. Seconding Eric Bittman's reply, I got 150 or so hits on my web site re "Quantitative Biomedical Imaging" in January, primarily from NIH-Image users. Some list-members use other software (eg, IPLab) for color-intensive work, although I'd expect Image/J to become much more important for color-based work, as Java 1.2 is loaded with wonderful new image-handling tools just waiting for someone to implement them in Image/J. The archives can be searched for specific topics,eg, "quantitative immuno" put into the gopher search of the NIH Image archives at URL = gopher://gopher.soils.umn.edu:7151/77/wais-sources/nih-image-archive My own web site is at URL = http://www-personal.umich.edu/~schuette/imaging/ and has some working papers on quantitation of dual-stained regions (eg immunoperoxidase counterstained with hematoxylin) and ideas about precisely what regions to measure. I'd personally love to see more active discussion of the issues and topics here and think they'd be in place on this list, or in side discussions sparked by a posting on the list, although those would not get archived and the archives are valuable. Wade Schuette University of Michigan Medical Center Ann Arbor, MI >>> Maaya A Yasuda 02/05 8:32 PM >>> Has anyone done - or heard of - doing quantitative immunocytochemistry with NIH Image software? Thanks, Maaya -------------------------------- End of nih-image-d Digest V99 Issue #35 *************************************** From nih-image-request@io.ece.drexel.edu Mon Feb 8 13:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA05064 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 13:41:15 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 13:41:15 -0500 (EST) Message-Id: <3.0.5.32.19990208132705.0094e4a0@mailserver.aecom.yu.edu> X-Sender: cammer@mailserver.aecom.yu.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 08 Feb 1999 13:27:05 -0800 To: nih-image@io.ece.drexel.edu From: Michael Cammer Subject: Re: Quantitative Immunocytochemistry In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"hVR93.0.Pn.vkols"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/965 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 622 At 03:17 PM 2/5/99 -1000, you wrote: >Has anyone done - or heard of - doing quantitative immunocytochemistry >with NIH Image software? Fluorescence? DAB? Immunogold (counting gold particles in certain locations)? Yes to all. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* From nih-image-request@io.ece.drexel.edu Mon Feb 8 17:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA28390 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 17:28:35 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 17:28:35 -0500 (EST) Date: Mon, 8 Feb 1999 12:13:24 -1000 From: Maaya A Yasuda X-Sender: maaya@uhunix2 To: nih-image listserve Subject: Which measurements? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"ZTJlF1.0.rY6.m6sls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/966 X-Loop: nih-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 I am trying to use nih-image to quantitate the amount of immunohistochemical stain in human cells fixed in Bouins, embedded in paraffin and stained with the ABC Dab-Nickel method. My question is what exactly should I measure? Mean density or integrated density? Which is the AVERAGE GRAY LEVEL? Also, I have had conflicting advise about use of the following log equation (i.e you should adjust the light so that the gray level for 0 ng of antigen is 255 (white) and then calculate optical density as the log (255/gv[Ab]) where gv[Ab] is your gray value measured for some concentration of antigen). Finally, how should the AREA of the cells being measured be handled? Should I divide the average gray level by the AREA and report measurements as GL/squred micron? Mahalo for the help. maaya From nih-image-request@io.ece.drexel.edu Mon Feb 8 17:34 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA29117 for cshtest@io.ece.drexel.edu; Mon, 8 Feb 1999 17:34:50 -0500 (EST) Resent-Date: Mon, 8 Feb 1999 17:34:50 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: kollmar@rockvax.rockefeller.edu, nih-image@io.ece.drexel.edu Date: Tue, 9 Feb 1999 9:26:39 +1100 Subject: Re: Set Count (?) macro command Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <8E813A65C8@rna.bio.mq.edu.au> Resent-Message-ID: <"ZNkTb2.0.do6.PFsls"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/967 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1903 > Am I missing something obvious here? Richard, :-) It seems like just the other day that I posted the response appended below erode; dilate; are the primatives for "Opening" and "Closing" hence: var i,n:integer; n:=5; for i:=1 to n do begin erode; dilate; end; or for i:=1 to n do begin dilate; erode; end; It is often obvious after you know the answer :-). >Date: Mon, 8 Feb 1999 09:05:25 -0500 >To: nih-image@io.ece.drexel.edu >From: Richard Kollmar >Subject: Set Count (?) macro command > >Dear Fellow Imagers, > >How does one set in a macro the number of iterations for the rank filters, >such as "Opening" and "Closing"? The NIH image documentation mentions the >command "Set Count", but only under the "SetBinaryCount(n)" command and >nowhere else. I have tried, e.g., "Set Count(5)" and "SetCount(5)", but >in both cases received errro messages. Am I missing something obvious here? > >Thank you for any help, > >Richard > > >Richard Kollmar, Ph.D. > >Laboratory of Sensory Neuroscience >The Rockefeller University >1230 York Ave., Box 314 >New York, NY 10021-6399 >Tel. (212) 327 7353 >FAX (212) 327 7352 >e-mail kollmar@rockvax.rockefeller.edu > From: Self To: gregoire@starlab.net,nih-image@io.ece.drexel.edu Subject: Re: 'Filter' macro command Date: Fri, 22 Jan 1999 9:04:34 >Date: Thu, 21 Jan 1999 15:10:32 +0100 >From: gregoire >To: nih-image@io.ece.drexel.edu >Subject: 'Filter' macro command >Just wondering if anybody knows how to change the number of iterations for >the Rank Filters from a macro (I'm using "Filter('min');"). >TIA >Gregoire var i,n:integer; n:=3; for i:=1 to n do Filter('min'); :-) 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 Feb 9 06:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA16388; Tue, 9 Feb 1999 06:15:36 -0500 (EST) Date: Tue, 9 Feb 1999 06:15:36 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902091115.GAA16388@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #36 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/36 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: 4650 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 36 Today's Topics: Re: Quantitative Immunocytochemistry [ Michael Cammer ] Re: Set Count (?) macro command [ GJOSS@rna.bio.mq.edu.au ] ------------------------------ Date: Mon, 08 Feb 1999 13:27:05 -0800 From: Michael Cammer To: nih-image@io.ece.drexel.edu Subject: Re: Quantitative Immunocytochemistry Message-Id: <3.0.5.32.19990208132705.0094e4a0@mailserver.aecom.yu.edu> Content-Type: text/plain; charset="us-ascii" At 03:17 PM 2/5/99 -1000, you wrote: >Has anyone done - or heard of - doing quantitative immunocytochemistry >with NIH Image software? Fluorescence? DAB? Immunogold (counting gold particles in certain locations)? Yes to all. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* ------------------------------ Date: Mon, 8 Feb 1999 12:13:24 -1000 From: Maaya A Yasuda To: nih-image listserve Subject: Which measurements? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying to use nih-image to quantitate the amount of immunohistochemical stain in human cells fixed in Bouins, embedded in paraffin and stained with the ABC Dab-Nickel method. My question is what exactly should I measure? Mean density or integrated density? Which is the AVERAGE GRAY LEVEL? Also, I have had conflicting advise about use of the following log equation (i.e you should adjust the light so that the gray level for 0 ng of antigen is 255 (white) and then calculate optical density as the log (255/gv[Ab]) where gv[Ab] is your gray value measured for some concentration of antigen). Finally, how should the AREA of the cells being measured be handled? Should I divide the average gray level by the AREA and report measurements as GL/squred micron? Mahalo for the help. maaya ------------------------------ Date: Tue, 9 Feb 1999 9:26:39 +1100 From: GJOSS@rna.bio.mq.edu.au To: kollmar@rockvax.rockefeller.edu, nih-image@io.ece.drexel.edu Subject: Re: Set Count (?) macro command Message-ID: <8E813A65C8@rna.bio.mq.edu.au> > Am I missing something obvious here? Richard, :-) It seems like just the other day that I posted the response appended below erode; dilate; are the primatives for "Opening" and "Closing" hence: var i,n:integer; n:=5; for i:=1 to n do begin erode; dilate; end; or for i:=1 to n do begin dilate; erode; end; It is often obvious after you know the answer :-). >Date: Mon, 8 Feb 1999 09:05:25 -0500 >To: nih-image@io.ece.drexel.edu >From: Richard Kollmar >Subject: Set Count (?) macro command > >Dear Fellow Imagers, > >How does one set in a macro the number of iterations for the rank filters, >such as "Opening" and "Closing"? The NIH image documentation mentions the >command "Set Count", but only under the "SetBinaryCount(n)" command and >nowhere else. I have tried, e.g., "Set Count(5)" and "SetCount(5)", but >in both cases received errro messages. Am I missing something obvious here? > >Thank you for any help, > >Richard > > >Richard Kollmar, Ph.D. > >Laboratory of Sensory Neuroscience >The Rockefeller University >1230 York Ave., Box 314 >New York, NY 10021-6399 >Tel. (212) 327 7353 >FAX (212) 327 7352 >e-mail kollmar@rockvax.rockefeller.edu > From: Self To: gregoire@starlab.net,nih-image@io.ece.drexel.edu Subject: Re: 'Filter' macro command Date: Fri, 22 Jan 1999 9:04:34 >Date: Thu, 21 Jan 1999 15:10:32 +0100 >From: gregoire >To: nih-image@io.ece.drexel.edu >Subject: 'Filter' macro command >Just wondering if anybody knows how to change the number of iterations for >the Rank Filters from a macro (I'm using "Filter('min');"). >TIA >Gregoire var i,n:integer; n:=3; for i:=1 to n do Filter('min'); :-) 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 V99 Issue #36 *************************************** From nih-image-request@io.ece.drexel.edu Tue Feb 9 07:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA26258 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 07:46:01 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 07:46:01 -0500 (EST) Date: Tue, 9 Feb 1999 07:26:35 -0500 (EST) From: Kanu P Singh To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #36 In-Reply-To: <199902091115.GAA16382@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Oc4mP1.0.5t5.zb2ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/968 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 54 i would like to unsubscribe from this list please. From nih-image-request@io.ece.drexel.edu Tue Feb 9 08:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA02102 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 08:40:25 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 08:40:25 -0500 (EST) X-Sender: mathias@ruby.unibe.ch Message-Id: Mime-Version: 1.0 Date: Tue, 9 Feb 1999 14:28:45 +0100 To: nih-image@io.ece.drexel.edu From: mathias rickli Subject: circularity factor Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id IAA00022 Resent-Message-ID: <"8rA4O2.0.d.HQ3ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/969 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: 755 When performing area and perimeter analysis on binary objects I may get some incorrect results for special cases. For instance, I like to use the circulatity factor cf=4*pi*Area/sqr(Perimeter). The cf for circular objects equals by definition 1. However, disregarding pixel irregularities for very small objects, cf obtained by NIH from area and perimeter analysis is about 0.9 for circular objects. This is an error of 10%. Does anybody know how the perimeter algorithm works? And has anybody already established something like a correction routine? Thanks for your answer mathias Mathias Rickli, dipl. Min. Mineralogisch-Petrographisches Institut Universität 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 Tue Feb 9 09:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA10239 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 09:59:29 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 09:59:29 -0500 (EST) Date: Tue, 09 Feb 1999 09:40:06 -0500 From: Bill Christens-Barry Subject: anyone ever implement auto-run macros? To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"tB4Mi.0.z-1.aZ4ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/970 X-Loop: nih-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 Years ago there was interest in creating the capacity for NIH Image to automaticly run a macro at startup. Did anyone ever implement this auto-run capability? What would be needed to implement this? Would it make sense for a user to specify in preferences which macro should be run at startup, or should it have some specified name? The auto-load feature in NIH Image requires a macro named 'Image macros' in the folder containing the application. 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 Tue Feb 9 10:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14203 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 10:40:10 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 10:40:10 -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, 9 Feb 1999 16:23:23 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: circularity factor Resent-Message-ID: <"XcY-4.0._v2.A65ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/971 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1720 >When performing area and perimeter analysis on binary objects I may get >some incorrect results for special cases. For instance, I like to use the >circulatity factor cf=4*pi*Area/sqr(Perimeter). > >The cf for circular objects equals by definition 1. However, disregarding >pixel irregularities for very small objects, cf obtained by NIH from area >and perimeter analysis is about 0.9 for circular objects. This is an error >of 10%. >Does anybody know how the perimeter algorithm works? And has anybody >already established something like a correction routine? NIH Image regards the perimeter as a composition of horizontal, vertical and 45 degrees line segments, which overestimates the perimeter of an average object. In a publication of Smeulders and Vossepoel, I found this formula for the perimeter: LP = (1-0.052) * Ne + sqrt(2) * No) = 0.948 * Ne + 1.340 * No Ne is the number of even Freemand codes (where the connection line between two adjacent pixels is horizontal or vertical) No is the number of odd Freemand codes (where connection line between two adjacent pixels is 45 degrees). The error of the above formula is indicated with 2.3%, while the error of the NIH method is indicated with 5.2% In NIH Image, it is possible to extract the freeman code from the XY coordinates array, but it may be cumbersome because line segments can be longer than a single pixel step. N. 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 Feb 9 11:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA21484 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 11:58:44 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 11:58:44 -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, 9 Feb 1999 17:28:45 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: circularity factor Resent-Message-ID: <"NTurr1.0.iU4.t46ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/972 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 226 After I sent my previous message, I realized that correcting with the formula I mentioned is nothing else than subtracting 5.2% from the perimeter, because this is the over-estimation of the perimeter of an average object. From nih-image-request@io.ece.drexel.edu Tue Feb 9 15:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA09702 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 15:08:43 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 15:08:43 -0500 (EST) From: rdr8@cornell.edu Date: Tue, 9 Feb 1999 14:52:08 -0500 (EST) X-Sender: rdr8@travelers.mail.cornell.edu To: nih-image@io.ece.drexel.edu cc: rdr8@cornell.edu Subject: background subtraction with scion image 1.62 (mac) Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"kadLF.0.Qx1.i79ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/973 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 773 >I have been using scion 1.62 on a mac for anaylizing images from a >microscope. I found that there is a command "background subtraction" and >in the manual it describes this as an adjustment for uneaven >illumination. How does this actually work? How does it distinguish "foreground" from background? What does the rolling ball do? What does "faster" do? Does >this correct for uneven background illumination? Over different frames should the actual illumination of the objects remain constant in respect to each >other? > >Thank you for any information you can give me. > >Sincerely, >Rebecca Riba >Cornell University ------------------------------------------------------------- ---------------------------------------------------------------------- From nih-image-request@io.ece.drexel.edu Tue Feb 9 15:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA10356 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 15:15:01 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 15:15:01 -0500 (EST) X-Sender: bruckner@bruckner.deskmail.washington.edu Message-Id: Mime-Version: 1.0 X-Face: ,5-1`[.GWu}Gki.@O4TcoJhGF6#|nery_y7r1rD2hcNr&wc=q(lM_x Y$66Oe)MYC*)Mar76RpUIgnbJn!<[ Subject: Interest in flow cell image analysis? Resent-Message-ID: <"pwAHM.0.KC2.OG9ms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/974 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1055 This message is a feeler to gauge this group's interest in or need for the following system: An instrument that takes images of objects in a flow cell, with a field of view of about 1 cm on a side (about 20 micron resolution). The light is captured by two monochrome CCD's, with appropriate filters for color discrimination. Currently, we are measuring the fluorescence of fibers in a moving stream. Labview controls the acquisition and particle analysis. What research areas have a need for such a system? I represent a research group, and am looking for ideas to generate proposals. There is room to change the specs, possibly even to use a microscope system. However, I'd like to stick to systems requiring moving streams. This system could fill a gap between cell sorting systems and static microscopy, in terms of the information that could be obtained. Any feedback is appreciated. ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- From nih-image-request@io.ece.drexel.edu Tue Feb 9 17:04 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA19920 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 17:04:29 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 17:04:29 -0500 (EST) X-Sender: jag@acs-mail.bu.edu Message-Id: Mime-Version: 1.0 Date: Tue, 9 Feb 1999 16:55:22 -0400 To: nih-image@io.ece.drexel.edu From: jag@bu.edu (Jagdeep Trivedi) Subject: object image 1.67 Resent-Message-ID: <"InYNc.0.TN4.RoAms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/975 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1084 I have been using Object Image for quite sometime and recently we tried to upgrade our computer with a newer technology card. We have a Power Mac 7100/80 and purchased the MAX Power G3 210 mhz card. For whatever reason the card didn't work, possibly because we are running OS 7.5.1, too old for the card. The technician played with our extensions folder and now when we go to open a movie with object image, or any image for that matter, instead of opening the entire movie in stack format (Quicktime movie) it opens the first frame and it says (Converted) next to the title. Does anyone know how to fix this problem. It is greatly delaying our analysis. Any suggestions would also be helpful. Thank You All. Sincerely, Jay =============================================================== JAGDEEP R. TRIVEDI Neurophysiology Lab Department of Health Sciences Boston University TEL: (617) 353-3467 FAX: (617) 353-7567 EMAIL: jag@bu.edu "May the best days of our past be the worst days of our future" =============================================================== From nih-image-request@io.ece.drexel.edu Tue Feb 9 17:33 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA23321 for cshtest@io.ece.drexel.edu; Tue, 9 Feb 1999 17:33:31 -0500 (EST) Resent-Date: Tue, 9 Feb 1999 17:33:31 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Tue, 9 Feb 1999 18:29:16 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: object image 1.67 Resent-Message-ID: <"ri61V.0.OL5.BKBms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/976 X-Loop: nih-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 >I have been using Object Image for quite sometime and recently we tried to >upgrade our computer with a newer technology card. We have a Power Mac >7100/80 and purchased the MAX Power G3 210 mhz card. For whatever reason >the card didn't work, possibly because we are running OS 7.5.1, too old for >the card. The technician played with our extensions folder and now when we >go to open a movie with object image, or any image for that matter, instead >of opening the entire movie in stack format (Quicktime movie) it opens the >first frame and it says (Converted) next to the title. > >Does anyone know how to fix this problem. It is greatly delaying our >analysis. Open the "Mac Easy Open" Control Panel and click on the "Delete Preferences" button. -wayne From nih-image-request@io.ece.drexel.edu Wed Feb 10 02:10 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA21648 for cshtest@io.ece.drexel.edu; Wed, 10 Feb 1999 02:10:38 -0500 (EST) Resent-Date: Wed, 10 Feb 1999 02:10:38 -0500 (EST) Message-ID: <36C12D3F.294E41E1@caspur.it> Date: Wed, 10 Feb 1999 07:54:55 +0100 From: Leopoldo Silvestroni X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Interest in flow cell image analysis? References: Content-Transfer-Encoding: 8bit Resent-Message-ID: <"gUtGs2.0.Qn4.ZsIms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/977 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: 1582 We are interested in biological application (cell suspensions / tissue strips or fragments). please specify instrument performance in quantitative terms. best regards Leopoldo Silvestroni,MD bruckner wrote: > This message is a feeler to gauge this group's interest in or need for the > following system: > > An instrument that takes images of objects in a flow cell, with a field of > view of about 1 cm on a side (about 20 micron resolution). The light is > captured by two monochrome CCD's, with appropriate filters for color > discrimination. Currently, we are measuring the fluorescence of fibers in > a moving stream. Labview controls the acquisition and particle analysis. > > What research areas have a need for such a system? I represent a research > group, and am looking for ideas to generate proposals. There is room to > change the specs, possibly even to use a microscope system. However, I'd > like to stick to systems requiring moving streams. This system could fill > a gap between cell sorting systems and static microscopy, in terms of the > information that could be obtained. > > Any feedback is appreciated. > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- -- Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html From nih-image-d-request@io.ece.drexel.edu Wed Feb 10 02:11 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id CAA21881; Wed, 10 Feb 1999 02:11:50 -0500 (EST) Date: Wed, 10 Feb 1999 02:11:50 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902100711.CAA21881@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #37 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/37 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: 12610 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 37 Today's Topics: Re: nih-image-d Digest V99 #36 [ Kanu P Singh ] circularity factor [ mathias rickli ] Re: Interest in flow cell image anal [ Leopoldo Silvestroni To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #36 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII i would like to unsubscribe from this list please. ------------------------------ Date: Tue, 9 Feb 1999 14:28:45 +0100 From: mathias rickli To: nih-image@io.ece.drexel.edu Subject: circularity factor Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit When performing area and perimeter analysis on binary objects I may get some incorrect results for special cases. For instance, I like to use the circulatity factor cf=4*pi*Area/sqr(Perimeter). The cf for circular objects equals by definition 1. However, disregarding pixel irregularities for very small objects, cf obtained by NIH from area and perimeter analysis is about 0.9 for circular objects. This is an error of 10%. Does anybody know how the perimeter algorithm works? And has anybody already established something like a correction routine? Thanks for your answer mathias Mathias Rickli, dipl. Min. Mineralogisch-Petrographisches Institut Universität Bern Baltzerstrasse 1 CH-3012 Bern Switzerland Tel: +41-31-631-8781 Fax: +41-31-631-4843 ------------------------------ Date: Tue, 09 Feb 1999 09:40:06 -0500 From: Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: anyone ever implement auto-run macros? Message-id: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Years ago there was interest in creating the capacity for NIH Image to automaticly run a macro at startup. Did anyone ever implement this auto-run capability? What would be needed to implement this? Would it make sense for a user to specify in preferences which macro should be run at startup, or should it have some specified name? The auto-load feature in NIH Image requires a macro named 'Image macros' in the folder containing the application. Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- ------------------------------ Date: Tue, 9 Feb 1999 16:23:23 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: circularity factor Message-Id: Content-Type: text/plain; charset="us-ascii" >When performing area and perimeter analysis on binary objects I may get >some incorrect results for special cases. For instance, I like to use the >circulatity factor cf=4*pi*Area/sqr(Perimeter). > >The cf for circular objects equals by definition 1. However, disregarding >pixel irregularities for very small objects, cf obtained by NIH from area >and perimeter analysis is about 0.9 for circular objects. This is an error >of 10%. >Does anybody know how the perimeter algorithm works? And has anybody >already established something like a correction routine? NIH Image regards the perimeter as a composition of horizontal, vertical and 45 degrees line segments, which overestimates the perimeter of an average object. In a publication of Smeulders and Vossepoel, I found this formula for the perimeter: LP = (1-0.052) * Ne + sqrt(2) * No) = 0.948 * Ne + 1.340 * No Ne is the number of even Freemand codes (where the connection line between two adjacent pixels is horizontal or vertical) No is the number of odd Freemand codes (where connection line between two adjacent pixels is 45 degrees). The error of the above formula is indicated with 2.3%, while the error of the NIH method is indicated with 5.2% In NIH Image, it is possible to extract the freeman code from the XY coordinates array, but it may be cumbersome because line segments can be longer than a single pixel step. N. 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, 9 Feb 1999 17:28:45 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: circularity factor Message-Id: Content-Type: text/plain; charset="us-ascii" After I sent my previous message, I realized that correcting with the formula I mentioned is nothing else than subtracting 5.2% from the perimeter, because this is the over-estimation of the perimeter of an average object. ------------------------------ Date: Tue, 9 Feb 1999 14:52:08 -0500 (EST) From: rdr8@cornell.edu To: nih-image@io.ece.drexel.edu cc: rdr8@cornell.edu Subject: background subtraction with scion image 1.62 (mac) Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII >I have been using scion 1.62 on a mac for anaylizing images from a >microscope. I found that there is a command "background subtraction" and >in the manual it describes this as an adjustment for uneaven >illumination. How does this actually work? How does it distinguish "foreground" from background? What does the rolling ball do? What does "faster" do? Does >this correct for uneven background illumination? Over different frames should the actual illumination of the objects remain constant in respect to each >other? > >Thank you for any information you can give me. > >Sincerely, >Rebecca Riba >Cornell University ------------------------------------------------------------- ---------------------------------------------------------------------- ------------------------------ Date: Tue, 9 Feb 1999 12:00:17 -0800 From: bruckner To: nih-image@io.ece.drexel.edu Subject: Interest in flow cell image analysis? Message-Id: Content-Type: text/plain; charset="us-ascii" This message is a feeler to gauge this group's interest in or need for the following system: An instrument that takes images of objects in a flow cell, with a field of view of about 1 cm on a side (about 20 micron resolution). The light is captured by two monochrome CCD's, with appropriate filters for color discrimination. Currently, we are measuring the fluorescence of fibers in a moving stream. Labview controls the acquisition and particle analysis. What research areas have a need for such a system? I represent a research group, and am looking for ideas to generate proposals. There is room to change the specs, possibly even to use a microscope system. However, I'd like to stick to systems requiring moving streams. This system could fill a gap between cell sorting systems and static microscopy, in terms of the information that could be obtained. Any feedback is appreciated. ----------------------- Carsten Bruckner U. of Washington Dept. of Chemistry Box 351700 Seattle, WA 98195-1700 Tel. 206-543-6144 ----------------------- ------------------------------ Date: Tue, 9 Feb 1999 16:55:22 -0400 From: jag@bu.edu (Jagdeep Trivedi) To: nih-image@io.ece.drexel.edu Subject: object image 1.67 Message-Id: Content-Type: text/plain; charset="us-ascii" I have been using Object Image for quite sometime and recently we tried to upgrade our computer with a newer technology card. We have a Power Mac 7100/80 and purchased the MAX Power G3 210 mhz card. For whatever reason the card didn't work, possibly because we are running OS 7.5.1, too old for the card. The technician played with our extensions folder and now when we go to open a movie with object image, or any image for that matter, instead of opening the entire movie in stack format (Quicktime movie) it opens the first frame and it says (Converted) next to the title. Does anyone know how to fix this problem. It is greatly delaying our analysis. Any suggestions would also be helpful. Thank You All. Sincerely, Jay =============================================================== JAGDEEP R. TRIVEDI Neurophysiology Lab Department of Health Sciences Boston University TEL: (617) 353-3467 FAX: (617) 353-7567 EMAIL: jag@bu.edu "May the best days of our past be the worst days of our future" =============================================================== ------------------------------ Date: Tue, 9 Feb 1999 18:29:16 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: object image 1.67 Message-Id: Content-Type: text/plain; charset="us-ascii" >I have been using Object Image for quite sometime and recently we tried to >upgrade our computer with a newer technology card. We have a Power Mac >7100/80 and purchased the MAX Power G3 210 mhz card. For whatever reason >the card didn't work, possibly because we are running OS 7.5.1, too old for >the card. The technician played with our extensions folder and now when we >go to open a movie with object image, or any image for that matter, instead >of opening the entire movie in stack format (Quicktime movie) it opens the >first frame and it says (Converted) next to the title. > >Does anyone know how to fix this problem. It is greatly delaying our >analysis. Open the "Mac Easy Open" Control Panel and click on the "Delete Preferences" button. -wayne ------------------------------ Date: Wed, 10 Feb 1999 07:54:55 +0100 From: Leopoldo Silvestroni To: nih-image@io.ece.drexel.edu Subject: Re: Interest in flow cell image analysis? Message-ID: <36C12D3F.294E41E1@caspur.it> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit We are interested in biological application (cell suspensions / tissue strips or fragments). please specify instrument performance in quantitative terms. best regards Leopoldo Silvestroni,MD bruckner wrote: > This message is a feeler to gauge this group's interest in or need for the > following system: > > An instrument that takes images of objects in a flow cell, with a field of > view of about 1 cm on a side (about 20 micron resolution). The light is > captured by two monochrome CCD's, with appropriate filters for color > discrimination. Currently, we are measuring the fluorescence of fibers in > a moving stream. Labview controls the acquisition and particle analysis. > > What research areas have a need for such a system? I represent a research > group, and am looking for ideas to generate proposals. There is room to > change the specs, possibly even to use a microscope system. However, I'd > like to stick to systems requiring moving streams. This system could fill > a gap between cell sorting systems and static microscopy, in terms of the > information that could be obtained. > > Any feedback is appreciated. > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- -- Laboratorio di Biofluorimetria Dipartimento di Fisiopatologia Medica Policlinico Umberto I Università di Roma 'La Sapienza' 00161-Roma tel. +39 6 49970710 fax +39 6 4461450 e-mail: l.silvestroni@caspur.it WWW address: http://w3.uniroma1.it/MEDICFISIO/labpag1.html -------------------------------- End of nih-image-d Digest V99 Issue #37 *************************************** From nih-image-request@io.ece.drexel.edu Wed Feb 10 06:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA22611 for cshtest@io.ece.drexel.edu; Wed, 10 Feb 1999 06:16:38 -0500 (EST) Resent-Date: Wed, 10 Feb 1999 06:16:38 -0500 (EST) Date: Wed, 10 Feb 1999 11:00:37 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor Reply-To: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: Re: Interest in flow cell image analysis? In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"5n8d.0.Lz4.8SMms"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/978 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1630 Hello, I'm doing flow cell work under a microscope to gather data on growth rates etc. of bacterial cells. I would be interested in your system if it would be equipped with a high-resolution light microscope, since I won't have the time to do much more of this work myself. Cheers, Jan. Dr. Jan-Ulrich 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, 9 Feb 1999, bruckner wrote: > This message is a feeler to gauge this group's interest in or need for the > following system: > > An instrument that takes images of objects in a flow cell, with a field of > view of about 1 cm on a side (about 20 micron resolution). The light is > captured by two monochrome CCD's, with appropriate filters for color > discrimination. Currently, we are measuring the fluorescence of fibers in > a moving stream. Labview controls the acquisition and particle analysis. > > What research areas have a need for such a system? I represent a research > group, and am looking for ideas to generate proposals. There is room to > change the specs, possibly even to use a microscope system. However, I'd > like to stick to systems requiring moving streams. This system could fill > a gap between cell sorting systems and static microscopy, in terms of the > information that could be obtained. > > Any feedback is appreciated. > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- > > > From nih-image-request@io.ece.drexel.edu Wed Feb 10 07:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA00079 for cshtest@io.ece.drexel.edu; Wed, 10 Feb 1999 07:14:15 -0500 (EST) Resent-Date: Wed, 10 Feb 1999 07:14:15 -0500 (EST) Message-Id: <3.0.3.32.19990210130020.00969320@uio-pop.uio.no> X-Sender: edgarr@uio-pop.uio.no X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Wed, 10 Feb 1999 13:00:20 +0100 To: nih-image@io.ece.drexel.edu From: Edgar Rivedal Subject: Western blots/scanners Mime-Version: 1.0 Resent-Message-ID: <"7Z4QS2.0.Xs6.kJNms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/979 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 973 Some of our nitrocellulose Western blots are stained with 4-chloro-1-naphtol as substrate for HRP and scanned using an Agfa Arcus II or HP ScanJet6100C for analysis by for example Image. Our problem is low sensitivity of the scanners, i.e. the the scanners are unable to detect whar appears to be reasonably clear bands. I have an impression that this may be related to properties of the nitrocellulose, perhaps having a fairly glossy surface. Is it possible to use filters to enhance the signal or would it be better to use a camera instead of a scanner, or a different type of scanner? Anyone with similar experience or suggestions? Regards Edgar ________________________________________________________ Edgar Rivedal, Ph.D. (edgar.rivedal@labmed.uio.no) Institute for Cancer Research The Norwegian Radium Hospital tel. +47 22 93 47 00 N-0310 Oslo, Norway fax +47 22 93 57 67 ________________________________________________________ From nih-image-request@io.ece.drexel.edu Wed Feb 10 10:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA22693 for cshtest@io.ece.drexel.edu; Wed, 10 Feb 1999 10:09:09 -0500 (EST) Resent-Date: Wed, 10 Feb 1999 10:09:09 -0500 (EST) Message-ID: <36C155C7.381CCF74@maine.rr.com> Date: Wed, 10 Feb 1999 09:47:54 +0000 From: Marcia Goldfarb X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Western blots/scanners References: <3.0.3.32.19990210130020.00969320@uio-pop.uio.no> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"y2LWq2.0.wi4.njPms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/980 X-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: 619 I have found capturing the image on a Western blot difficult. I was not any more successful with a camera than most scanners. I solved the problem by getting the scans done at a company set up for graphic design work, which had a drum scanner (very expensive) that is indeed very sensitive. I saw spots that were not easily seen with my eye. The technician was able to wrap the nitrocellose around the drum without any problem . He kept it there by putting a piece of clear wrap around it, which he could tape. Hope this helps. Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com From nih-image-request@io.ece.drexel.edu Wed Feb 10 18:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA15314 for cshtest@io.ece.drexel.edu; Wed, 10 Feb 1999 18:17:21 -0500 (EST) Resent-Date: Wed, 10 Feb 1999 18:17:21 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Wed, 10 Feb 1999 17:15:00 -0700 To: nih-image@io.ece.drexel.edu From: "G. Wesley Vick, III M.D., PhD." Subject: "Converted" Quicktime images Resent-Message-ID: <"5l_cd.0.-L3.l1Xms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/981 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 624 Re: "Converted" Quicktime images jag@bu.edu (Jagdeep Trivedi) Try going to the extensions manager control panel and turning off Mac OS Easy Open. You may also need to delete the Mac OS Easy Open preferences file. I had a similar problem a couple of years ago and that seemed to solve it, as I recall. Hope this works! Thanks, Wes Vick G. Wesley Vick, III M.D., Ph.D. Assistant Professor Sections of Cardiology and Atherosclerosis Departments of Pediatrics and Medicine Baylor College of Medicine Associate in Pediatric Cardiology Texas Children's Hospital Phone: 713-770-5915 Fax: 713-770-5923 email: gvick@bcm.tmc.edu From nih-image-d-request@io.ece.drexel.edu Thu Feb 11 06:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA13255; Thu, 11 Feb 1999 06:17:43 -0500 (EST) Date: Thu, 11 Feb 1999 06:17:43 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902111117.GAA13255@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #38 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/38 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: 5637 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 38 Today's Topics: Re: Interest in flow cell image anal [ Jan Kreft ] Western blots/scanners [ Edgar Rivedal To: nih-image@io.ece.drexel.edu Subject: Re: Interest in flow cell image analysis? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I'm doing flow cell work under a microscope to gather data on growth rates etc. of bacterial cells. I would be interested in your system if it would be equipped with a high-resolution light microscope, since I won't have the time to do much more of this work myself. Cheers, Jan. Dr. Jan-Ulrich 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, 9 Feb 1999, bruckner wrote: > This message is a feeler to gauge this group's interest in or need for the > following system: > > An instrument that takes images of objects in a flow cell, with a field of > view of about 1 cm on a side (about 20 micron resolution). The light is > captured by two monochrome CCD's, with appropriate filters for color > discrimination. Currently, we are measuring the fluorescence of fibers in > a moving stream. Labview controls the acquisition and particle analysis. > > What research areas have a need for such a system? I represent a research > group, and am looking for ideas to generate proposals. There is room to > change the specs, possibly even to use a microscope system. However, I'd > like to stick to systems requiring moving streams. This system could fill > a gap between cell sorting systems and static microscopy, in terms of the > information that could be obtained. > > Any feedback is appreciated. > > ----------------------- > Carsten Bruckner > U. of Washington > Dept. of Chemistry > Box 351700 > Seattle, WA 98195-1700 > > Tel. 206-543-6144 > ----------------------- > > > ------------------------------ Date: Wed, 10 Feb 1999 13:00:20 +0100 From: Edgar Rivedal To: nih-image@io.ece.drexel.edu Subject: Western blots/scanners Message-Id: <3.0.3.32.19990210130020.00969320@uio-pop.uio.no> Content-Type: text/plain; charset="us-ascii" Some of our nitrocellulose Western blots are stained with 4-chloro-1-naphtol as substrate for HRP and scanned using an Agfa Arcus II or HP ScanJet6100C for analysis by for example Image. Our problem is low sensitivity of the scanners, i.e. the the scanners are unable to detect whar appears to be reasonably clear bands. I have an impression that this may be related to properties of the nitrocellulose, perhaps having a fairly glossy surface. Is it possible to use filters to enhance the signal or would it be better to use a camera instead of a scanner, or a different type of scanner? Anyone with similar experience or suggestions? Regards Edgar ________________________________________________________ Edgar Rivedal, Ph.D. (edgar.rivedal@labmed.uio.no) Institute for Cancer Research The Norwegian Radium Hospital tel. +47 22 93 47 00 N-0310 Oslo, Norway fax +47 22 93 57 67 ________________________________________________________ ------------------------------ Date: Wed, 10 Feb 1999 09:47:54 +0000 From: Marcia Goldfarb To: nih-image@io.ece.drexel.edu Subject: Re: Western blots/scanners Message-ID: <36C155C7.381CCF74@maine.rr.com> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I have found capturing the image on a Western blot difficult. I was not any more successful with a camera than most scanners. I solved the problem by getting the scans done at a company set up for graphic design work, which had a drum scanner (very expensive) that is indeed very sensitive. I saw spots that were not easily seen with my eye. The technician was able to wrap the nitrocellose around the drum without any problem . He kept it there by putting a piece of clear wrap around it, which he could tape. Hope this helps. Marcia Goldfarb Anatek-EP 17 Bishop St Portland,ME 04103 email: anatekep@maine.rr.com ------------------------------ Date: Wed, 10 Feb 1999 17:15:00 -0700 From: "G. Wesley Vick, III M.D., PhD." To: nih-image@io.ece.drexel.edu Subject: "Converted" Quicktime images Message-Id: Content-Type: text/plain; charset="us-ascii" Re: "Converted" Quicktime images jag@bu.edu (Jagdeep Trivedi) Try going to the extensions manager control panel and turning off Mac OS Easy Open. You may also need to delete the Mac OS Easy Open preferences file. I had a similar problem a couple of years ago and that seemed to solve it, as I recall. Hope this works! Thanks, Wes Vick G. Wesley Vick, III M.D., Ph.D. Assistant Professor Sections of Cardiology and Atherosclerosis Departments of Pediatrics and Medicine Baylor College of Medicine Associate in Pediatric Cardiology Texas Children's Hospital Phone: 713-770-5915 Fax: 713-770-5923 email: gvick@bcm.tmc.edu -------------------------------- End of nih-image-d Digest V99 Issue #38 *************************************** From nih-image-request@io.ece.drexel.edu Thu Feb 11 22:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA23140 for cshtest@io.ece.drexel.edu; Thu, 11 Feb 1999 22:08:31 -0500 (EST) Resent-Date: Thu, 11 Feb 1999 22:08:31 -0500 (EST) Date: Thu, 11 Feb 1999 16:57:05 -1000 From: Maaya A Yasuda X-Sender: maaya@uhunix1 To: nih-image listserve Subject: How to apply calibration data Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"zmYNA2.0.2K5.UYvms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/982 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 712 I am using NIH Image 1.61 and am having a problem making my calibration data stick. From the ANALYZE pull-down menu, I select CALIBRATE, and the calibrate menu comes up. I have a known concentrations of protein which I measure the gray level of and the numbers go into the calibration table. THe problem arises when I try to SAVE and APPLY the data to an unknown sample. How do you make NIH accept the calibration and report subsequent readings according to teh calibratation? I got some advice on this, but it did not work for my version. (The advice was to check a box that says "apply calibration", but there is no such box in the calibration window for my NIH image version). Many thanks, Maaya From nih-image-request@io.ece.drexel.edu Thu Feb 11 23:58 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA05358 for cshtest@io.ece.drexel.edu; Thu, 11 Feb 1999 23:58:07 -0500 (EST) Resent-Date: Thu, 11 Feb 1999 23:58:07 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: maaya@hawaii.edu, nih-image@io.ece.drexel.edu Date: Fri, 12 Feb 1999 15:51:44 +1100 Subject: Re: How to apply calibration data Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <2E2C86595E@rna.bio.mq.edu.au> Resent-Message-ID: <"pvN5L3.0.Q_.IAxms"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/983 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1647 >Date: Thu, 11 Feb 1999 16:57:05 -1000 >From: Maaya A Yasuda >To: nih-image listserve >Subject: How to apply calibration data > >I am using NIH Image 1.61 and am having a problem making my calibration >data stick. From the ANALYZE pull-down menu, I select CALIBRATE, and the >calibrate menu comes up. I have a known concentrations of protein which I >measure the gray level of and the numbers go into the calibration table. >THe problem arises when I try to SAVE and APPLY the data to an unknown >sample. How do you make NIH accept the calibration and report subsequent >readings according to teh calibratation? > > I got some advice on this, but it did not work for my version. >(The advice was to check a box that says "apply calibration", but there is >no such box in the calibration window for my NIH image version). > >Many thanks, Maaya > "Standards" can be save'd and open'ed to/from text files via save/open check boxes in calibrate dialogue window. Clicking OK will apply the currently chosen mode of calibration eg'2rd degree polynomial' (also including 'uncalibrated') to the current window. Density calibration of the current window can also be propagated to all open windows via Options(Propagate(Density Calibration. If you do not have a copy of the NIH-Image manual or "Image Engineering" I suggest you download one via the NIH-Image homepage http://rsb.info.nih.gov/nih-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-request@io.ece.drexel.edu Fri Feb 12 10:27 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14068 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 10:27:43 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 10:27:43 -0500 (EST) Message-ID: <36C44664.4D1F@huemul.ffyb.uba.ar> Date: Fri, 12 Feb 1999 12:19:02 -0300 From: Ruben Iacono X-Mailer: Mozilla 3.01-C-MACOS8 (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Question Content-Transfer-Encoding: 8bit Resent-Message-ID: <"g5cNI1.0.F03.qJ4ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/985 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: 246 Dear Friends I downloaded scionimage-win95 version, and I couldn´t run it because I don´t have ddraw.dll file. Could anybody help me?. Thank´s in advance Ruben F Iacono rubeniac@huemul.ffyb.uba.ar School of Biochemistry Buenos Aires University From nih-image-request@io.ece.drexel.edu Fri Feb 12 10:27 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA14110 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 10:27:58 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 10:27:58 -0500 (EST) From: Nicholas Price Sender: nprice@rpms.ac.uk Reply-To: n.price@rpms.ac.uk To: nih-image@io.ece.drexel.edu Subject: calibration of nih-image Message-ID: Date: Fri, 12 Feb 1999 15:22:27 +0000 () Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.0.7 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"Kofag2.0.-z2.vI4ns"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/984 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 723 I have installed the Scion PC version of NIH image and would like to use this to semiquantitate matrix metalloproteinase activity on zymogram gels. I am having difficulty at the calibration stage. The values measured for each step on the Kodak tablet, decrease (instead of increase) going from light to dark. Secondly, when I "plot lanes" after analysing a gel, I do not see any measurements in the boxes. I suspect the two problems may be connected. I would be very grateful if anyone could help. Nick Price ---------------------- Dr Nicholas Price, Medical Research Council Fellow, Department of Infectious Diseases, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, LONDON W12 ONN From nih-image-request@io.ece.drexel.edu Fri Feb 12 11:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA18747 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 11:08:54 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 11:08:54 -0500 (EST) Date: Fri, 12 Feb 1999 10:52:45 -0500 From: Bill Christens-Barry Subject: Q: given these coercions, why the distinctions between integer and real in var declarations? To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Content-transfer-encoding: 7BIT Resent-Message-ID: <"TMLDx2.0.Q54.dv4ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/986 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1402 Here's a macro that declares several integers and a real: macro 'test_coercion'; var anInt, aSecondInt: integer; aReal: real; begin anInt:= 3; aSecondInt:= anInt; ShowMessage('before', chr(13), 'anInt ', anInt, chr(13), 'aSecondInt ', aSecondInt); Wait(3); aReal:= 3.3; anInt:= aReal; ShowMessage('in-between', chr(13), 'anInt ', anInt, chr(13), 'aSecondInt ', aSecondInt); Wait(3); ShowMessage('final', chr(13), 'aSecondInt ', aSecondInt); end; Running this in NIH Image 1.62/fat yields a real result for the integer variable 'aSecondInt' (the values of the integer variables are shown in the info window) at one point. Why? No reassignment is made to 'aSecondInt' after it is initially set equal to the integer variable 'anInt', which at that time has an integer value). Is this a typing or ShowMessage problem? We noticed that the MakeMovie() command accepted and used a dialog-derived real value for a variable declared as an integer. Can we ever expect this variable to behave like an integer again, or are coercions persistent? And, why bother typing variables such as these as integers if they can be coerced into reals? Why not just have a single 'intOrReal' type? 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 Feb 12 11:30 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA22557 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 11:30:46 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 11:30:46 -0500 (EST) Date: Fri, 12 Feb 1999 16:13:32 +0000 (GMT) From: Jan Kreft X-Sender: sabjk@thor To: nih-image@io.ece.drexel.edu Subject: Re: Question In-Reply-To: <36C44664.4D1F@huemul.ffyb.uba.ar> Message-ID: X-MIME-Autoconverted: from 8bit to quoted-printable by thor.cf.ac.uk id QAA23005 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id LAA19717 Resent-Message-ID: <"9IWxQ2.0.Cq4.rD5ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/987 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: 714 I guess you need to install DirectX from the Microsoft website. Somewhere on the Scion image website they mention that the software requires DirectX, though it's a long time ago and I hardly remember. Hope this 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 Fri, 12 Feb 1999, Ruben Iacono wrote: > Dear Friends > I downloaded scionimage-win95 version, and I couldn´t run it because I > don´t have ddraw.dll file. Could anybody help me?. > Thank´s in advance > > Ruben F Iacono > rubeniac@huemul.ffyb.uba.ar > School of Biochemistry > Buenos Aires University > > From nih-image-request@io.ece.drexel.edu Fri Feb 12 12:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA28346 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 12:26:54 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 12:26:54 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Fri, 12 Feb 1999 11:07:57 -0600 From: "Vince Hardy" To: Subject: Nuclear stains used for density slicing 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 MAA26401 Resent-Message-ID: <"fuQX03.0.iS6.906ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/988 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 633 I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber. We are seeking to learn of a nuclear stain (or some other way) to stain (or label) various germ cell nuclei of the testis which have been embedded in Epon sectioned at 0.5 microns. Is there some kind of nuclear stain (or label) that we can use on Epon sections? Is there some way to etch or treat the sections that will cause them to take up more stain? We want to use the density slicing funtion of Image to estimate volume densities of the various nuclei. Any suggestions?? Vince Hardy Texas A&M University College Station, Texas From nih-image-request@io.ece.drexel.edu Fri Feb 12 12:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA28556 for cshtest@io.ece.drexel.edu; Fri, 12 Feb 1999 12:28:12 -0500 (EST) Resent-Date: Fri, 12 Feb 1999 12:28:12 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Fri, 12 Feb 1999 11:08:18 -0600 From: "Vince Hardy" To: Subject: Digitizing pads 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 MAA26482 Resent-Message-ID: <"fJZz51.0.wT6.V06ns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/989 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 408 I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber. We are wondering if there are any digitizing pads that work in conjuction with NIH Image whereby we can project a microscopic image directly from the microscope onto the pad, and then make diameter measurements of individual cells. Thanks for your help. Vince Hardy Texas A&M University College Station, Texas From nih-image-request@io.ece.drexel.edu Sat Feb 13 05:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA16560 for cshtest@io.ece.drexel.edu; Sat, 13 Feb 1999 05:16:39 -0500 (EST) Resent-Date: Sat, 13 Feb 1999 05:16:39 -0500 (EST) Date: Sat, 13 Feb 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199902131005.FAA14667@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"URFFH3.0.Qb3.FvKns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/990 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3727 NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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-d-request@io.ece.drexel.edu Sat Feb 13 05:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA16828; Sat, 13 Feb 1999 05:17:58 -0500 (EST) Date: Sat, 13 Feb 1999 05:17:58 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902131017.FAA16828@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #39 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/39 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: 13851 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 39 Today's Topics: How to apply calibration data [ Maaya A Yasuda ] Re: How to apply calibration data [ GJOSS@rna.bio.mq.edu.au ] calibration of nih-image [ Nicholas Price ] Question [ Ruben Iacono ] Nuclear stains used for density slic [ "Vince Hardy" ] Digitizing pads [ "Vince Hardy" ] ADMIN: list commands [ nih-image-owner@io.ece.drexel.edu ] ------------------------------ Date: Thu, 11 Feb 1999 16:57:05 -1000 From: Maaya A Yasuda To: nih-image listserve Subject: How to apply calibration data Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am using NIH Image 1.61 and am having a problem making my calibration data stick. From the ANALYZE pull-down menu, I select CALIBRATE, and the calibrate menu comes up. I have a known concentrations of protein which I measure the gray level of and the numbers go into the calibration table. THe problem arises when I try to SAVE and APPLY the data to an unknown sample. How do you make NIH accept the calibration and report subsequent readings according to teh calibratation? I got some advice on this, but it did not work for my version. (The advice was to check a box that says "apply calibration", but there is no such box in the calibration window for my NIH image version). Many thanks, Maaya ------------------------------ Date: Fri, 12 Feb 1999 15:51:44 +1100 From: GJOSS@rna.bio.mq.edu.au To: maaya@hawaii.edu, nih-image@io.ece.drexel.edu Subject: Re: How to apply calibration data Message-ID: <2E2C86595E@rna.bio.mq.edu.au> >Date: Thu, 11 Feb 1999 16:57:05 -1000 >From: Maaya A Yasuda >To: nih-image listserve >Subject: How to apply calibration data > >I am using NIH Image 1.61 and am having a problem making my calibration >data stick. From the ANALYZE pull-down menu, I select CALIBRATE, and the >calibrate menu comes up. I have a known concentrations of protein which I >measure the gray level of and the numbers go into the calibration table. >THe problem arises when I try to SAVE and APPLY the data to an unknown >sample. How do you make NIH accept the calibration and report subsequent >readings according to teh calibratation? > > I got some advice on this, but it did not work for my version. >(The advice was to check a box that says "apply calibration", but there is >no such box in the calibration window for my NIH image version). > >Many thanks, Maaya > "Standards" can be save'd and open'ed to/from text files via save/open check boxes in calibrate dialogue window. Clicking OK will apply the currently chosen mode of calibration eg'2rd degree polynomial' (also including 'uncalibrated') to the current window. Density calibration of the current window can also be propagated to all open windows via Options(Propagate(Density Calibration. If you do not have a copy of the NIH-Image manual or "Image Engineering" I suggest you download one via the NIH-Image homepage http://rsb.info.nih.gov/nih-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 ------------------------------ Date: Fri, 12 Feb 1999 15:22:27 +0000 () From: Nicholas Price To: nih-image@io.ece.drexel.edu Subject: calibration of nih-image Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I have installed the Scion PC version of NIH image and would like to use this to semiquantitate matrix metalloproteinase activity on zymogram gels. I am having difficulty at the calibration stage. The values measured for each step on the Kodak tablet, decrease (instead of increase) going from light to dark. Secondly, when I "plot lanes" after analysing a gel, I do not see any measurements in the boxes. I suspect the two problems may be connected. I would be very grateful if anyone could help. Nick Price ---------------------- Dr Nicholas Price, Medical Research Council Fellow, Department of Infectious Diseases, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, LONDON W12 ONN ------------------------------ Date: Fri, 12 Feb 1999 12:19:02 -0300 From: Ruben Iacono To: nih-image@io.ece.drexel.edu Subject: Question Message-ID: <36C44664.4D1F@huemul.ffyb.uba.ar> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Friends I downloaded scionimage-win95 version, and I couldn´t run it because I don´t have ddraw.dll file. Could anybody help me?. Thank´s in advance Ruben F Iacono rubeniac@huemul.ffyb.uba.ar School of Biochemistry Buenos Aires University ------------------------------ Date: Fri, 12 Feb 1999 10:52:45 -0500 From: Bill Christens-Barry To: nih-image@io.ece.drexel.edu Subject: Q: given these coercions, why the distinctions between integer and real in var declarations? Message-id: Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Here's a macro that declares several integers and a real: macro 'test_coercion'; var anInt, aSecondInt: integer; aReal: real; begin anInt:= 3; aSecondInt:= anInt; ShowMessage('before', chr(13), 'anInt ', anInt, chr(13), 'aSecondInt ', aSecondInt); Wait(3); aReal:= 3.3; anInt:= aReal; ShowMessage('in-between', chr(13), 'anInt ', anInt, chr(13), 'aSecondInt ', aSecondInt); Wait(3); ShowMessage('final', chr(13), 'aSecondInt ', aSecondInt); end; Running this in NIH Image 1.62/fat yields a real result for the integer variable 'aSecondInt' (the values of the integer variables are shown in the info window) at one point. Why? No reassignment is made to 'aSecondInt' after it is initially set equal to the integer variable 'anInt', which at that time has an integer value). Is this a typing or ShowMessage problem? We noticed that the MakeMovie() command accepted and used a dialog-derived real value for a variable declared as an integer. Can we ever expect this variable to behave like an integer again, or are coercions persistent? And, why bother typing variables such as these as integers if they can be coerced into reals? Why not just have a single 'intOrReal' type? Thanks. Bill Christens-Barry ------------------------- Bill Christens-Barry, PhD Johns Hopkins University Applied Physics Laboratory wacb@aplcomm.jhuapl.edu ------------------------- ------------------------------ Date: Fri, 12 Feb 1999 16:13:32 +0000 (GMT) From: Jan Kreft To: nih-image@io.ece.drexel.edu Subject: Re: Question Message-ID: Content-type: text/PLAIN; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit I guess you need to install DirectX from the Microsoft website. Somewhere on the Scion image website they mention that the software requires DirectX, though it's a long time ago and I hardly remember. Hope this 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 Fri, 12 Feb 1999, Ruben Iacono wrote: > Dear Friends > I downloaded scionimage-win95 version, and I couldn´t run it because I > don´t have ddraw.dll file. Could anybody help me?. > Thank´s in advance > > Ruben F Iacono > rubeniac@huemul.ffyb.uba.ar > School of Biochemistry > Buenos Aires University > > ------------------------------ Date: Fri, 12 Feb 1999 11:07:57 -0600 From: "Vince Hardy" To: Subject: Nuclear stains used for density slicing Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber. We are seeking to learn of a nuclear stain (or some other way) to stain (or label) various germ cell nuclei of the testis which have been embedded in Epon sectioned at 0.5 microns. Is there some kind of nuclear stain (or label) that we can use on Epon sections? Is there some way to etch or treat the sections that will cause them to take up more stain? We want to use the density slicing funtion of Image to estimate volume densities of the various nuclei. Any suggestions?? Vince Hardy Texas A&M University College Station, Texas ------------------------------ Date: Fri, 12 Feb 1999 11:08:18 -0600 From: "Vince Hardy" To: Subject: Digitizing pads Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber. We are wondering if there are any digitizing pads that work in conjuction with NIH Image whereby we can project a microscopic image directly from the microscope onto the pad, and then make diameter measurements of individual cells. Thanks for your help. Vince Hardy Texas A&M University College Station, Texas ------------------------------ Date: Sat, 13 Feb 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: <199902131005.FAA14667@io.ece.drexel.edu> NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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 V99 Issue #39 *************************************** From nih-image-request@io.ece.drexel.edu Sat Feb 13 22:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA15489 for cshtest@io.ece.drexel.edu; Sat, 13 Feb 1999 22:23:50 -0500 (EST) Resent-Date: Sat, 13 Feb 1999 22:23:50 -0500 (EST) From: gjoss@rna.bio.mq.edu.au Comments: Authenticated sender is To: nih-image@io.ece.drexel.edu, wacb@aplcomm.jhuapl.edu Date: Sun, 14 Feb 1999 11:23:23 +0000 Subject: Re: Q: given these coercions, why the distinctions between inte Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <5C97CF1623@rna.bio.mq.edu.au> Resent-Message-ID: <"yDTnt.0.3Q3.GyZns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/991 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3513 > Date: Fri, 12 Feb 1999 10:52:45 -0500 > From: Bill Christens-Barry > Subject: Q: given these coercions, why the distinctions between integer and > real in var declarations? > To: nih-image@io.ece.drexel.edu > Reply-to: nih-image@io.ece.drexel.edu > Here's a macro that declares several integers and a real: > > macro 'test_coercion'; > var > anInt, aSecondInt: integer; > aReal: real; > begin > anInt:= 3; > aSecondInt:= anInt; > ShowMessage('before', chr(13), 'anInt ', anInt, chr(13), > 'aSecondInt ', aSecondInt); > Wait(3); > aReal:= 3.3; > anInt:= aReal; > ShowMessage('in-between', chr(13), 'anInt ', anInt, chr(13), > 'aSecondInt ', aSecondInt); > Wait(3); > ShowMessage('final', chr(13), 'aSecondInt ', aSecondInt); > end; > > Running this in NIH Image 1.62/fat yields a real result for the integer > variable 'aSecondInt' (the values of the integer variables are shown in the > info window) at one point. > > Why? No reassignment is made to 'aSecondInt' after it is initially set > equal to the integer variable 'anInt', which at that time has an integer > value). Is this a typing or ShowMessage problem? > > We noticed that the MakeMovie() command accepted and used a dialog-derived > real value for a variable declared as an integer. Can we ever expect this > variable to behave like an integer again, or are coercions persistent? And, > why bother typing variables such as these as integers if they can be > coerced into reals? Why not just have a single 'intOrReal' type? > > Thanks. > > Bill Christens-Barry > ------------------------- > Bill Christens-Barry, PhD > Johns Hopkins University Applied Physics Laboratory > wacb@aplcomm.jhuapl.edu > ------------------------- Bill, I am just checking out setup of a pop-mailer at home so I dont have ready access to references but I recall that: the macro appendix preamble in the manual states that all macro numeric variables are processed as 4 byte 'real's regardless of specification as 'real' or 'integer'. (although, as I recall a problem, numeric macro constants are not stored with that precision). Coercion to integer only occurs when values are assigned to intrinsically integer items eg in putpixel(x,y,c),lineBuffer[i],redLut[i], rX[i] etc x,y,c,i are processed as integers. Also, with 'for' loop variables, the increment is an implied integer one but the variable may be (inadvertantly) fractional. Explicit coercion can be controled using the round() and trunc() functions. There is also a mod() {modulus} function. The point of having 'real' and 'integer' variable specifications is to maximise the compatibility between macro code and Pascal. The idea is to minimise the need to change working tested macro code if/when they are converted into compiled Pascal code for 'User.p' implementation. Another aspect of this is the formating of numeric values for output eg via the ShowMessage() command. When NIH-Image switched from being THINK Pascal to Metroworks Pascal, (ie after V1.55?) the rules governing default format specification of output numeric values seemed to change to a less convenient arrangement. The formatting using a ':f:d' {fieldwidth,decimals}needs to be reasserted for integers to output in the 'desired' form after a real is output. eg ShowMessage('final\aSecondInt ', aSecondInt:0); ShowMessage('final\aSecondInt', aSecondInt:4:0); {note also '\' for chr(13)} From nih-image-d-request@io.ece.drexel.edu Sun Feb 14 13:47 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA07396; Sun, 14 Feb 1999 13:47:47 -0500 (EST) Date: Sun, 14 Feb 1999 13:47:47 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902141847.NAA07396@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #40 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/40 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: 4963 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 40 Today's Topics: Re: Q: given these coercions, why th [ gjoss@rna.bio.mq.edu.au ] question re. features of ImageJ [ "Samuel Zeichner" > Date: Fri, 12 Feb 1999 10:52:45 -0500 > From: Bill Christens-Barry > Subject: Q: given these coercions, why the distinctions between integer and > real in var declarations? > To: nih-image@io.ece.drexel.edu > Reply-to: nih-image@io.ece.drexel.edu > Here's a macro that declares several integers and a real: > > macro 'test_coercion'; > var > anInt, aSecondInt: integer; > aReal: real; > begin > anInt:= 3; > aSecondInt:= anInt; > ShowMessage('before', chr(13), 'anInt ', anInt, chr(13), > 'aSecondInt ', aSecondInt); > Wait(3); > aReal:= 3.3; > anInt:= aReal; > ShowMessage('in-between', chr(13), 'anInt ', anInt, chr(13), > 'aSecondInt ', aSecondInt); > Wait(3); > ShowMessage('final', chr(13), 'aSecondInt ', aSecondInt); > end; > > Running this in NIH Image 1.62/fat yields a real result for the integer > variable 'aSecondInt' (the values of the integer variables are shown in the > info window) at one point. > > Why? No reassignment is made to 'aSecondInt' after it is initially set > equal to the integer variable 'anInt', which at that time has an integer > value). Is this a typing or ShowMessage problem? > > We noticed that the MakeMovie() command accepted and used a dialog-derived > real value for a variable declared as an integer. Can we ever expect this > variable to behave like an integer again, or are coercions persistent? And, > why bother typing variables such as these as integers if they can be > coerced into reals? Why not just have a single 'intOrReal' type? > > Thanks. > > Bill Christens-Barry > ------------------------- > Bill Christens-Barry, PhD > Johns Hopkins University Applied Physics Laboratory > wacb@aplcomm.jhuapl.edu > ------------------------- Bill, I am just checking out setup of a pop-mailer at home so I dont have ready access to references but I recall that: the macro appendix preamble in the manual states that all macro numeric variables are processed as 4 byte 'real's regardless of specification as 'real' or 'integer'. (although, as I recall a problem, numeric macro constants are not stored with that precision). Coercion to integer only occurs when values are assigned to intrinsically integer items eg in putpixel(x,y,c),lineBuffer[i],redLut[i], rX[i] etc x,y,c,i are processed as integers. Also, with 'for' loop variables, the increment is an implied integer one but the variable may be (inadvertantly) fractional. Explicit coercion can be controled using the round() and trunc() functions. There is also a mod() {modulus} function. The point of having 'real' and 'integer' variable specifications is to maximise the compatibility between macro code and Pascal. The idea is to minimise the need to change working tested macro code if/when they are converted into compiled Pascal code for 'User.p' implementation. Another aspect of this is the formating of numeric values for output eg via the ShowMessage() command. When NIH-Image switched from being THINK Pascal to Metroworks Pascal, (ie after V1.55?) the rules governing default format specification of output numeric values seemed to change to a less convenient arrangement. The formatting using a ':f:d' {fieldwidth,decimals}needs to be reasserted for integers to output in the 'desired' form after a real is output. eg ShowMessage('final\aSecondInt ', aSecondInt:0); ShowMessage('final\aSecondInt', aSecondInt:4:0); {note also '\' for chr(13)} ------------------------------ Date: Sun, 14 Feb 1999 10:37:53 PST From: "Samuel Zeichner" To: nih-image@io.ece.drexel.edu Subject: question re. features of ImageJ Message-ID: <19990214183753.24163.qmail@hotmail.com> Content-type: text/plain Perhaps someone can enlighten me. I have been using NIH Image to process medical images. I frequently use the "Stacks Menu" to register images, project and reslice. Recently, I explored the features of ImageJ v0.98. Image J does not appear to support these functions. Can anyone tell me if these functions are possible with ImageJ? Can they be implemented with macros or plugins or must code be written? Thanks ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com -------------------------------- End of nih-image-d Digest V99 Issue #40 *************************************** From nih-image-request@io.ece.drexel.edu Sun Feb 14 13:50 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA07915 for cshtest@io.ece.drexel.edu; Sun, 14 Feb 1999 13:50:42 -0500 (EST) Resent-Date: Sun, 14 Feb 1999 13:50:42 -0500 (EST) Message-ID: <19990214183753.24163.qmail@hotmail.com> X-Originating-IP: [204.58.30.2] From: "Samuel Zeichner" To: nih-image@io.ece.drexel.edu Subject: question re. features of ImageJ Date: Sun, 14 Feb 1999 10:37:53 PST Mime-Version: 1.0 Resent-Message-ID: <"ZcxKV1.0.QT1.pWnns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/992 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 529 Perhaps someone can enlighten me. I have been using NIH Image to process medical images. I frequently use the "Stacks Menu" to register images, project and reslice. Recently, I explored the features of ImageJ v0.98. Image J does not appear to support these functions. Can anyone tell me if these functions are possible with ImageJ? Can they be implemented with macros or plugins or must code be written? Thanks ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Sun Feb 14 19:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA20094 for cshtest@io.ece.drexel.edu; Sun, 14 Feb 1999 19:41:22 -0500 (EST) Resent-Date: Sun, 14 Feb 1999 19:41:22 -0500 (EST) Message-Id: <3.0.5.32.19990214193534.008c34e0@codon.nih.gov> X-Sender: wayne@codon.nih.gov X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sun, 14 Feb 1999 19:35:34 -0500 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: question re. features of ImageJ In-Reply-To: <19990214183753.24163.qmail@hotmail.com> Mime-Version: 1.0 Resent-Message-ID: <"AhiCJ3.0.nU4.8fsns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/993 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 738 At 10:37 AM 2/14/99 PST, you wrote: >Perhaps someone can enlighten me. I have been using NIH Image to process >medical images. I frequently use the "Stacks Menu" to register images, >project and reslice. Recently, I explored the features of ImageJ v0.98. >Image J does not appear to support these functions. Can anyone tell me >if these functions are possible with ImageJ? Can they be implemented >with macros or plugins or must code be written? ImageJ, which is a work in progress, does not yet have Project, Register or Reslice commands. These commands could be implemented as plug-ins by translating the NIH Image Pascal source to Java (macros would be too slow), but I don't expect to get to this for at least a year. -wayne From nih-image-request@io.ece.drexel.edu Mon Feb 15 01:31 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id BAA02032 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 01:31:01 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 01:31:01 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 15 Feb 1999 08:26:04 +0200 To: nih-image@io.ece.drexel.edu From: langsjo@hytti.uku.fi (Teemu =?iso-8859-1?Q?L=E5ngsj=F6?= ) Subject: stereology/morphometry lists... Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id BAA00660 Resent-Message-ID: <"75yLS2.0.RA.Xpxns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/994 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: 234 Hello! My question doesn't actually relate to nih-image but perhaps some of the list users can answer it. Is there any mailing list just for stereology and/or morphometry ? Thanks in advance. Yours, Teemu Långsjö From nih-image-request@io.ece.drexel.edu Mon Feb 15 03:40 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA17294 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 03:40:38 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 03:40:38 -0500 (EST) X-Sender: steinr@pop.chembio.ntnu.no Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Mon, 15 Feb 1999 10:27:50 +0200 To: nih-image@io.ece.drexel.edu From: Stein Roervik Subject: Re: anyone ever implement auto-run macros? Resent-Message-ID: <"TNez_1.0.9p3.5gzns"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/995 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2148 >Years ago there was interest in creating the capacity for NIH Image to >automaticly run a macro at startup. Did anyone ever implement this auto-run >capability? > >What would be needed to implement this? Would it make sense for a user to >specify in preferences which macro should be run at startup, or should it >have some specified name? The auto-load feature in NIH Image requires a >macro named 'Image macros' in the folder containing the application. > Some years ago I implemented this in my own modified version of NIH image. The way I did it was to use a reserved key in the macro shortcut brackets and have the code that loads the macro from file automcatically if that key was found. I used a tilde ~ for this feature. Only eight lines of code is required as additions to the NIH source code. You need a forward/external declaration since the load macro function is declared before the run macro function. Bad programming practice, but it works well. Note that the autorun macro can be called anything you like. In source file Macros2.p, add these lines: const AutoRunKey = '~'; {a key that is unlikely to be used for other macros} procedure RunMacro (nMacro: integer); external; {defined in Macros1.p} procedure LoadMacros2; var ... i: integer; begin ... for i := 1 to nMacros do if (MacroKey[i] = AutoRunKey) then begin RunMacro(i); exit(LoadMacros2); end; end; {LoadMacros2} In your macro file, declare your autorun macro as: macro 'autorun macro [~]'; begin ... end; The autorun feature is very useful for initializing variables. Beware of making something happen here because that may confuse unaware users. +---------------------------------------------------------+ | 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 Feb 15 11:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA11308 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 11:15:21 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 11:15:21 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Mon, 15 Feb 1999 09:44:23 -0600 To: nih-image@io.ece.drexel.edu From: "John A. Cooper" Subject: Change defaults in Save As? Resent-Message-ID: <"YZcek1.0.8p1.S34os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/996 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1075 We routinely generate large stacks that we immediately convert to quicktime, in order to make them smaller and to perform subsequent manipulations. We do a Save As... and need to change many of the settings. At present, we use a QuicKeys macro to do this. It works OK but is not very efficient and occasionally goes wacko, needing to be re-recorded. Is there a way to have the Save As... options be changed permanently? Presumably, we could edit the source code to do this. If so, which section? How difficult will this be if we have little experience? The academic price for Code Warrior is pretty reasonable, I just don't want to waste too much time. TIA. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ John Cooper Dept. of Cell Biology & Physiology Washington University School of Medicine St. Louis, MO 63110-1093 US Post Office address: Box 8228, 660 S Euclid Ave Shipping (FedEx) address: Dept of Cell Biology, 4566 Scott Ave Phone (314) 362-3964 Fax (314) 362-0098 E-mail: jcooper@cellbio.wustl.edu World Wide Web site: http://www.cooperlab.wustl.edu/ From nih-image-d-request@io.ece.drexel.edu Mon Feb 15 11:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA12463; Mon, 15 Feb 1999 11:25:22 -0500 (EST) Date: Mon, 15 Feb 1999 11:25:22 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902151625.LAA12463@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #41 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/41 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: 5968 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 41 Today's Topics: Re: question re. features of ImageJ [ Wayne Rasband ] stereology/morphometry lists... [ langsjo@hytti.uku.fi (Teemu =?iso-8 ] Re: anyone ever implement auto-run m [ Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: question re. features of ImageJ Message-Id: <3.0.5.32.19990214193534.008c34e0@codon.nih.gov> Content-Type: text/plain; charset="us-ascii" At 10:37 AM 2/14/99 PST, you wrote: >Perhaps someone can enlighten me. I have been using NIH Image to process >medical images. I frequently use the "Stacks Menu" to register images, >project and reslice. Recently, I explored the features of ImageJ v0.98. >Image J does not appear to support these functions. Can anyone tell me >if these functions are possible with ImageJ? Can they be implemented >with macros or plugins or must code be written? ImageJ, which is a work in progress, does not yet have Project, Register or Reslice commands. These commands could be implemented as plug-ins by translating the NIH Image Pascal source to Java (macros would be too slow), but I don't expect to get to this for at least a year. -wayne ------------------------------ Date: Mon, 15 Feb 1999 08:26:04 +0200 From: langsjo@hytti.uku.fi (Teemu =?iso-8859-1?Q?L=E5ngsj=F6?= ) To: nih-image@io.ece.drexel.edu Subject: stereology/morphometry lists... Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hello! My question doesn't actually relate to nih-image but perhaps some of the list users can answer it. Is there any mailing list just for stereology and/or morphometry ? Thanks in advance. Yours, Teemu Långsjö ------------------------------ Date: Mon, 15 Feb 1999 10:27:50 +0200 From: Stein Roervik To: nih-image@io.ece.drexel.edu Subject: Re: anyone ever implement auto-run macros? Message-Id: Content-Type: text/plain; charset="us-ascii" >Years ago there was interest in creating the capacity for NIH Image to >automaticly run a macro at startup. Did anyone ever implement this auto-run >capability? > >What would be needed to implement this? Would it make sense for a user to >specify in preferences which macro should be run at startup, or should it >have some specified name? The auto-load feature in NIH Image requires a >macro named 'Image macros' in the folder containing the application. > Some years ago I implemented this in my own modified version of NIH image. The way I did it was to use a reserved key in the macro shortcut brackets and have the code that loads the macro from file automcatically if that key was found. I used a tilde ~ for this feature. Only eight lines of code is required as additions to the NIH source code. You need a forward/external declaration since the load macro function is declared before the run macro function. Bad programming practice, but it works well. Note that the autorun macro can be called anything you like. In source file Macros2.p, add these lines: const AutoRunKey = '~'; {a key that is unlikely to be used for other macros} procedure RunMacro (nMacro: integer); external; {defined in Macros1.p} procedure LoadMacros2; var ... i: integer; begin ... for i := 1 to nMacros do if (MacroKey[i] = AutoRunKey) then begin RunMacro(i); exit(LoadMacros2); end; end; {LoadMacros2} In your macro file, declare your autorun macro as: macro 'autorun macro [~]'; begin ... end; The autorun feature is very useful for initializing variables. Beware of making something happen here because that may confuse unaware users. +---------------------------------------------------------+ | 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, 15 Feb 1999 09:44:23 -0600 From: "John A. Cooper" To: nih-image@io.ece.drexel.edu Subject: Change defaults in Save As? Message-Id: Content-Type: text/plain; charset="us-ascii" We routinely generate large stacks that we immediately convert to quicktime, in order to make them smaller and to perform subsequent manipulations. We do a Save As... and need to change many of the settings. At present, we use a QuicKeys macro to do this. It works OK but is not very efficient and occasionally goes wacko, needing to be re-recorded. Is there a way to have the Save As... options be changed permanently? Presumably, we could edit the source code to do this. If so, which section? How difficult will this be if we have little experience? The academic price for Code Warrior is pretty reasonable, I just don't want to waste too much time. TIA. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ John Cooper Dept. of Cell Biology & Physiology Washington University School of Medicine St. Louis, MO 63110-1093 US Post Office address: Box 8228, 660 S Euclid Ave Shipping (FedEx) address: Dept of Cell Biology, 4566 Scott Ave Phone (314) 362-3964 Fax (314) 362-0098 E-mail: jcooper@cellbio.wustl.edu World Wide Web site: http://www.cooperlab.wustl.edu/ -------------------------------- End of nih-image-d Digest V99 Issue #41 *************************************** From nih-image-request@io.ece.drexel.edu Mon Feb 15 12:30 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA19413 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 12:30:23 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 12:30:23 -0500 (EST) Message-Id: <3.0.5.32.19990215115822.009702a0@mailserver.aecom.yu.edu> X-Sender: cammer@mailserver.aecom.yu.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Mon, 15 Feb 1999 11:58:22 -0800 To: nih-image@io.ece.drexel.edu From: Michael Cammer Subject: Re: Change defaults in Save As? In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"8_lVK3.0.Fq3.E55os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/997 X-Loop: nih-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 >Is there a way to have the Save As... options be changed permanently? Write a macro that sets the SaveAs options you need. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* From nih-image-request@io.ece.drexel.edu Mon Feb 15 12:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA21526 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 12:44:23 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 12:44:23 -0500 (EST) Message-ID: <36C85827.4CDF@pop.uky.edu> Date: Mon, 15 Feb 1999 12:23:50 -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: Re: anyone ever implement auto-run macros? Content-Transfer-Encoding: 7bit Resent-Message-ID: <"1lEjr3.0.4Y4.4W5os"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/998 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 122 NIH Image VDM (Perceptrics Corp; available from Image ftp site) runs the first macro in "Image Macros" after launch. AG From nih-image-request@io.ece.drexel.edu Mon Feb 15 22:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA23882 for cshtest@io.ece.drexel.edu; Mon, 15 Feb 1999 22:02:56 -0500 (EST) Resent-Date: Mon, 15 Feb 1999 22:02:56 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: cammer@aecom.yu.edu, jcooper@cellbio.wustl.edu, nih-image@io.ece.drexel.edu Date: Tue, 16 Feb 1999 11:51:42 +1100 Subject: Re: Change defaults in Save As? Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <8A32D37176@rna.bio.mq.edu.au> Resent-Message-ID: <"Z5_fj.0.TT5.vqDos"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/999 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2783 >Date: Mon, 15 Feb 1999 11:58:22 -0800 >To: nih-image@io.ece.drexel.edu >From: Michael Cammer >Subject: Re: Change defaults in Save As? > >>Is there a way to have the Save As... options be changed permanently? > >Write a macro that sets the SaveAs options you need. >******************************************************* >* Michael Cammer Analytical Imaging Facility * >* Albert Einstein College of Medicine * >* Bronx, NY 10461 (718) 430-2890 * >* work URL: http://www.ca.aecom.yu.edu/aif/ * >* personal URL: http://cammer.home.mindspring.com/ * >******************************************************* > While a macro such as: macro'/m SaveAs quickTime';begin selectPic(picNumber);setSaveAs('quick');saveAs(windowtitle,'.Moov');end will initiate the 'saveas', there is no way (that I can determine) that will allow the Quicktime compression parameters to be set via macros or to avoid the dialogue box. As "John A. Cooper" said: >We do a Save As... and need to change many of the settings. At present, we >use a QuicKeys macro to do this. It works OK but is not very efficient and >occasionally goes wacko, needing to be re-recorded. it would be desirable to automatically setup parameters. The source module File2.p uses .... ToolUtils, Resources, ... Components, ImageCompression, Movies, QuickTimeComponents,...GestaltEqu function OpenMovieToolbox:boolean; ..... if Gestalt(gestaltQuickTime, result) <> noErr then begin ShowMessage('QuickTime Required'); ..... procedure SaveAsQuickTime (fname: str255; fRefNum: integer); {Written by Eric A. Shelden (shelden@umich.edu) 3/23/94} .............. myComponentInstance := OpenDefaultComponent('scdi', 'imag'); myResult := SCRequestSequenceSettings(myComponentInstance); ..... myResult := SCGetInfo(myComponentInstance, 'sptl', ptr(@theSpaceSettings)); myResult := SCGetInfo(myComponentInstance, scTemporalSettingsType , ptr(@theTimeSettings)); myResult := SCGetInfo(myComponentInstance, scDataRateSettingsType , ptr(@theRateSettings)); myResult := CloseComponent(myComponentInstance); The above code appears to access system (ie external to NIH-Image source) QuickTime services. Perhaps a knowledgeable Mac programmer could tell us how to access and modify default settings presumeablely accessed via myComponentInstance := OpenDefaultComponent('scdi', 'imag'); Given the string references, they are presumeably keys in a control file somewhere? 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 Feb 16 06:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24878; Tue, 16 Feb 1999 06:17:12 -0500 (EST) Date: Tue, 16 Feb 1999 06:17:12 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902161117.GAA24878@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #42 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/42 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: 4813 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 42 Today's Topics: Re: Change defaults in Save As? [ Michael Cammer To: nih-image@io.ece.drexel.edu Subject: Re: Change defaults in Save As? Message-Id: <3.0.5.32.19990215115822.009702a0@mailserver.aecom.yu.edu> Content-Type: text/plain; charset="us-ascii" >Is there a way to have the Save As... options be changed permanently? Write a macro that sets the SaveAs options you need. ******************************************************* * Michael Cammer Analytical Imaging Facility * * Albert Einstein College of Medicine * * Bronx, NY 10461 (718) 430-2890 * * work URL: http://www.ca.aecom.yu.edu/aif/ * * personal URL: http://cammer.home.mindspring.com/ * ******************************************************* ------------------------------ Date: Mon, 15 Feb 1999 12:23:50 -0500 From: alex gimelbrant To: NIH-Image mailing list Subject: Re: anyone ever implement auto-run macros? Message-ID: <36C85827.4CDF@pop.uky.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NIH Image VDM (Perceptrics Corp; available from Image ftp site) runs the first macro in "Image Macros" after launch. AG ------------------------------ Date: Tue, 16 Feb 1999 11:51:42 +1100 From: GJOSS@rna.bio.mq.edu.au To: cammer@aecom.yu.edu, jcooper@cellbio.wustl.edu, nih-image@io.ece.drexel.edu Subject: Re: Change defaults in Save As? Message-ID: <8A32D37176@rna.bio.mq.edu.au> >Date: Mon, 15 Feb 1999 11:58:22 -0800 >To: nih-image@io.ece.drexel.edu >From: Michael Cammer >Subject: Re: Change defaults in Save As? > >>Is there a way to have the Save As... options be changed permanently? > >Write a macro that sets the SaveAs options you need. >******************************************************* >* Michael Cammer Analytical Imaging Facility * >* Albert Einstein College of Medicine * >* Bronx, NY 10461 (718) 430-2890 * >* work URL: http://www.ca.aecom.yu.edu/aif/ * >* personal URL: http://cammer.home.mindspring.com/ * >******************************************************* > While a macro such as: macro'/m SaveAs quickTime';begin selectPic(picNumber);setSaveAs('quick');saveAs(windowtitle,'.Moov');end will initiate the 'saveas', there is no way (that I can determine) that will allow the Quicktime compression parameters to be set via macros or to avoid the dialogue box. As "John A. Cooper" said: >We do a Save As... and need to change many of the settings. At present, we >use a QuicKeys macro to do this. It works OK but is not very efficient and >occasionally goes wacko, needing to be re-recorded. it would be desirable to automatically setup parameters. The source module File2.p uses .... ToolUtils, Resources, ... Components, ImageCompression, Movies, QuickTimeComponents,...GestaltEqu function OpenMovieToolbox:boolean; ..... if Gestalt(gestaltQuickTime, result) <> noErr then begin ShowMessage('QuickTime Required'); ..... procedure SaveAsQuickTime (fname: str255; fRefNum: integer); {Written by Eric A. Shelden (shelden@umich.edu) 3/23/94} .............. myComponentInstance := OpenDefaultComponent('scdi', 'imag'); myResult := SCRequestSequenceSettings(myComponentInstance); ..... myResult := SCGetInfo(myComponentInstance, 'sptl', ptr(@theSpaceSettings)); myResult := SCGetInfo(myComponentInstance, scTemporalSettingsType , ptr(@theTimeSettings)); myResult := SCGetInfo(myComponentInstance, scDataRateSettingsType , ptr(@theRateSettings)); myResult := CloseComponent(myComponentInstance); The above code appears to access system (ie external to NIH-Image source) QuickTime services. Perhaps a knowledgeable Mac programmer could tell us how to access and modify default settings presumeablely accessed via myComponentInstance := OpenDefaultComponent('scdi', 'imag'); Given the string references, they are presumeably keys in a control file somewhere? 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 V99 Issue #42 *************************************** From nih-image-request@io.ece.drexel.edu Tue Feb 16 18:51 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA20649 for cshtest@io.ece.drexel.edu; Tue, 16 Feb 1999 18:51:46 -0500 (EST) Resent-Date: Tue, 16 Feb 1999 18:51:46 -0500 (EST) Mime-Version: 1.0 X-Sender: scm@128.250.6.196 Message-Id: In-Reply-To: <8A32D37176@rna.bio.mq.edu.au> Date: Wed, 17 Feb 1999 10:38:53 +1100 To: nih-image@io.ece.drexel.edu From: Steve Martin Subject: Re: Change defaults in Save As? Resent-Message-ID: <"OCyT83.0.og4.P6Wos"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1000 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3567 Michael, you might wish to check http://pascal-central.com/merlin.html for my Codewarrior Make QT movie project. It is a Pascal port of the example Inside Macintosh routines (which Apple now publishes in C :-( ), and would provide a simple starting point for trialling changes in movie options, before moving on to Image. The Inside Macintosh volumes on qt are freely available as PDF files from and good luck, Steve At 11:51 AM +1100 on 16/2/99, GJOSS@rna.bio.mq.edu.au wrote: > >Date: Mon, 15 Feb 1999 11:58:22 -0800 > >To: nih-image@io.ece.drexel.edu > >From: Michael Cammer > >Subject: Re: Change defaults in Save As? > > > >>Is there a way to have the Save As... options be changed permanently? > > > >Write a macro that sets the SaveAs options you need. > >******************************************************* > >* Michael Cammer Analytical Imaging Facility * > >* Albert Einstein College of Medicine * > >* Bronx, NY 10461 (718) 430-2890 * > >* work URL: http://www.ca.aecom.yu.edu/aif/ * > >* personal URL: http://cammer.home.mindspring.com/ * > >******************************************************* > > > > While a macro such as: > > macro'/m SaveAs quickTime';begin > selectPic(picNumber);setSaveAs('quick');saveAs(windowtitle,'.Moov');end > > will initiate the 'saveas', there is no way (that I can determine) that >will allow > the Quicktime compression parameters to be set via macros or to avoid the >dialogue > box. > > As "John A. Cooper" said: > > >We do a Save As... and need to change many of the settings. At present, we > >use a QuicKeys macro to do this. It works OK but is not very efficient and > >occasionally goes wacko, needing to be re-recorded. > > it would be desirable to automatically setup parameters. > > The source module File2.p > uses > .... ToolUtils, Resources, > ... Components, ImageCompression, > Movies, QuickTimeComponents,...GestaltEqu > > function OpenMovieToolbox:boolean; > ..... > if Gestalt(gestaltQuickTime, result) <> noErr then begin > ShowMessage('QuickTime Required'); > ..... > > procedure SaveAsQuickTime (fname: str255; fRefNum: integer); > {Written by Eric A. Shelden (shelden@umich.edu) 3/23/94} > .............. > myComponentInstance := >OpenDefaultComponent('scdi', 'imag'); > myResult := >SCRequestSequenceSettings(myComponentInstance); > ..... > myResult := SCGetInfo(myComponentInstance, 'sptl', >ptr(@theSpaceSettings)); > myResult := SCGetInfo(myComponentInstance, scTemporalSettingsType > > , ptr(@theTimeSettings)); > myResult := SCGetInfo(myComponentInstance, scDataRateSettingsType > , ptr(@theRateSettings)); > myResult := CloseComponent(myComponentInstance); > > The above code appears to access system (ie external to NIH-Image source) >QuickTime > services. > > Perhaps a knowledgeable Mac programmer could tell us how to access and >modify > default settings presumeablely accessed via > myComponentInstance := OpenDefaultComponent('scdi', 'imag'); > > Given the string references, they are presumeably keys in a control file >somewhere? > > > > 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 Feb 16 23:03 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA17813 for cshtest@io.ece.drexel.edu; Tue, 16 Feb 1999 23:03:13 -0500 (EST) Resent-Date: Tue, 16 Feb 1999 23:03:13 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: VHardy@cvm.tamu.edu, nih-image@io.ece.drexel.edu Date: Wed, 17 Feb 1999 14:55:57 +1100 Subject: Re: Digitizing pads Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"E0uA22.0.C_3.ipZos"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1001 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1471 >Date: Fri, 12 Feb 1999 11:08:18 -0600 >From: "Vince Hardy" >To: >Subject: Digitizing pads > >I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame >grabber. We are wondering if there are any digitizing pads that work in >conjuction with NIH Image whereby we can pr >ject a microscopic image directly from the microscope onto the pad, and then make >diameter measurements of individual cells. Thanks for your help. > >Vince Hardy >Texas A&M University >College Station, Texas > I am rather bemused by your post but cant resist a reply :-) If you have a "Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber" then presumeably you have a c-mount video camera mounted on your microscope and connected to the "LG-3 frame grabber";that is what the "LG-3 frame grabber" is for. You can then "project a microscopic image directly from the microscope onto the " computer monitor ", and then make diameter measurements of individual cells " using NIH Image 1.61 by a number of alternative methods eg manual selection using mouse, densitySlice/analyzeParticles etc. I cant imagine why you would want to go back to the old technology of a digitizing pad. Am I missing something? (again :-) 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 Feb 17 05:34 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA01097 for cshtest@io.ece.drexel.edu; Wed, 17 Feb 1999 05:34:32 -0500 (EST) Resent-Date: Wed, 17 Feb 1999 05:34:32 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk Reply-To: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu Subject: Re: Quick time movies for the PC In-Reply-To: Message-ID: Date: Wed, 17 Feb 1999 10:19:23 -0600 (Central 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: <"aulb8.0.l67.0Vfos"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1002 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 980 I realize that this area has been discussed in some detail but I could not find any answers on the FAQ gopher list. I need to save NIH movies in Quick Time format which I can then open on a PC. I have the free download of QT but when I try to open the movie I get the message that the file is not a movie file. I have tried to save in a number of the formats in the QT options list. I then go into explorer or DOS and manually add the .mov extension. In a response to the same question by Matthew Warfel, Euginio de Hostos suggested "saving the movie as a flattened movie". I did not see anything obvious in the QT saving options on NIH image. Any ideas, thanks for your help. Paul. ---------------------- 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-request@io.ece.drexel.edu Wed Feb 17 20:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA28791 for cshtest@io.ece.drexel.edu; Wed, 17 Feb 1999 20:02:08 -0500 (EST) Resent-Date: Wed, 17 Feb 1999 20:02:08 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: P.Stoodley@exeter.ac.uk, nih-image@io.ece.drexel.edu Date: Thu, 18 Feb 1999 11:51:43 +1100 Subject: Re: Quick time movies for the PC Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"aAWHe2.0.Cb6.GDsos"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1003 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2549 >To: nih-image@io.ece.drexel.edu >Subject: Re: Quick time movies for the PC >Date: Wed, 17 Feb 1999 10:19:23 -0600 (Central Standard Time) > >I realize that this area has been discussed in some detail >but I could not find any answers on the FAQ gopher list. >I need to save NIH movies in Quick Time format which I can >then open on a PC. I have the free download of QT but when >I try to open the movie I get the message that the file is >not a movie file. I have tried to save in a number of the >formats in the QT options list. I then go into explorer or >DOS and manually add the .mov extension. In a response to >the same question by Matthew Warfel, Euginio de Hostos >suggested "saving the movie as a flattened movie". I did >not see anything obvious in the QT saving options on NIH >image. Any ideas, thanks for your help. >Paul. > >---------------------- >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. > Paul, "flatten" refers to converting Mac file structure of data and resource fork to a "flat" ie unstructured file. If you had gone back to gopher with "flatten" you would have found the following: (MoviePlayer works) From: Cengizhan Ozturk You have to flatten the movie... (MoviePlayer does this!) Use only standard compression schemes if you have to use one and make sure it is self-contained.. . Date: Tue, 7 May 1996 08:12:46 +0100 (BST) From: Kit Erlebach > You have to convert all the images to Pict format and open the whole folder > by using "MovieMaker". It works well. . How ever for those interested Apple have a PC version of Quicktime avalible on their ftp site, You also need to flatten the Quicktime movie before you transfer it to PC.... From: shawn@bioserver.vsb.usu.edu (Shawn Swaner) Date: Mon, 25 Aug 1997 15:31:57 -0600 When I have done as you describe, the movies will not work unless they are flattened. I use a shareware program called flattenmoov. I think you can download it from www.shareware.com Run this program on the Mac, flatten the movie files, then FTP them to the PC. They will then play with QuickTime for Windows. 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 Feb 17 20:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA28889; Wed, 17 Feb 1999 20:02:41 -0500 (EST) Date: Wed, 17 Feb 1999 20:02:41 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902180102.UAA28889@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #43 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/43 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: 10196 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 43 Today's Topics: Re: Change defaults in Save As? [ Steve Martin To: nih-image@io.ece.drexel.edu Subject: Re: Change defaults in Save As? Message-Id: Content-Type: text/plain; charset="us-ascii" Michael, you might wish to check http://pascal-central.com/merlin.html for my Codewarrior Make QT movie project. It is a Pascal port of the example Inside Macintosh routines (which Apple now publishes in C :-( ), and would provide a simple starting point for trialling changes in movie options, before moving on to Image. The Inside Macintosh volumes on qt are freely available as PDF files from and good luck, Steve At 11:51 AM +1100 on 16/2/99, GJOSS@rna.bio.mq.edu.au wrote: > >Date: Mon, 15 Feb 1999 11:58:22 -0800 > >To: nih-image@io.ece.drexel.edu > >From: Michael Cammer > >Subject: Re: Change defaults in Save As? > > > >>Is there a way to have the Save As... options be changed permanently? > > > >Write a macro that sets the SaveAs options you need. > >******************************************************* > >* Michael Cammer Analytical Imaging Facility * > >* Albert Einstein College of Medicine * > >* Bronx, NY 10461 (718) 430-2890 * > >* work URL: http://www.ca.aecom.yu.edu/aif/ * > >* personal URL: http://cammer.home.mindspring.com/ * > >******************************************************* > > > > While a macro such as: > > macro'/m SaveAs quickTime';begin > selectPic(picNumber);setSaveAs('quick');saveAs(windowtitle,'.Moov');end > > will initiate the 'saveas', there is no way (that I can determine) that >will allow > the Quicktime compression parameters to be set via macros or to avoid the >dialogue > box. > > As "John A. Cooper" said: > > >We do a Save As... and need to change many of the settings. At present, we > >use a QuicKeys macro to do this. It works OK but is not very efficient and > >occasionally goes wacko, needing to be re-recorded. > > it would be desirable to automatically setup parameters. > > The source module File2.p > uses > .... ToolUtils, Resources, > ... Components, ImageCompression, > Movies, QuickTimeComponents,...GestaltEqu > > function OpenMovieToolbox:boolean; > ..... > if Gestalt(gestaltQuickTime, result) <> noErr then begin > ShowMessage('QuickTime Required'); > ..... > > procedure SaveAsQuickTime (fname: str255; fRefNum: integer); > {Written by Eric A. Shelden (shelden@umich.edu) 3/23/94} > .............. > myComponentInstance := >OpenDefaultComponent('scdi', 'imag'); > myResult := >SCRequestSequenceSettings(myComponentInstance); > ..... > myResult := SCGetInfo(myComponentInstance, 'sptl', >ptr(@theSpaceSettings)); > myResult := SCGetInfo(myComponentInstance, scTemporalSettingsType > > , ptr(@theTimeSettings)); > myResult := SCGetInfo(myComponentInstance, scDataRateSettingsType > , ptr(@theRateSettings)); > myResult := CloseComponent(myComponentInstance); > > The above code appears to access system (ie external to NIH-Image source) >QuickTime > services. > > Perhaps a knowledgeable Mac programmer could tell us how to access and >modify > default settings presumeablely accessed via > myComponentInstance := OpenDefaultComponent('scdi', 'imag'); > > Given the string references, they are presumeably keys in a control file >somewhere? > > > > 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: Wed, 17 Feb 1999 14:55:57 +1100 From: GJOSS@rna.bio.mq.edu.au To: VHardy@cvm.tamu.edu, nih-image@io.ece.drexel.edu Subject: Re: Digitizing pads Message-ID: >Date: Fri, 12 Feb 1999 11:08:18 -0600 >From: "Vince Hardy" >To: >Subject: Digitizing pads > >I am a very NEW user of the Scion Mac version of NIH Image 1.61 with a LG-3 frame >grabber. We are wondering if there are any digitizing pads that work in >conjuction with NIH Image whereby we can pr >ject a microscopic image directly from the microscope onto the pad, and then make >diameter measurements of individual cells. Thanks for your help. > >Vince Hardy >Texas A&M University >College Station, Texas > I am rather bemused by your post but cant resist a reply :-) If you have a "Scion Mac version of NIH Image 1.61 with a LG-3 frame grabber" then presumeably you have a c-mount video camera mounted on your microscope and connected to the "LG-3 frame grabber";that is what the "LG-3 frame grabber" is for. You can then "project a microscopic image directly from the microscope onto the " computer monitor ", and then make diameter measurements of individual cells " using NIH Image 1.61 by a number of alternative methods eg manual selection using mouse, densitySlice/analyzeParticles etc. I cant imagine why you would want to go back to the old technology of a digitizing pad. Am I missing something? (again :-) 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: Wed, 17 Feb 1999 10:19:23 -0600 (Central Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu Subject: Re: Quick time movies for the PC Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I realize that this area has been discussed in some detail but I could not find any answers on the FAQ gopher list. I need to save NIH movies in Quick Time format which I can then open on a PC. I have the free download of QT but when I try to open the movie I get the message that the file is not a movie file. I have tried to save in a number of the formats in the QT options list. I then go into explorer or DOS and manually add the .mov extension. In a response to the same question by Matthew Warfel, Euginio de Hostos suggested "saving the movie as a flattened movie". I did not see anything obvious in the QT saving options on NIH image. Any ideas, thanks for your help. Paul. ---------------------- 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. ------------------------------ Date: Thu, 18 Feb 1999 11:51:43 +1100 From: GJOSS@rna.bio.mq.edu.au To: P.Stoodley@exeter.ac.uk, nih-image@io.ece.drexel.edu Subject: Re: Quick time movies for the PC Message-ID: >To: nih-image@io.ece.drexel.edu >Subject: Re: Quick time movies for the PC >Date: Wed, 17 Feb 1999 10:19:23 -0600 (Central Standard Time) > >I realize that this area has been discussed in some detail >but I could not find any answers on the FAQ gopher list. >I need to save NIH movies in Quick Time format which I can >then open on a PC. I have the free download of QT but when >I try to open the movie I get the message that the file is >not a movie file. I have tried to save in a number of the >formats in the QT options list. I then go into explorer or >DOS and manually add the .mov extension. In a response to >the same question by Matthew Warfel, Euginio de Hostos >suggested "saving the movie as a flattened movie". I did >not see anything obvious in the QT saving options on NIH >image. Any ideas, thanks for your help. >Paul. > >---------------------- >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. > Paul, "flatten" refers to converting Mac file structure of data and resource fork to a "flat" ie unstructured file. If you had gone back to gopher with "flatten" you would have found the following: (MoviePlayer works) From: Cengizhan Ozturk You have to flatten the movie... (MoviePlayer does this!) Use only standard compression schemes if you have to use one and make sure it is self-contained.. . Date: Tue, 7 May 1996 08:12:46 +0100 (BST) From: Kit Erlebach > You have to convert all the images to Pict format and open the whole folder > by using "MovieMaker". It works well. . How ever for those interested Apple have a PC version of Quicktime avalible on their ftp site, You also need to flatten the Quicktime movie before you transfer it to PC.... From: shawn@bioserver.vsb.usu.edu (Shawn Swaner) Date: Mon, 25 Aug 1997 15:31:57 -0600 When I have done as you describe, the movies will not work unless they are flattened. I use a shareware program called flattenmoov. I think you can download it from www.shareware.com Run this program on the Mac, flatten the movie files, then FTP them to the PC. They will then play with QuickTime for Windows. 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 V99 Issue #43 *************************************** From nih-image-request@io.ece.drexel.edu Thu Feb 18 11:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26317 for cshtest@io.ece.drexel.edu; Thu, 18 Feb 1999 11:02:59 -0500 (EST) Resent-Date: Thu, 18 Feb 1999 11:02:59 -0500 (EST) From: Martyn_Evans-1@sbphrd.com X-Lotus-FromDomain: SB_PHARM_RD To: nih-image@io.ece.drexel.edu Message-ID: <8025671C.00555FC6.00@uksmtp01.ha.uk.sbphrd.com> Date: Thu, 18 Feb 1999 15:46:40 +0000 Subject: more movie ... Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"EDKpI3.0.Xs5.aF3ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1004 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 218 Hi All - following on from the recent QT discussion, I need to find a way to make *.avi movies from a TIFF stack from SCION Image for NT. Anyone have any suggestions ? Martyn Evans NeuroImaging Research Harlow UK From nih-image-request@io.ece.drexel.edu Thu Feb 18 15:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA15222 for cshtest@io.ece.drexel.edu; Thu, 18 Feb 1999 15:01:05 -0500 (EST) Resent-Date: Thu, 18 Feb 1999 15:01:05 -0500 (EST) Date: Thu, 18 Feb 1999 14:44:23 -0500 (EST) From: Cengizhan Ozturk X-Sender: cozturk@henryv To: nih-image@io.ece.drexel.edu Subject: Re: more movie ... In-Reply-To: <8025671C.00555FC6.00@uksmtp01.ha.uk.sbphrd.com> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"fINtx2.0._J3.Ss6ps"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1005 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 836 Hi, Since conversion form quicktime directly to avi is still a big mystery to me I use "Platypus Animator" program (www.c-point.com) in a PC. I am using in a windows 98 but it will probably work in NT. It will do what you want and more. Good luck ... Cengizhan -------------------------------------------- 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, 18 Feb 1999 Martyn_Evans-1@sbphrd.com wrote: > Hi All - following on from the recent QT discussion, I need to find a way > to make *.avi movies from a TIFF stack from SCION Image for NT. Anyone > have any suggestions ? > > > Martyn Evans > NeuroImaging Research > Harlow UK > > > From nih-image-d-request@io.ece.drexel.edu Fri Feb 19 06:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA24953; Fri, 19 Feb 1999 06:21:28 -0500 (EST) Date: Fri, 19 Feb 1999 06:21:28 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902191121.GAA24953@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #44 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/44 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: 2012 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 44 Today's Topics: more movie ... [ Martyn_Evans-1@sbphrd.com ] Re: more movie ... [ Cengizhan Ozturk Content-type: text/plain; charset=us-ascii Content-Disposition: inline Hi All - following on from the recent QT discussion, I need to find a way to make *.avi movies from a TIFF stack from SCION Image for NT. Anyone have any suggestions ? Martyn Evans NeuroImaging Research Harlow UK ------------------------------ Date: Thu, 18 Feb 1999 14:44:23 -0500 (EST) From: Cengizhan Ozturk To: nih-image@io.ece.drexel.edu Subject: Re: more movie ... Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Since conversion form quicktime directly to avi is still a big mystery to me I use "Platypus Animator" program (www.c-point.com) in a PC. I am using in a windows 98 but it will probably work in NT. It will do what you want and more. Good luck ... Cengizhan -------------------------------------------- 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, 18 Feb 1999 Martyn_Evans-1@sbphrd.com wrote: > Hi All - following on from the recent QT discussion, I need to find a way > to make *.avi movies from a TIFF stack from SCION Image for NT. Anyone > have any suggestions ? > > > Martyn Evans > NeuroImaging Research > Harlow UK > > > -------------------------------- End of nih-image-d Digest V99 Issue #44 *************************************** From nih-image-request@io.ece.drexel.edu Sun Feb 21 14:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA04218 for cshtest@io.ece.drexel.edu; Sun, 21 Feb 1999 14:01:09 -0500 (EST) Resent-Date: Sun, 21 Feb 1999 14:01:09 -0500 (EST) Message-Id: <199902211839.TAA01963@dns.cisea.it> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Sun, 21 Feb 1999 19:41:40 +0100 Subject: export in JPEG format from NIH-Image From: "mimmo" To: nih-image@io.ece.drexel.edu Mime-version: 1.0 X-Priority: 3 Content-transfer-encoding: 7bit Resent-Message-ID: <"oXcG9.0.sb.6E5qs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1006 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 139 hi, anybody knows as to export images in JPEG format with compression level control from NIH-Image? any help will be appreciated TIA -dom From nih-image-request@io.ece.drexel.edu Sun Feb 21 18:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA01371 for cshtest@io.ece.drexel.edu; Sun, 21 Feb 1999 18:25:27 -0500 (EST) Resent-Date: Sun, 21 Feb 1999 18:25:27 -0500 (EST) Message-Id: <3.0.5.32.19990221182004.008cece0@codon.nih.gov> X-Sender: wayne@codon.nih.gov X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Sun, 21 Feb 1999 18:20:04 -0500 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: export in JPEG format from NIH-Image In-Reply-To: <199902211839.TAA01963@dns.cisea.it> Mime-Version: 1.0 Resent-Message-ID: <"V8z6R3.0.5I7.uB9qs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1007 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 485 At 07:41 PM 2/21/99 +0100, you wrote: >hi, >anybody knows as to export images in JPEG format with compression level >control from NIH-Image? >any help will be appreciated NIH Image cannot save in JPEG format but my new ImageJ program can. Use ImageJ's Edit/Options/Jpeg Quality command to specify the compression level. The ImageJ home page is at "http://rsb.info.nih.gov/ij/". ImageJ requires MRJ 2.1, available from "http://www.apple.com/java/", and Mac OS 7.6.1 or later. -wayne From nih-image-request@io.ece.drexel.edu Mon Feb 22 05:38 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA10947 for cshtest@io.ece.drexel.edu; Mon, 22 Feb 1999 05:38:30 -0500 (EST) Resent-Date: Mon, 22 Feb 1999 05:38:30 -0500 (EST) From: paul stoodley Sender: P.Stoodley@exeter.ac.uk Reply-To: P.Stoodley@exeter.ac.uk To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: export in JPEG format from NIH-Image In-Reply-To: <3.0.5.32.19990221182004.008cece0@codon.nih.gov> Message-ID: Date: Mon, 22 Feb 1999 09:21:00 +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: <"oPxT33.0.A42.QxIqs"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1008 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 905 > >hi, > >anybody knows as to export images in JPEG format with compression level > >control from NIH-Image? > >any help will be appreciated > > NIH Image cannot save in JPEG format but my new ImageJ program can. Use ImageJ's Edit/Options/Jpeg Quality command to specify the compression level. The ImageJ home page is at "http://rsb.info.nih.gov/ij/". ImageJ requires MRJ 2.1, available from "http://www.apple.com/java/", and Mac OS 7.6.1 or later. > > -wayne Another option is to open the tif file in Image Tool (free down load can be found in NIH-image links). You can then save in various jpeg formats. Paul. ---------------------- 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 Mon Feb 22 05:41 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA11436; Mon, 22 Feb 1999 05:41:41 -0500 (EST) Date: Mon, 22 Feb 1999 05:41:41 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902221041.FAA11436@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #45 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/45 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: 2942 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 45 Today's Topics: export in JPEG format from NIH-Image [ "mimmo" ] Re: export in JPEG format from NIH-I [ Wayne Rasband ] Re: export in JPEG format from NIH-I [ paul stoodley To: nih-image@io.ece.drexel.edu Subject: export in JPEG format from NIH-Image Message-Id: <199902211839.TAA01963@dns.cisea.it> Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit hi, anybody knows as to export images in JPEG format with compression level control from NIH-Image? any help will be appreciated TIA -dom ------------------------------ Date: Sun, 21 Feb 1999 18:20:04 -0500 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: export in JPEG format from NIH-Image Message-Id: <3.0.5.32.19990221182004.008cece0@codon.nih.gov> Content-Type: text/plain; charset="us-ascii" At 07:41 PM 2/21/99 +0100, you wrote: >hi, >anybody knows as to export images in JPEG format with compression level >control from NIH-Image? >any help will be appreciated NIH Image cannot save in JPEG format but my new ImageJ program can. Use ImageJ's Edit/Options/Jpeg Quality command to specify the compression level. The ImageJ home page is at "http://rsb.info.nih.gov/ij/". ImageJ requires MRJ 2.1, available from "http://www.apple.com/java/", and Mac OS 7.6.1 or later. -wayne ------------------------------ Date: Mon, 22 Feb 1999 09:21:00 +0000 (GMT Standard Time) From: paul stoodley To: nih-image@io.ece.drexel.edu cc: nih-image@io.ece.drexel.edu Subject: Re: export in JPEG format from NIH-Image Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > >hi, > >anybody knows as to export images in JPEG format with compression level > >control from NIH-Image? > >any help will be appreciated > > NIH Image cannot save in JPEG format but my new ImageJ program can. Use ImageJ's Edit/Options/Jpeg Quality command to specify the compression level. The ImageJ home page is at "http://rsb.info.nih.gov/ij/". ImageJ requires MRJ 2.1, available from "http://www.apple.com/java/", and Mac OS 7.6.1 or later. > > -wayne Another option is to open the tif file in Image Tool (free down load can be found in NIH-image links). You can then save in various jpeg formats. Paul. ---------------------- 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 V99 Issue #45 *************************************** From nih-image-request@io.ece.drexel.edu Tue Feb 23 05:19 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA27272 for cshtest@io.ece.drexel.edu; Tue, 23 Feb 1999 05:19:50 -0500 (EST) Resent-Date: Tue, 23 Feb 1999 05:19:50 -0500 (EST) Date: Tue, 23 Feb 1999 05:05:01 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199902231005.FAA25533@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"gyGcU.0.9F6.Frdqs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1009 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3727 NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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 Feb 23 12:43 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA11476 for cshtest@io.ece.drexel.edu; Tue, 23 Feb 1999 12:43:52 -0500 (EST) Resent-Date: Tue, 23 Feb 1999 12:43:52 -0500 (EST) Date: Tue, 23 Feb 1999 09:23:50 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Mac to OMDR serial connection Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"sqbf73.0.2L2.jGkqs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1010 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 682 Has anyone successfully cabled a Mac to a Panasonic 3038 OMDR? According to the OMDR manual, there are several possibilities for serial card jumpers and Type 1 versus Type 2 communications on the OMDR, plus the usual choices on Mac RS-422 to RS-232 serial cable wiring. I have images recorded onto the OMDR at frame rate from an intensified CCD. My plan is to use a macro to step through them so that they can be captured into a stack. Thanks, 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-d-request@io.ece.drexel.edu Wed Feb 24 06:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12412; Wed, 24 Feb 1999 06:21:18 -0500 (EST) Date: Wed, 24 Feb 1999 06:21:18 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902241121.GAA12412@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #46 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/46 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: 5350 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 46 Today's Topics: ADMIN: list commands [ nih-image-owner@io.ece.drexel.edu ] Mac to OMDR serial connection [ "G. Macdonald" NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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, 23 Feb 1999 09:23:50 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Mac to OMDR serial connection Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone successfully cabled a Mac to a Panasonic 3038 OMDR? According to the OMDR manual, there are several possibilities for serial card jumpers and Type 1 versus Type 2 communications on the OMDR, plus the usual choices on Mac RS-422 to RS-232 serial cable wiring. I have images recorded onto the OMDR at frame rate from an intensified CCD. My plan is to use a macro to step through them so that they can be captured into a stack. Thanks, 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 -------------------------------- End of nih-image-d Digest V99 Issue #46 *************************************** From nih-image-request@io.ece.drexel.edu Wed Feb 24 06:22 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA12596 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 06:22:14 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 06:22:14 -0500 (EST) Message-ID: <19990224110221.22465.qmail@hotmail.com> X-Originating-IP: [139.165.30.103] From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Filters KODAK WRATTEN Date: Wed, 24 Feb 1999 03:02:20 PST Mime-Version: 1.0 Resent-Message-ID: <"kWlJz1.0.Kb2.Xnzqs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1011 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 904 Dear Imagers I'm working with a gray scale CCD on Mac and I need to aquire three images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, 47B blue). I would like to know at what wavelenght these filters works, what's the distribution of the spectrum, or where can I found some information about this. Someone can help me? Thanks ************************************************************ Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ************************************************************ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-request@io.ece.drexel.edu Wed Feb 24 07:01 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA16417 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 07:01:50 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 07:01:50 -0500 (EST) X-Sender: jorgen@mail.datakom.su.se Message-Id: In-Reply-To: <19990224110221.22465.qmail@hotmail.com> Mime-Version: 1.0 Content-Transfer-Encoding: 8bit Date: Wed, 24 Feb 1999 12:57:17 +0100 To: nih-image@io.ece.drexel.edu From: =?iso-8859-1?Q?J=F6rgen?= Ullberg Subject: Re: Filters KODAK WRATTEN Resent-Message-ID: <"sN4182.0.Ej3.BU-qs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1012 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: 615 >Dear Imagers > >I'm working with a gray scale CCD on Mac and I need to aquire three >images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >47B blue). > >I would like to know at what wavelenght these filters works, what's the >distribution of the spectrum, or where can I found some information >about this. > >Someone can help me? > >Thanks > Hi Enrico! Have you tried the Kodak homepage? Should be kodak.com or something. Jörgen Jörgen Ullberg Phone: + 46 8 164001 Dept. of Zoology Fax: + 46 8 167715 Stockholm University e-mail: Jorgen.Ullberg@zoologi.su.se 106 91 STOCKHOLM SWEDEN From nih-image-request@io.ece.drexel.edu Wed Feb 24 09:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA27674 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 09:02:28 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 09:02:28 -0500 (EST) Message-ID: From: "Purdy, Sam" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Filters KODAK WRATTEN Date: Wed, 24 Feb 1999 08:47:45 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.995.52 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Resent-Message-ID: <"HVYVB2.0.6B6.v50rs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1013 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1420 Kodak publication B-3, Kodak Filters for Scientific and Technical Uses, contains transmittance curves for all Kodak filters. The particular filters: filter 25 transmits at wavelengths above 600 nanometers, 47B transmits at 430 nanometers, and 58 at 525 nonometers. Hope this helps. Sam Purdy National Steel Corp. Trenton, MI, USA >---------- >From: Enrico BONINO >Sent: Wednesday, February 24, 1999 6:02 AM >To: nih-image@io.ece.drexel.edu >Subject: Filters KODAK WRATTEN > >Dear Imagers > >I'm working with a gray scale CCD on Mac and I need to aquire three >images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >47B blue). > >I would like to know at what wavelenght these filters works, what's the >distribution of the spectrum, or where can I found some information >about this. > >Someone can help me? > >Thanks > >************************************************************ >Enrico BONINO, geologist >University of Liege >Dept. of Applied Geology >Lab. MICA Geomaterials Characterization >http://www.ulg.ac.be/mica >Avenue des Tilleuls, 45 >B-4000 LIEGE >BELGIUM >tel. 0032 (0)4 3669526 >fax 0032 (0)4 3669520 >E-mail: e_bonino@hotmail.com >CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 >************************************************************ > > >______________________________________________________ >Get Your Private, Free Email at http://www.hotmail.com > > From nih-image-request@io.ece.drexel.edu Wed Feb 24 17:03 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA13158 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 17:03:14 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 17:03:14 -0500 (EST) Date: Wed, 24 Feb 1999 13:52:15 -0800 From: David Linker To: nih-image@io.ece.drexel.edu Subject: Overview of Video Capture options for B&W G3's Message-ID: <354393.3128853135@huginn.medicine.washington.edu> Originator-Info: login-id=dtlinker; server=dtlinker.deskmail.washington.edu X-Mailer: Mulberry (MacOS) [1.4.0, s/n U-300938] MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline Resent-Message-ID: <"JI2Uf1.0.hx2.KI7rs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1014 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1820 I am looking for video capture solutions to use with one of the new B/W G3's and NIH Image. I have done some research as to the options, and have summarized some of the issues below, for those who are interested, but I also have a question for the list. We have been capturing grayscale images from a VCR via S-Video input, using a serial control line to advance the VCR to another frame, and capturing still frames that are then put in a stack. If we could capture full motion video with excellent (or as good) quality, it might be preferable. We would like to preserve the option of capturing still frames with no compression, though, as our fall-back. We measure dimensions on the images, not gray values. >From the table below, it would appeart that Buz would be best, but so far, I have heard only problems with Buz and the new macs. Aurora Fuse looks good, but I would like to hear from someone using it with Image. Has anyone used the Sony DVMC-DA1? Any other related thoughts would also be welcome. David Linker Device Inputs Resolution Compression FF Cost Scion LG-3 RS-170 640x480 None Yes $895 Aurora Fuse S-Video 640x480 2:1 -> 50:1 Yes? $499 Iomega Buz Comp & S-Video 720x480 3:1 -> 100:1 Yes $299 Miro DC30 Comp & S-Video 680x480 2.2 -> 5:1 ?? $720 Media 100qx S-Video ?? ?? ?? $1970 Sony DVMC-DA1 S-Video ?? ?? ?? <$400 Newer Firestorm S-Video ?? ?? ?? ?? Targa 2000 S-Video 720x480 ?? ?? ?? Notes: This is NOT a complete list of features, only a summary of the features important to my application. I was unable to connect to Data Translations site, so I could not get detailed specifications for Media 100qx. Ditto Targa. The Newer solution has not been released yet, but it will use Firewire input. The Sony system is released, I believe, and also uses Firewire. From nih-image-request@io.ece.drexel.edu Wed Feb 24 17:48 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA17361 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 17:48:15 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 17:48:15 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: SPurdy@nationalsteel.com, nih-image@io.ece.drexel.edu, e_bonino@hotmail.com Date: Thu, 25 Feb 1999 9:42:39 +1100 Subject: RE: Filters KODAK WRATTEN Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <3A49F85713@rna.bio.mq.edu.au> Resent-Message-ID: <"Z79pE.0.E04.sz7rs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1015 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2297 Following previous enquires of my own, I have recent Web reference KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 ) http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml and access to Kodak Data Book of applied photography vol1 sheet FT-6 which gives spectrophotometric absorption curves for 25,47B,58 and 29,47b,61. I will email separately an attachment image of the curves to e_bonino and have copied Kodak support requesting that they extend their website to include such data. Greg Joss >From: "Purdy, Sam" >To: "'nih-image@io.ece.drexel.edu'" >Subject: RE: Filters KODAK WRATTEN >Date: Wed, 24 Feb 1999 08:47:45 -0500 >X-Mailing-List: archive/latest/1013 > >Kodak publication B-3, Kodak Filters for Scientific and Technical Uses, >contains transmittance curves for all Kodak filters. The particular >filters: >filter 25 transmits at wavelengths above 600 nanometers, 47B transmits >at 430 nanometers, and 58 at 525 nonometers. Hope this helps. >Sam Purdy >National Steel Corp. >Trenton, MI, USA >>---------- >>From: Enrico BONINO >>Sent: Wednesday, February 24, 1999 6:02 AM >>To: nih-image@io.ece.drexel.edu >>Subject: Filters KODAK WRATTEN >> >>Dear Imagers >> >>I'm working with a gray scale CCD on Mac and I need to aquire three >>images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >>47B blue). >> >>I would like to know at what wavelenght these filters works, what's the >>distribution of the spectrum, or where can I found some information >>about this. >> >>Someone can help me? >> >>Thanks >> >>************************************************************ >>Enrico BONINO, geologist >>University of Liege >>Dept. of Applied Geology >>Lab. MICA Geomaterials Characterization >>http://www.ulg.ac.be/mica >>Avenue des Tilleuls, 45 >>B-4000 LIEGE >>BELGIUM >>tel. 0032 (0)4 3669526 >>fax 0032 (0)4 3669520 >>E-mail: e_bonino@hotmail.com >>CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 >>************************************************************ 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 Feb 24 18:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA19889 for cshtest@io.ece.drexel.edu; Wed, 24 Feb 1999 18:16:50 -0500 (EST) Resent-Date: Wed, 24 Feb 1999 18:16:50 -0500 (EST) From: "Darryl C. Sutton" Date: Wed, 24 Feb 1999 18:04:17 -0500 (EST) Message-Id: <199902242304.SAA12465@K.coe.neu.edu> To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: SlQ+a7QxpNZqOSCAWTqrQg== Resent-Message-ID: <"bgdsj1.0.Wa4.EN8rs"@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/1016 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 466 I presently have an imaging system which is abut 9 years old. It includes a Dage 72 series camera, Hamatushi video processors, an EPIX 4MegVid 10-20 framegrabber board, Compac PC. The present system software is Optimas. Does NIH IMAGE offer a software package that will support the EPIX 4MegVid 10-20 framegrabber. The framegrabber uses a Texas Instrument TMS320C25 signal processor. If additional information is required to a answer this, please specify. From nih-image-d-request@io.ece.drexel.edu Thu Feb 25 06:17 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA23465; Thu, 25 Feb 1999 06:17:25 -0500 (EST) Date: Thu, 25 Feb 1999 06:17:25 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902251117.GAA23465@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #47 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/47 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: 10216 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 47 Today's Topics: Filters KODAK WRATTEN [ "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Filters KODAK WRATTEN Message-ID: <19990224110221.22465.qmail@hotmail.com> Content-type: text/plain Dear Imagers I'm working with a gray scale CCD on Mac and I need to aquire three images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, 47B blue). I would like to know at what wavelenght these filters works, what's the distribution of the spectrum, or where can I found some information about this. Someone can help me? Thanks ************************************************************ Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ************************************************************ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com ------------------------------ Date: Wed, 24 Feb 1999 12:57:17 +0100 From: =?iso-8859-1?Q?J=F6rgen?= Ullberg To: nih-image@io.ece.drexel.edu Subject: Re: Filters KODAK WRATTEN Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit >Dear Imagers > >I'm working with a gray scale CCD on Mac and I need to aquire three >images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >47B blue). > >I would like to know at what wavelenght these filters works, what's the >distribution of the spectrum, or where can I found some information >about this. > >Someone can help me? > >Thanks > Hi Enrico! Have you tried the Kodak homepage? Should be kodak.com or something. Jörgen Jörgen Ullberg Phone: + 46 8 164001 Dept. of Zoology Fax: + 46 8 167715 Stockholm University e-mail: Jorgen.Ullberg@zoologi.su.se 106 91 STOCKHOLM SWEDEN ------------------------------ Date: Wed, 24 Feb 1999 08:47:45 -0500 From: "Purdy, Sam" To: "'nih-image@io.ece.drexel.edu'" Subject: RE: Filters KODAK WRATTEN Message-ID: Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Kodak publication B-3, Kodak Filters for Scientific and Technical Uses, contains transmittance curves for all Kodak filters. The particular filters: filter 25 transmits at wavelengths above 600 nanometers, 47B transmits at 430 nanometers, and 58 at 525 nonometers. Hope this helps. Sam Purdy National Steel Corp. Trenton, MI, USA >---------- >From: Enrico BONINO >Sent: Wednesday, February 24, 1999 6:02 AM >To: nih-image@io.ece.drexel.edu >Subject: Filters KODAK WRATTEN > >Dear Imagers > >I'm working with a gray scale CCD on Mac and I need to aquire three >images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >47B blue). > >I would like to know at what wavelenght these filters works, what's the >distribution of the spectrum, or where can I found some information >about this. > >Someone can help me? > >Thanks > >************************************************************ >Enrico BONINO, geologist >University of Liege >Dept. of Applied Geology >Lab. MICA Geomaterials Characterization >http://www.ulg.ac.be/mica >Avenue des Tilleuls, 45 >B-4000 LIEGE >BELGIUM >tel. 0032 (0)4 3669526 >fax 0032 (0)4 3669520 >E-mail: e_bonino@hotmail.com >CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 >************************************************************ > > >______________________________________________________ >Get Your Private, Free Email at http://www.hotmail.com > > ------------------------------ Date: Wed, 24 Feb 1999 13:52:15 -0800 From: David Linker To: nih-image@io.ece.drexel.edu Subject: Overview of Video Capture options for B&W G3's Message-ID: <354393.3128853135@huginn.medicine.washington.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Disposition: inline I am looking for video capture solutions to use with one of the new B/W G3's and NIH Image. I have done some research as to the options, and have summarized some of the issues below, for those who are interested, but I also have a question for the list. We have been capturing grayscale images from a VCR via S-Video input, using a serial control line to advance the VCR to another frame, and capturing still frames that are then put in a stack. If we could capture full motion video with excellent (or as good) quality, it might be preferable. We would like to preserve the option of capturing still frames with no compression, though, as our fall-back. We measure dimensions on the images, not gray values. >From the table below, it would appeart that Buz would be best, but so far, I have heard only problems with Buz and the new macs. Aurora Fuse looks good, but I would like to hear from someone using it with Image. Has anyone used the Sony DVMC-DA1? Any other related thoughts would also be welcome. David Linker Device Inputs Resolution Compression FF Cost Scion LG-3 RS-170 640x480 None Yes $895 Aurora Fuse S-Video 640x480 2:1 -> 50:1 Yes? $499 Iomega Buz Comp & S-Video 720x480 3:1 -> 100:1 Yes $299 Miro DC30 Comp & S-Video 680x480 2.2 -> 5:1 ?? $720 Media 100qx S-Video ?? ?? ?? $1970 Sony DVMC-DA1 S-Video ?? ?? ?? <$400 Newer Firestorm S-Video ?? ?? ?? ?? Targa 2000 S-Video 720x480 ?? ?? ?? Notes: This is NOT a complete list of features, only a summary of the features important to my application. I was unable to connect to Data Translations site, so I could not get detailed specifications for Media 100qx. Ditto Targa. The Newer solution has not been released yet, but it will use Firewire input. The Sony system is released, I believe, and also uses Firewire. ------------------------------ Date: Thu, 25 Feb 1999 9:42:39 +1100 From: GJOSS@rna.bio.mq.edu.au To: SPurdy@nationalsteel.com, nih-image@io.ece.drexel.edu, e_bonino@hotmail.com Subject: RE: Filters KODAK WRATTEN Message-ID: <3A49F85713@rna.bio.mq.edu.au> Following previous enquires of my own, I have recent Web reference KSIS: Kodak Wratten Gelatin Filters, ( May 28 1998 ) http://www.kodak.com:80/country/US/en/digital/sis/wratten.shtml and access to Kodak Data Book of applied photography vol1 sheet FT-6 which gives spectrophotometric absorption curves for 25,47B,58 and 29,47b,61. I will email separately an attachment image of the curves to e_bonino and have copied Kodak support requesting that they extend their website to include such data. Greg Joss >From: "Purdy, Sam" >To: "'nih-image@io.ece.drexel.edu'" >Subject: RE: Filters KODAK WRATTEN >Date: Wed, 24 Feb 1999 08:47:45 -0500 >X-Mailing-List: archive/latest/1013 > >Kodak publication B-3, Kodak Filters for Scientific and Technical Uses, >contains transmittance curves for all Kodak filters. The particular >filters: >filter 25 transmits at wavelengths above 600 nanometers, 47B transmits >at 430 nanometers, and 58 at 525 nonometers. Hope this helps. >Sam Purdy >National Steel Corp. >Trenton, MI, USA >>---------- >>From: Enrico BONINO >>Sent: Wednesday, February 24, 1999 6:02 AM >>To: nih-image@io.ece.drexel.edu >>Subject: Filters KODAK WRATTEN >> >>Dear Imagers >> >>I'm working with a gray scale CCD on Mac and I need to aquire three >>images R,G,B using the gelatin filter WRATTEN KODAK (25 red, 58 green, >>47B blue). >> >>I would like to know at what wavelenght these filters works, what's the >>distribution of the spectrum, or where can I found some information >>about this. >> >>Someone can help me? >> >>Thanks >> >>************************************************************ >>Enrico BONINO, geologist >>University of Liege >>Dept. of Applied Geology >>Lab. MICA Geomaterials Characterization >>http://www.ulg.ac.be/mica >>Avenue des Tilleuls, 45 >>B-4000 LIEGE >>BELGIUM >>tel. 0032 (0)4 3669526 >>fax 0032 (0)4 3669520 >>E-mail: e_bonino@hotmail.com >>CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 >>************************************************************ 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: Wed, 24 Feb 1999 18:04:17 -0500 (EST) From: "Darryl C. Sutton" To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: <199902242304.SAA12465@K.coe.neu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: SlQ+a7QxpNZqOSCAWTqrQg== I presently have an imaging system which is abut 9 years old. It includes a Dage 72 series camera, Hamatushi video processors, an EPIX 4MegVid 10-20 framegrabber board, Compac PC. The present system software is Optimas. Does NIH IMAGE offer a software package that will support the EPIX 4MegVid 10-20 framegrabber. The framegrabber uses a Texas Instrument TMS320C25 signal processor. If additional information is required to a answer this, please specify. -------------------------------- End of nih-image-d Digest V99 Issue #47 *************************************** From nih-image-request@io.ece.drexel.edu Thu Feb 25 12:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA24142 for cshtest@io.ece.drexel.edu; Thu, 25 Feb 1999 12:14:29 -0500 (EST) Resent-Date: Thu, 25 Feb 1999 12:14:29 -0500 (EST) Message-ID: <36D5815E.6F19@wxs.nl> Date: Thu, 25 Feb 1999 17:59:22 +0100 From: "P.M. Houpt" X-Mailer: Mozilla 3.01-C-WXS-Mac (Macintosh; I; PPC) MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: Overview of Video Capture options for B&W G3's References: <354393.3128853135@huginn.medicine.washington.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"Cucrq3.0.mS5.P2Ors"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1017 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 367 Dear David, For scientific purposes it's better to use a framegrabber board without compression.In my opinion the best choose in your list is the SCION LG3 . I use it for several years for capturing microscopy BW images. With compression you always will lose information, best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 31703504466 From nih-image-request@io.ece.drexel.edu Thu Feb 25 15:26 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA09978 for cshtest@io.ece.drexel.edu; Thu, 25 Feb 1999 15:26:03 -0500 (EST) Resent-Date: Thu, 25 Feb 1999 15:26:03 -0500 (EST) Date: Thu, 25 Feb 1999 15:10:41 -0500 (EST) X-Sender: mechawan@alize.ere.umontreal.ca Message-Id: Mime-Version: 1.0 X-Mailer: Eudora F1.5.5 To: nih-image@io.ece.drexel.edu From: mechawan@ERE.UMontreal.CA (Naguib MECHAWAR) Subject: Help! Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by io.ece.drexel.edu id PAA08525 Resent-Message-ID: <"mlCSn3.0.L52.AvQrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1018 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: 1588 Hello! I recently started working with NIH Image (version 1.60) and have encountered a problem which seemed initially easy enough to solve rapidly. But I still havn't found a solution, which brings my project to a stand-still!!! So I would very much appreciate if someone could give me a hand with this. Here goes: I am trying to analyze 2-D images solely composed of lines (all of them having the same width, but with different individual lenghts and random directions). What interests me is to know the total lenght of the lines composing the images. I have managed to do it for the images which contain only a few of them. But some of the images have a higher density of lines, which gives rise to a tight network of intersecting lines in which many closed surfaces are created. The problem is that such closed surfaces seem to be an obstacle. The program gives me very different values for the lenght of the lines intersecting to form, let's say, a triangle and for the same lines if I "open" the triangle by removing a pixel or two... Another problem with those closed areas is that I sometimes have lines passing through them and the portion of the line comprised in the area cannot be selected for a lenght measurement... I am sure that there is a very simple way to get around this... but what is it?! I hope I was clear enough in describing my problem and that someone out there knows the solution to it. Thanking you in advance, ************************************* Naguib Mechawar Sc. neurologiques Université de Montréal ************************************* From nih-image-request@io.ece.drexel.edu Thu Feb 25 16:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA13487 for cshtest@io.ece.drexel.edu; Thu, 25 Feb 1999 16:02:46 -0500 (EST) Resent-Date: Thu, 25 Feb 1999 16:02:46 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Thu, 25 Feb 1999 15:48:18 -0500 From: "Wade Schuette" To: mechawan@ERE.UMontreal.CA, nih-image@io.ece.drexel.edu Subject: Re: Help! 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 PAA12003 Resent-Message-ID: <"6MMNq2.0.mx2.kSRrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1019 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: 2411 This is not a solution but a "work-around." If the lines are truly in random directions, and the length is not correlated with direction, then I believe you could "skeletonize" the image and simply count pixels to get a value that would be close to proportional to the sum of line lengths in your original image for images with many lines on them. ( I don't know the proportion but it probably involves "pi"). You could test the concept and bracket its accuracy by generating a number of such images with known line lengths and plot the resulting measure versus known lengths. (That's not much additional work, since you probably want to do that to test ANY proposed solution after your experience so far.) Wade Schuette (schuette@umich.edu) >>> Naguib MECHAWAR 02/25 3:25 PM >>> Hello! I recently started working with NIH Image (version 1.60) and have encountered a problem which seemed initially easy enough to solve rapidly. But I still havn't found a solution, which brings my project to a stand-still!!! So I would very much appreciate if someone could give me a hand with this. Here goes: I am trying to analyze 2-D images solely composed of lines (all of them having the same width, but with different individual lenghts and random directions). What interests me is to know the total lenght of the lines composing the images. I have managed to do it for the images which contain only a few of them. But some of the images have a higher density of lines, which gives rise to a tight network of intersecting lines in which many closed surfaces are created. The problem is that such closed surfaces seem to be an obstacle. The program gives me very different values for the lenght of the lines intersecting to form, let's say, a triangle and for the same lines if I "open" the triangle by removing a pixel or two... Another problem with those closed areas is that I sometimes have lines passing through them and the portion of the line comprised in the area cannot be selected for a lenght measurement... I am sure that there is a very simple way to get around this... but what is it?! I hope I was clear enough in describing my problem and that someone out there knows the solution to it. Thanking you in advance, ************************************* Naguib Mechawar Sc. neurologiques Université de Montréal ************************************* From nih-image-request@io.ece.drexel.edu Thu Feb 25 16:57 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA17924 for cshtest@io.ece.drexel.edu; Thu, 25 Feb 1999 16:57:32 -0500 (EST) Resent-Date: Thu, 25 Feb 1999 16:57:32 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Thu, 25 Feb 1999 16:38:43 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Help! Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"HVJYb.0.a44.AGSrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1020 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1176 In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: > If the lines are truly in random > >directions, and the length is not correlated with direction, then I believe >you > >could "skeletonize" the image and simply count pixels to get a value that >would > >be close to proportional to the sum of line lengths in your original image >for images > >with many lines on them. ( I don't know the proportion but it probably >involves "pi"). It's actually a little more complicated than that. The skeleton consists of links that are 1.0 and 1.414 pixels long. If you just count the number of pixels you will seriously underestimate the length. If you count the face- touching and corner touching links separately and multiply the latter by sqrt(2), and sum everything up, you will slightly overestimate the length. Smeulders has published correction factors for this case (and also for the 3D case in which you look at a projection of 3D lines in a 2D image). Of course, if you know that you are dealing with straight lines you could just find the end points (points in the skeleton with exactly one neighbor) and just use the Pythagorean distance. John Russ From nih-image-request@io.ece.drexel.edu Thu Feb 25 18:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA27544 for cshtest@io.ece.drexel.edu; Thu, 25 Feb 1999 18:18:57 -0500 (EST) Resent-Date: Thu, 25 Feb 1999 18:18:57 -0500 (EST) Message-Id: <3.0.5.32.19990226100841.007c2ce0@pop3.unsw.edu.au> X-Sender: s9500316@pop3.unsw.edu.au (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 26 Feb 1999 10:08:41 +1100 To: nih-image@io.ece.drexel.edu From: John Jamieson Subject: Surface area from voxels? Mime-Version: 1.0 Resent-Message-ID: <"RSCi-1.0.7L6.cRTrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1021 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 983 My query does not relate to NIH Image directly, but here goes anyway... There have been some papers in the last few years reporting cell surface area measurements from fluorescence confocal microscopy imaging. The surface area measurements have relied on counting surface-voxel external surfaces. Does anyone know how reliable this kind of measure is? or can anyone point me to literature on the subject? As I would expect, these "3D" measurements give higher surface area measurements than comparable measures based on 2D optical microscopy projection images (eg representation of the cell as a collection of regular objects), but is it likely that simply counting voxel surfaces is an overestimate? Or does it depend on the confocal imaging parameters etc? Any ideas on the subject will be greatly appreciated. Thanks, John Jamieson Prince of Wales Medical Research Institute Randwick NSW AUSTRALIA tel: 61-2-9382-2696 fax: 61-2-9382-2723 email: j.jamieson@unsw.edu.au From nih-image-request@io.ece.drexel.edu Fri Feb 26 00:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01007 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 00:16:12 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 00:16:12 -0500 (EST) Message-Id: <3.0.5.32.19990226050141.0093e9a0@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: Fri, 26 Feb 1999 05:01:41 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Help! In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"H7y_w3.0.-87.MjYrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1022 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1674 At 04:38 PM 2/25/99 EST, John Russ wrote: > >In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: >>...could "skeletonize" the image and simply count pixels to get a value that >>...would be close to proportional to the sum of line lengths >It's actually a little more complicated than that. The skeleton consists of >links that are 1.0 and 1.414 pixels long. If you ...> >John Russ Hmm. I didn't get whether that meant you disagreed with my workaround or not, John. The complexity of the relationship between number of pixels and line length as a function of angle is irrelevant, if it's constant for any particular angle, and essentially a linear function of length for that angle, for long lines. It still seems to me that, if you have a large number of lines, randomly oriented, of random lengths, the total count of pixels of skeletonized lines should be close to proportional to total line length, and would be an EASY figure to obtain, and relatively easy to experiment with and bracket the accuracy which, for all we know, may be "good enough" for the intended purpose. If the lines were ALL one fixed angle theta to horizontal, this would clearly be true, no? Twice as long would mean twice as many skeletonized pixels, plus or minus an end effect. So, for each angle, we have a function that is linear in total line length for that angle. The SUM of such functions would also be a linear function if a constant fraction of new lines were distributed in each direction. For a large number of lines, randomly oriented, that would be true. No? Wade Schuette Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Fri Feb 26 00:18 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id AAA01376 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 00:18:33 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 00:18:33 -0500 (EST) Message-Id: <3.0.5.32.19990226000141.0097a7c0@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: Fri, 26 Feb 1999 00:01:41 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Help! In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"YxyYn3.0.aF7.imYrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1023 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1674 At 04:38 PM 2/25/99 EST, John Russ wrote: > >In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: >>...could "skeletonize" the image and simply count pixels to get a value that >>...would be close to proportional to the sum of line lengths >It's actually a little more complicated than that. The skeleton consists of >links that are 1.0 and 1.414 pixels long. If you ...> >John Russ Hmm. I didn't get whether that meant you disagreed with my workaround or not, John. The complexity of the relationship between number of pixels and line length as a function of angle is irrelevant, if it's constant for any particular angle, and essentially a linear function of length for that angle, for long lines. It still seems to me that, if you have a large number of lines, randomly oriented, of random lengths, the total count of pixels of skeletonized lines should be close to proportional to total line length, and would be an EASY figure to obtain, and relatively easy to experiment with and bracket the accuracy which, for all we know, may be "good enough" for the intended purpose. If the lines were ALL one fixed angle theta to horizontal, this would clearly be true, no? Twice as long would mean twice as many skeletonized pixels, plus or minus an end effect. So, for each angle, we have a function that is linear in total line length for that angle. The SUM of such functions would also be a linear function if a constant fraction of new lines were distributed in each direction. For a large number of lines, randomly oriented, that would be true. No? Wade Schuette Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-d-request@io.ece.drexel.edu Fri Feb 26 06:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA04849; Fri, 26 Feb 1999 06:15:10 -0500 (EST) Date: Fri, 26 Feb 1999 06:15:10 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902261115.GAA04849@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #48 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/48 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: 12728 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 48 Today's Topics: Re: Overview of Video Capture option [ "P.M. Houpt" ] Help! [ mechawan@ERE.UMontreal.CA (Naguib M ] Re: Help! [ "Wade Schuette" To: nih-image@io.ece.drexel.edu Subject: Re: Overview of Video Capture options for B&W G3's Message-ID: <36D5815E.6F19@wxs.nl> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear David, For scientific purposes it's better to use a framegrabber board without compression.In my opinion the best choose in your list is the SCION LG3 . I use it for several years for capturing microscopy BW images. With compression you always will lose information, best wishes, Pieter Houpt -- BIOMET The Hague , The Netherlands. voice/fax : 31703504466 ------------------------------ Date: Thu, 25 Feb 1999 15:10:41 -0500 (EST) From: mechawan@ERE.UMontreal.CA (Naguib MECHAWAR) To: nih-image@io.ece.drexel.edu Subject: Help! Message-Id: Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hello! I recently started working with NIH Image (version 1.60) and have encountered a problem which seemed initially easy enough to solve rapidly. But I still havn't found a solution, which brings my project to a stand-still!!! So I would very much appreciate if someone could give me a hand with this. Here goes: I am trying to analyze 2-D images solely composed of lines (all of them having the same width, but with different individual lenghts and random directions). What interests me is to know the total lenght of the lines composing the images. I have managed to do it for the images which contain only a few of them. But some of the images have a higher density of lines, which gives rise to a tight network of intersecting lines in which many closed surfaces are created. The problem is that such closed surfaces seem to be an obstacle. The program gives me very different values for the lenght of the lines intersecting to form, let's say, a triangle and for the same lines if I "open" the triangle by removing a pixel or two... Another problem with those closed areas is that I sometimes have lines passing through them and the portion of the line comprised in the area cannot be selected for a lenght measurement... I am sure that there is a very simple way to get around this... but what is it?! I hope I was clear enough in describing my problem and that someone out there knows the solution to it. Thanking you in advance, ************************************* Naguib Mechawar Sc. neurologiques Université de Montréal ************************************* ------------------------------ Date: Thu, 25 Feb 1999 15:48:18 -0500 From: "Wade Schuette" To: mechawan@ERE.UMontreal.CA, nih-image@io.ece.drexel.edu Subject: Re: Help! Message-Id: Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit This is not a solution but a "work-around." If the lines are truly in random directions, and the length is not correlated with direction, then I believe you could "skeletonize" the image and simply count pixels to get a value that would be close to proportional to the sum of line lengths in your original image for images with many lines on them. ( I don't know the proportion but it probably involves "pi"). You could test the concept and bracket its accuracy by generating a number of such images with known line lengths and plot the resulting measure versus known lengths. (That's not much additional work, since you probably want to do that to test ANY proposed solution after your experience so far.) Wade Schuette (schuette@umich.edu) >>> Naguib MECHAWAR 02/25 3:25 PM >>> Hello! I recently started working with NIH Image (version 1.60) and have encountered a problem which seemed initially easy enough to solve rapidly. But I still havn't found a solution, which brings my project to a stand-still!!! So I would very much appreciate if someone could give me a hand with this. Here goes: I am trying to analyze 2-D images solely composed of lines (all of them having the same width, but with different individual lenghts and random directions). What interests me is to know the total lenght of the lines composing the images. I have managed to do it for the images which contain only a few of them. But some of the images have a higher density of lines, which gives rise to a tight network of intersecting lines in which many closed surfaces are created. The problem is that such closed surfaces seem to be an obstacle. The program gives me very different values for the lenght of the lines intersecting to form, let's say, a triangle and for the same lines if I "open" the triangle by removing a pixel or two... Another problem with those closed areas is that I sometimes have lines passing through them and the portion of the line comprised in the area cannot be selected for a lenght measurement... I am sure that there is a very simple way to get around this... but what is it?! I hope I was clear enough in describing my problem and that someone out there knows the solution to it. Thanking you in advance, ************************************* Naguib Mechawar Sc. neurologiques Université de Montréal ************************************* ------------------------------ Date: Thu, 25 Feb 1999 16:38:43 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Help! Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: > If the lines are truly in random > >directions, and the length is not correlated with direction, then I believe >you > >could "skeletonize" the image and simply count pixels to get a value that >would > >be close to proportional to the sum of line lengths in your original image >for images > >with many lines on them. ( I don't know the proportion but it probably >involves "pi"). It's actually a little more complicated than that. The skeleton consists of links that are 1.0 and 1.414 pixels long. If you just count the number of pixels you will seriously underestimate the length. If you count the face- touching and corner touching links separately and multiply the latter by sqrt(2), and sum everything up, you will slightly overestimate the length. Smeulders has published correction factors for this case (and also for the 3D case in which you look at a projection of 3D lines in a 2D image). Of course, if you know that you are dealing with straight lines you could just find the end points (points in the skeleton with exactly one neighbor) and just use the Pythagorean distance. John Russ ------------------------------ Date: Fri, 26 Feb 1999 10:08:41 +1100 From: John Jamieson To: nih-image@io.ece.drexel.edu Subject: Surface area from voxels? Message-Id: <3.0.5.32.19990226100841.007c2ce0@pop3.unsw.edu.au> Content-Type: text/plain; charset="us-ascii" My query does not relate to NIH Image directly, but here goes anyway... There have been some papers in the last few years reporting cell surface area measurements from fluorescence confocal microscopy imaging. The surface area measurements have relied on counting surface-voxel external surfaces. Does anyone know how reliable this kind of measure is? or can anyone point me to literature on the subject? As I would expect, these "3D" measurements give higher surface area measurements than comparable measures based on 2D optical microscopy projection images (eg representation of the cell as a collection of regular objects), but is it likely that simply counting voxel surfaces is an overestimate? Or does it depend on the confocal imaging parameters etc? Any ideas on the subject will be greatly appreciated. Thanks, John Jamieson Prince of Wales Medical Research Institute Randwick NSW AUSTRALIA tel: 61-2-9382-2696 fax: 61-2-9382-2723 email: j.jamieson@unsw.edu.au ------------------------------ Date: Fri, 26 Feb 1999 05:01:41 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Help! Message-Id: <3.0.5.32.19990226050141.0093e9a0@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" At 04:38 PM 2/25/99 EST, John Russ wrote: > >In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: >>...could "skeletonize" the image and simply count pixels to get a value that >>...would be close to proportional to the sum of line lengths >It's actually a little more complicated than that. The skeleton consists of >links that are 1.0 and 1.414 pixels long. If you ...> >John Russ Hmm. I didn't get whether that meant you disagreed with my workaround or not, John. The complexity of the relationship between number of pixels and line length as a function of angle is irrelevant, if it's constant for any particular angle, and essentially a linear function of length for that angle, for long lines. It still seems to me that, if you have a large number of lines, randomly oriented, of random lengths, the total count of pixels of skeletonized lines should be close to proportional to total line length, and would be an EASY figure to obtain, and relatively easy to experiment with and bracket the accuracy which, for all we know, may be "good enough" for the intended purpose. If the lines were ALL one fixed angle theta to horizontal, this would clearly be true, no? Twice as long would mean twice as many skeletonized pixels, plus or minus an end effect. So, for each angle, we have a function that is linear in total line length for that angle. The SUM of such functions would also be a linear function if a constant fraction of new lines were distributed in each direction. For a large number of lines, randomly oriented, that would be true. No? Wade Schuette Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Fri, 26 Feb 1999 00:01:41 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Help! Message-Id: <3.0.5.32.19990226000141.0097a7c0@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" At 04:38 PM 2/25/99 EST, John Russ wrote: > >In a message dated 2/25/99 8:56:41 PM, schuette@umich.edu writes: >>...could "skeletonize" the image and simply count pixels to get a value that >>...would be close to proportional to the sum of line lengths >It's actually a little more complicated than that. The skeleton consists of >links that are 1.0 and 1.414 pixels long. If you ...> >John Russ Hmm. I didn't get whether that meant you disagreed with my workaround or not, John. The complexity of the relationship between number of pixels and line length as a function of angle is irrelevant, if it's constant for any particular angle, and essentially a linear function of length for that angle, for long lines. It still seems to me that, if you have a large number of lines, randomly oriented, of random lengths, the total count of pixels of skeletonized lines should be close to proportional to total line length, and would be an EASY figure to obtain, and relatively easy to experiment with and bracket the accuracy which, for all we know, may be "good enough" for the intended purpose. If the lines were ALL one fixed angle theta to horizontal, this would clearly be true, no? Twice as long would mean twice as many skeletonized pixels, plus or minus an end effect. So, for each angle, we have a function that is linear in total line length for that angle. The SUM of such functions would also be a linear function if a constant fraction of new lines were distributed in each direction. For a large number of lines, randomly oriented, that would be true. No? Wade Schuette Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 -------------------------------- End of nih-image-d Digest V99 Issue #48 *************************************** From nih-image-request@io.ece.drexel.edu Fri Feb 26 10:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA01471 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 10:54:58 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 10:54:58 -0500 (EST) Message-ID: <36D6BFFF.45A3053@ucdavis.edu> Date: Fri, 26 Feb 1999 07:38:39 -0800 From: Jana Gut X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #48 References: <199902261116.GAA04992@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"FZu5g2.0.SC7.H-hrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1024 X-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: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Fri Feb 26 11:16 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA03696 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 11:16:28 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 11:16:28 -0500 (EST) Date: Fri, 26 Feb 1999 15:57:25 +0000 (GMT) From: "A.G.H.Podoleanu" X-Sender: ap11@kiwi To: nih-image@io.ece.drexel.edu Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"uGdY82.0.ES.OIirs"@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/1025 X-Loop: nih-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 Fri Feb 26 12:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12153 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 12:39:16 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 12:39:16 -0500 (EST) From: rdr8@cornell.edu Date: Fri, 26 Feb 1999 12:24:53 -0500 (EST) X-Sender: rdr8@travelers.mail.cornell.edu To: nih-image@io.ece.drexel.edu cc: rdr8@cornell.edu Subject: Re: nih-image-d Digest V99 #48 In-Reply-To: <199902261115.GAA04865@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"DkUnv.0.aU2.hZjrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1026 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 91 How does background subtraction fix uneven background illumination? Thanks, Rebecca Riba From nih-image-request@io.ece.drexel.edu Fri Feb 26 12:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA12243 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 12:39:30 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 12:39:30 -0500 (EST) Subject: Re: Help! Date: Fri, 26 Feb 99 12:25:57 -0500 x-sender: jlr$biol.biol.qc@qc1.qc.edu x-mailer: Claris Emailer 1.1 From: "Jared L. Rifkin" To: , Mime-Version: 1.0 Message-ID: <409E8CC248F@qc1.qc.edu> Resent-Message-ID: <"yWFYf3.0.MY2.Qbjrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1027 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="US-ASCII" Content-Length: 471 at the risk of hopping on angels footprints-> pixels appear to be square and therefore at any angle other than horizontal or vertical- (wherein width and height of pixel are equal and therefore the number of pixels per unit line length is the same whether vertical or horizontal) the number of pixels covered by a unit line will always be less (than that covered by horixontal or vertical line). even if pixels were round, you run in the non-close-packing problem! From nih-image-request@io.ece.drexel.edu Fri Feb 26 17:15 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA08351 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 17:15:18 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 17:15:18 -0500 (EST) Message-Id: X-Mailer: Novell GroupWise 5.2 Date: Fri, 26 Feb 1999 17:01:43 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu, jared_rifkin@qc.edu Subject: Re: Help! Mime-Version: 1.0 Content-Disposition: inline Resent-Message-ID: <"pcE4v1.0.1i1.Mdnrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1028 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 2613 I agree with your comment, but my point was that it shouldn't matter. Yes, the pixel representation of a line at 45 degrees has fewer pixels per centimeter of line length than a horizontal one. And the pixel representation of a line at 37.25 degrees has some totally strange number of pixels per centimeter. BUT, so what? Imagine ANY grid of random length lines at random angles, as represented by these pixels. Say the total of all line lengths is "L" and the total number of pixels in the skeletonized "lines" is P. If you now doubled the length of every line, you'd have a total line length of 2*L. You'd also have, to a very close approximation, 2*P pixels. Triple every line length, and total length is 3*L, total number of black pixels is 3*P. The ratio of line-length to pixels remains constant for this scenario, regardless what you multiply the line length by --ie, 3*L/3*P = 2*L/2*P = L/P. establish that ratio, measure, P, and you can deduce L, for any length lines. Ahh, yes, you may say, but what if there were DIFFERENT lines, wouldn't the ratio change? This is why I said for "a large number of randomly oriented lines whose lengths are not correlated with their direction", because, for such lines, there are essentially a constant fraction of them in any angular range. Therefore, measure the fraction (L/P) for any such grid, and you can use that to approximate L/P for ALL such grids. It's not exactly accurate, both from end effects and single-counting each point where two lines intersect - but it is FAST, it is EASY, it can be TESTED, and could give an ADEQUATE approximation. As the number of lines gets fewer, the approximation gets worse. Unless I'm wrong, of course. So far, I haven't heard anything that dissuades me from this point, which is becoming academic, since the original user with the problem left long ago. : ) Still, I'll run a simulation this weekend and see how close the approximation is, in case I'm missing some point and being incredilbly dense here. regards. Wade >>> "Jared L. Rifkin" 02/26 12:39 PM >>> at the risk of hopping on angels footprints-> pixels appear to be square and therefore at any angle other than horizontal or vertical- (wherein width and height of pixel are equal and therefore the number of pixels per unit line length is the same whether vertical or horizontal) the number of pixels covered by a unit line will always be less (than that covered by horixontal or vertical line). even if pixels were round, you run in the non-close-packing problem! From nih-image-request@io.ece.drexel.edu Fri Feb 26 17:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA09141 for cshtest@io.ece.drexel.edu; Fri, 26 Feb 1999 17:21:26 -0500 (EST) Resent-Date: Fri, 26 Feb 1999 17:21:26 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Fri, 26 Feb 1999 17:07:05 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Re: Help! Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"D4kmd.0.Ky1.ymnrs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1029 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1081 In a message dated 2/26/99 5:13:28 AM, schuette@s.imap.itd.umich.edu writes: >If the lines were ALL one fixed angle theta to horizontal, this would >clearly be true, no? Twice as long would mean twice as many skeletonized >pixels, plus or minus an end effect. So, for each angle, we have a >function that is linear in total line length for that angle. The SUM >of such functions would also be a linear function if a constant fraction >of new lines were distributed in each direction. For a large number of >lines, randomly oriented, that would be true. No? Simply speaking, no. the problem is that the skeleton actually consists of an aliased set of pixels lying along a line. The number of corner-connected and edge-connected pairs varies with the angle of the line. The length of the line and the number of pixels are not strictly proportional. I actually have a paper in press (Journal of Computer Assisted Microscopy, but who knows when it will finally be reviewed) that presents a new and extremely accurate way to measure such lines (straight or curved). John From nih-image-d-request@io.ece.drexel.edu Sat Feb 27 06:08 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA20727; Sat, 27 Feb 1999 06:08:20 -0500 (EST) Date: Sat, 27 Feb 1999 06:08:20 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902271108.GAA20727@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #49 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/49 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: 6740 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 49 Today's Topics: Re: nih-image-d Digest V99 #48 [ Jana Gut ] Unidentified subject! [ "A.G.H.Podoleanu" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #48 Message-ID: <36D6BFFF.45A3053@ucdavis.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Fri, 26 Feb 1999 15:57:25 +0000 (GMT) From: "A.G.H.Podoleanu" To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII unsubscribe ------------------------------ Date: Fri, 26 Feb 1999 12:24:53 -0500 (EST) From: rdr8@cornell.edu To: nih-image@io.ece.drexel.edu cc: rdr8@cornell.edu Subject: Re: nih-image-d Digest V99 #48 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII How does background subtraction fix uneven background illumination? Thanks, Rebecca Riba ------------------------------ Date: Fri, 26 Feb 99 12:25:57 -0500 From: "Jared L. Rifkin" To: , Subject: Re: Help! Message-ID: <409E8CC248F@qc1.qc.edu> Content-Type: text/plain; charset="US-ASCII" at the risk of hopping on angels footprints-> pixels appear to be square and therefore at any angle other than horizontal or vertical- (wherein width and height of pixel are equal and therefore the number of pixels per unit line length is the same whether vertical or horizontal) the number of pixels covered by a unit line will always be less (than that covered by horixontal or vertical line). even if pixels were round, you run in the non-close-packing problem! ------------------------------ Date: Fri, 26 Feb 1999 17:01:43 -0500 From: "Wade Schuette" To: nih-image@io.ece.drexel.edu, jared_rifkin@qc.edu Subject: Re: Help! Message-Id: Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline I agree with your comment, but my point was that it shouldn't matter. Yes, the pixel representation of a line at 45 degrees has fewer pixels per centimeter of line length than a horizontal one. And the pixel representation of a line at 37.25 degrees has some totally strange number of pixels per centimeter. BUT, so what? Imagine ANY grid of random length lines at random angles, as represented by these pixels. Say the total of all line lengths is "L" and the total number of pixels in the skeletonized "lines" is P. If you now doubled the length of every line, you'd have a total line length of 2*L. You'd also have, to a very close approximation, 2*P pixels. Triple every line length, and total length is 3*L, total number of black pixels is 3*P. The ratio of line-length to pixels remains constant for this scenario, regardless what you multiply the line length by --ie, 3*L/3*P = 2*L/2*P = L/P. establish that ratio, measure, P, and you can deduce L, for any length lines. Ahh, yes, you may say, but what if there were DIFFERENT lines, wouldn't the ratio change? This is why I said for "a large number of randomly oriented lines whose lengths are not correlated with their direction", because, for such lines, there are essentially a constant fraction of them in any angular range. Therefore, measure the fraction (L/P) for any such grid, and you can use that to approximate L/P for ALL such grids. It's not exactly accurate, both from end effects and single-counting each point where two lines intersect - but it is FAST, it is EASY, it can be TESTED, and could give an ADEQUATE approximation. As the number of lines gets fewer, the approximation gets worse. Unless I'm wrong, of course. So far, I haven't heard anything that dissuades me from this point, which is becoming academic, since the original user with the problem left long ago. : ) Still, I'll run a simulation this weekend and see how close the approximation is, in case I'm missing some point and being incredilbly dense here. regards. Wade >>> "Jared L. Rifkin" 02/26 12:39 PM >>> at the risk of hopping on angels footprints-> pixels appear to be square and therefore at any angle other than horizontal or vertical- (wherein width and height of pixel are equal and therefore the number of pixels per unit line length is the same whether vertical or horizontal) the number of pixels covered by a unit line will always be less (than that covered by horixontal or vertical line). even if pixels were round, you run in the non-close-packing problem! ------------------------------ Date: Fri, 26 Feb 1999 17:07:05 EST From: DrJohnRuss@aol.com To: nih-image@io.ece.drexel.edu Subject: Re: Help! Message-ID: Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 2/26/99 5:13:28 AM, schuette@s.imap.itd.umich.edu writes: >If the lines were ALL one fixed angle theta to horizontal, this would >clearly be true, no? Twice as long would mean twice as many skeletonized >pixels, plus or minus an end effect. So, for each angle, we have a >function that is linear in total line length for that angle. The SUM >of such functions would also be a linear function if a constant fraction >of new lines were distributed in each direction. For a large number of >lines, randomly oriented, that would be true. No? Simply speaking, no. the problem is that the skeleton actually consists of an aliased set of pixels lying along a line. The number of corner-connected and edge-connected pairs varies with the angle of the line. The length of the line and the number of pixels are not strictly proportional. I actually have a paper in press (Journal of Computer Assisted Microscopy, but who knows when it will finally be reviewed) that presents a new and extremely accurate way to measure such lines (straight or curved). John -------------------------------- End of nih-image-d Digest V99 Issue #49 *************************************** From nih-image-request@io.ece.drexel.edu Sat Feb 27 13:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id NAA02413 for cshtest@io.ece.drexel.edu; Sat, 27 Feb 1999 13:25:19 -0500 (EST) Resent-Date: Sat, 27 Feb 1999 13:25:19 -0500 (EST) Date: Sat, 27 Feb 1999 19:10:09 +0100 (CET) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Re: Help! In-Reply-To: Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"KYNSM1.0.KC.WK3ss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1030 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1098 I have the same problems with my lines. I am trying to measure only vertical lines(one pixel widht) with different lengths, but I cant get the right length. If I measure the lines manually I can get a value of e.g 37 pixels, but if i use Analyse particles the value is changed to Area:38, Length:76, major 43. I know that length refers to the perimeter around the llne and therefore the high value of this parameter, but what about area and major, should it not be the same??. Anyway, How can i get the right results (37 pixels)???? thanks.... Gary. > > > Simply speaking, no. the problem is that the skeleton actually consists of an > aliased set of pixels lying along a line. The number of corner-connected and > edge-connected pairs varies with the angle of the line. The length of the line > and the number of pixels are not strictly proportional. > > I actually have a paper in press (Journal of Computer Assisted Microscopy, but > who knows when it will finally be reviewed) that presents a new and extremely > accurate way to measure such lines (straight or curved). > > John > From nih-image-d-request@io.ece.drexel.edu Sun Feb 28 06:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA06007; Sun, 28 Feb 1999 06:14:04 -0500 (EST) Date: Sun, 28 Feb 1999 06:14:04 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199902281114.GAA06007@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #50 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/50 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: 1687 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 50 Today's Topics: Re: Help! [ Gary Chinga ] ------------------------------ Date: Sat, 27 Feb 1999 19:10:09 +0100 (CET) From: Gary Chinga To: nih-image@io.ece.drexel.edu Subject: Re: Help! Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I have the same problems with my lines. I am trying to measure only vertical lines(one pixel widht) with different lengths, but I cant get the right length. If I measure the lines manually I can get a value of e.g 37 pixels, but if i use Analyse particles the value is changed to Area:38, Length:76, major 43. I know that length refers to the perimeter around the llne and therefore the high value of this parameter, but what about area and major, should it not be the same??. Anyway, How can i get the right results (37 pixels)???? thanks.... Gary. > > > Simply speaking, no. the problem is that the skeleton actually consists of an > aliased set of pixels lying along a line. The number of corner-connected and > edge-connected pairs varies with the angle of the line. The length of the line > and the number of pixels are not strictly proportional. > > I actually have a paper in press (Journal of Computer Assisted Microscopy, but > who knows when it will finally be reviewed) that presents a new and extremely > accurate way to measure such lines (straight or curved). > > John > -------------------------------- End of nih-image-d Digest V99 Issue #50 *************************************** From nih-image-request@io.ece.drexel.edu Sun Feb 28 18:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id SAA11881 for cshtest@io.ece.drexel.edu; Sun, 28 Feb 1999 18:14:51 -0500 (EST) Resent-Date: Sun, 28 Feb 1999 18:14:51 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gary@nvg.ntnu.no, nih-image@io.ece.drexel.edu Date: Mon, 1 Mar 1999 10:02:19 +1100 Subject: Re: Help! Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: <9AA57C5402@rna.bio.mq.edu.au> Resent-Message-ID: <"YUmJc.0.gW2.ReSss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1031 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1618 >Date: Sat, 27 Feb 1999 19:10:09 +0100 (CET) >From: Gary Chinga >To: nih-image@io.ece.drexel.edu >Subject: Re: Help! > >I have the same problems with my lines. I am trying to measure >only vertical lines(one pixel widht) with different lengths, but I cant >get the right length. If I measure the lines manually I can >get a value of e.g 37 pixels, but if i use Analyse particles the value is >changed to Area:38, Length:76, major 43. I know that length refers to >the perimeter around the llne and therefore the high value of this >parameter, but what about area and major, should it not be the same??. Ah! an opportunity for me to also stumble "into the footprints of angels" :-) Area of a vertical/horizontal line is 1 > length as length is distance between centres of end pixels ie number of pixels - 2 * 1/2 pixels Analyse particles doesn't return length but perimeter as you say so for a vertical/horizontal line perimeter=2* number of pixels. major/minor axis is calculated on a best-fitting ellipse where "best-fitting" refers to a matching of 'moments on inertia' of corresponding binary objects (not a linear dimensional fit). >Anyway, How can i get the right results (37 pixels)???? vertical/horizontal line length = rLength[rCount]/2; or = rArea[rCount]-1; If not vertical/horizontal, then you need current "Help!" thread. :-) > >thanks.... ? :-) > >Gary. > 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 Sun Feb 28 19:03 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id TAA16474 for cshtest@io.ece.drexel.edu; Sun, 28 Feb 1999 19:03:47 -0500 (EST) Resent-Date: Sun, 28 Feb 1999 19:03:47 -0500 (EST) Date: Sun, 28 Feb 1999 18:49:45 -0500 (EST) From: R Wade Schuette X-Sender: schuette@joust.rs.itd.umich.edu To: nih-image@io.ece.drexel.edu cc: gary@nvg.ntnu.no Subject: Re: Help! In-Reply-To: <9AA57C5402@rna.bio.mq.edu.au> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"sYS-U1.0.ug3.WOTss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1032 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 269 On Mon, 1 Mar 1999 Greg Joss GJOSS@rna.bio.mq.edu.au wrote: ... > Ah! an opportunity for me to also stumble "into the footprints of angels" :-) > ... > If not vertical/horizontal, then you need current "Help!" thread. :-) > > > >thanks.... Oh, no! Help! Wade From nih-image-request@io.ece.drexel.edu Mon Mar 1 09:35 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA11775 for cshtest@io.ece.drexel.edu; Mon, 1 Mar 1999 09:35:46 -0500 (EST) Resent-Date: Mon, 1 Mar 1999 09:35:46 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <7245c86e.36daa03b@aol.com> Date: Mon, 1 Mar 1999 09:12:11 EST To: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: 3RD ANNOUNCEMENT: Image analysis workshops Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"EVRNb.0.lH2.Z4gss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1033 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1450 Workshops on Quantitative Image Analysis May 20-22 and May 24-26, 1999 North Carolina State University Raleigh, North Carolina, USA and June 14-16, 1998 Danish Technological Institute Taastrup, Denmark This highly regarded hands-on course taught by expert faculty has been presented annually for more than 15 years. It deals with all phases of quantitative and computer-assisted imaging from acquisition and processing through measurement and stereological interpretation. Attendees receive The Image Processing Handbook plus a CD-ROM containing images, algorithms (Photoshop-compatible for Mac and Windows) and an extensive on-line tutorial and course notes on stereology and statistical analysis. The course is appropriate for scientists, technicians and administrators using or intending to use these techniques. Attendees typically come from materials science, geology, biological and medical sciences, pharmaceuticals, food science, industrial quality control, remote sensing, and other disciplines. You are encouraged to bring your own images for the hands-on lab sessions. For detailed information and registration contact Cindy Allen, Dept. of Continuing and Professional Education, N. C. State University, Raleigh, NC 27695-7401, 919-515-8171, fax 919-515-7614, email: Cindy_Allen@NCSU.edu Information is available on-line at the following sites: http://members.aol.com/IPCourse/ http://evu.dti.dk/hojslet/ipcourse.htm From nih-image-d-request@io.ece.drexel.edu Mon Mar 1 09:36 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA11871; Mon, 1 Mar 1999 09:36:18 -0500 (EST) Date: Mon, 1 Mar 1999 09:36:18 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903011436.JAA11871@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #51 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/51 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: 4643 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 51 Today's Topics: Re: Help! [ GJOSS@rna.bio.mq.edu.au ] Re: Help! [ R Wade Schuette >Date: Sat, 27 Feb 1999 19:10:09 +0100 (CET) >From: Gary Chinga >To: nih-image@io.ece.drexel.edu >Subject: Re: Help! > >I have the same problems with my lines. I am trying to measure >only vertical lines(one pixel widht) with different lengths, but I cant >get the right length. If I measure the lines manually I can >get a value of e.g 37 pixels, but if i use Analyse particles the value is >changed to Area:38, Length:76, major 43. I know that length refers to >the perimeter around the llne and therefore the high value of this >parameter, but what about area and major, should it not be the same??. Ah! an opportunity for me to also stumble "into the footprints of angels" :-) Area of a vertical/horizontal line is 1 > length as length is distance between centres of end pixels ie number of pixels - 2 * 1/2 pixels Analyse particles doesn't return length but perimeter as you say so for a vertical/horizontal line perimeter=2* number of pixels. major/minor axis is calculated on a best-fitting ellipse where "best-fitting" refers to a matching of 'moments on inertia' of corresponding binary objects (not a linear dimensional fit). >Anyway, How can i get the right results (37 pixels)???? vertical/horizontal line length = rLength[rCount]/2; or = rArea[rCount]-1; If not vertical/horizontal, then you need current "Help!" thread. :-) > >thanks.... ? :-) > >Gary. > 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, 28 Feb 1999 18:49:45 -0500 (EST) From: R Wade Schuette To: nih-image@io.ece.drexel.edu cc: gary@nvg.ntnu.no Subject: Re: Help! Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 1 Mar 1999 Greg Joss GJOSS@rna.bio.mq.edu.au wrote: ... > Ah! an opportunity for me to also stumble "into the footprints of angels" :-) > ... > If not vertical/horizontal, then you need current "Help!" thread. :-) > > > >thanks.... Oh, no! Help! Wade ------------------------------ Date: Mon, 1 Mar 1999 09:12:11 EST From: DrJohnRuss@aol.com To: Microscopy@sparc5.microscopy.com, nih-image@io.ece.drexel.edu Subject: 3RD ANNOUNCEMENT: Image analysis workshops Message-ID: <7245c86e.36daa03b@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit Workshops on Quantitative Image Analysis May 20-22 and May 24-26, 1999 North Carolina State University Raleigh, North Carolina, USA and June 14-16, 1998 Danish Technological Institute Taastrup, Denmark This highly regarded hands-on course taught by expert faculty has been presented annually for more than 15 years. It deals with all phases of quantitative and computer-assisted imaging from acquisition and processing through measurement and stereological interpretation. Attendees receive The Image Processing Handbook plus a CD-ROM containing images, algorithms (Photoshop-compatible for Mac and Windows) and an extensive on-line tutorial and course notes on stereology and statistical analysis. The course is appropriate for scientists, technicians and administrators using or intending to use these techniques. Attendees typically come from materials science, geology, biological and medical sciences, pharmaceuticals, food science, industrial quality control, remote sensing, and other disciplines. You are encouraged to bring your own images for the hands-on lab sessions. For detailed information and registration contact Cindy Allen, Dept. of Continuing and Professional Education, N. C. State University, Raleigh, NC 27695-7401, 919-515-8171, fax 919-515-7614, email: Cindy_Allen@NCSU.edu Information is available on-line at the following sites: http://members.aol.com/IPCourse/ http://evu.dti.dk/hojslet/ipcourse.htm -------------------------------- End of nih-image-d Digest V99 Issue #51 *************************************** From nih-image-request@io.ece.drexel.edu Mon Mar 1 09:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA13305 for cshtest@io.ece.drexel.edu; Mon, 1 Mar 1999 09:46:47 -0500 (EST) Resent-Date: Mon, 1 Mar 1999 09:46:47 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: Date: Mon, 1 Mar 1999 09:12:53 EST To: nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Updates to Image Processing Tool Kit Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"zjZ2Z2.0.Ul2.-Jgss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1034 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 574 A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ Recent updates include Phong shading of surface reconstructions (with adjustable illumination) and an advanced Convolve routine that provides autoscaling and accepts floating point kernels. Several tutorials (pdf files) have also been posted, covering a variety of topics beyond those in the tutorial distributed on the CD. The site also has other updates, new plug-ins, bug fixes, and other information, all identical for both Mac and PC users. From nih-image-request@io.ece.drexel.edu Mon Mar 1 10:05 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA15523 for cshtest@io.ece.drexel.edu; Mon, 1 Mar 1999 10:05:45 -0500 (EST) Resent-Date: Mon, 1 Mar 1999 10:05:45 -0500 (EST) X-Sender: jjp3@pop.cwru.edu Message-Id: Mime-Version: 1.0 Date: Mon, 1 Mar 1999 09:50:45 -0400 To: nih-image@io.ece.drexel.edu From: jjp3@po.cwru.edu (James Plantner) Resent-Message-ID: <"X9PQj1.0.wJ3.IZgss"@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/1035 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 164 UNSUBSCRIBE James J. Plantner, Ph.D. Center for Vision Research Case Western Reserve University Cleveland, OH 44106-5068 (216)844-3612; fax: (216)844-5297/3196 From nih-image-request@io.ece.drexel.edu Mon Mar 1 10:28 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id KAA18024 for cshtest@io.ece.drexel.edu; Mon, 1 Mar 1999 10:28:08 -0500 (EST) Resent-Date: Mon, 1 Mar 1999 10:28:08 -0500 (EST) Message-ID: <36DAADD9.3154AD90@ucdavis.edu> Date: Mon, 01 Mar 1999 07:11:28 -0800 From: Jana Gut X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu CC: nih-image-d@io.ece.drexel.edu Subject: unsubscribe References: <199903011440.JAA12315@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"uiFLv2.0.1u3.crgss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1036 X-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: 13 unsubscribe From nih-image-request@io.ece.drexel.edu Mon Mar 1 20:30 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id UAA18432 for cshtest@io.ece.drexel.edu; Mon, 1 Mar 1999 20:30:42 -0500 (EST) Resent-Date: Mon, 1 Mar 1999 20:30:42 -0500 (EST) From: GJOSS@rna.bio.mq.edu.au Organization: Dept. of Biological Sciences To: gary.chinga@pfi.no, nih-image@io.ece.drexel.edu Date: Tue, 2 Mar 1999 12:19:01 +1100 Subject: Re: help! Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.1) Message-ID: Resent-Message-ID: <"fcPvx.0.D94.inpss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1037 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 2319 >From: Gary Chinga >To: "'GJOSS@rna.bio.mq.edu.au'" >Subject: help! >Date: Mon, 1 Mar 1999 10:05:26 +0100 > >hi! > >Thanks for your answer, but the following procedure > >vertical/horizontal line length = rLength[rCount]/2; >or = rArea[rCount]-1; > > >doesnt give the right length. I have measured two lines both manually >and with analyze particles, and if you see, dividing the perimeter by 2 >doesnt give the result i need. > > Area length {Measured with analyza particles} > 2.18 12.96 > 1.61 9.57 > > Area length {Measured manually} > 2.18 6.44 > 1.61 4.75 > >Gary. > I began my previous post with "Ah! an opportunity for me to also stumble "into the footprints of angels" :-)" in response to "Jared L. Rifkin" "at the risk of hopping on angels footprints->"; and stumble I did! :-) On checking, rather than off the top of my head, I find that analyzeParticles in Image returns the perimeter of the particle in the column labeled rLength and the perimeter counts around the outside of the vertical/horizontal line pixels counting corner pixels as sqrt(2) so that vertical/horizontal line length = rLength[rCount]/2-2*(sqrt(2)-1); or = rArea[rCount]-1; if length is measured between centres of end pixels; add 1 if length is to be measured between extremities of line. I should have emphasised however that the above works only on a pixel scale. analyzeParticles operates with scaled values {except in the case of analyzeParticles('rawXY');} so that the scalefactor is squared in the area measurement but not in the perimeter/length field. I expect this explains the above results. It usually seems easier to me to use getScale(scale,unit,AspectRatio); to retrieve scaling setScale(0,'pixel'); to disable scale prior to analyzeParticles in those cases where you need/want to play with integer pixel results. I suspect I am still floundering about. :-) 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 Mar 2 03:27 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA02494 for cshtest@io.ece.drexel.edu; Tue, 2 Mar 1999 03:27:40 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 03:27:40 -0500 (EST) Message-ID: <19990302081417.22483.qmail@hotmail.com> X-Originating-IP: [139.165.30.129] From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Problems with LG3 Date: Tue, 02 Mar 1999 00:14:15 PST Mime-Version: 1.0 Resent-Message-ID: <"BceUX3.0.p9.ytvss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1038 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain Content-Length: 965 Dear Imagers I work with a JAI camera and frame grabber LG3, these work well when drived with the soft Scion Image, but if I'd like to acquire images with NIH-Image (or Image SXM), I have some problems when I start the command 'Start Camera'. The image is flashing between the 'real image' and a b/w grid (like 'chess game')... Someone can say me why? Thanks ....and sorry for my bad english. Enrico ************************************************************ Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ************************************************************ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From nih-image-d-request@io.ece.drexel.edu Tue Mar 2 03:35 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id DAA03489; Tue, 2 Mar 1999 03:35:01 -0500 (EST) Date: Tue, 2 Mar 1999 03:35:01 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903020835.DAA03489@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #52 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/52 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: 6024 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 52 Today's Topics: Updates to Image Processing Tool Kit [ DrJohnRuss@aol.com ] Unidentified subject! [ jjp3@po.cwru.edu (James Plantner) ] unsubscribe [ Jana Gut ] Re: help! [ GJOSS@rna.bio.mq.edu.au ] Problems with LG3 [ "Enrico BONINO" Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit A new update package for the Image Processing Tool Kit has been posted on the web site at http://members.aol.com/ImagProcTK/ Recent updates include Phong shading of surface reconstructions (with adjustable illumination) and an advanced Convolve routine that provides autoscaling and accepts floating point kernels. Several tutorials (pdf files) have also been posted, covering a variety of topics beyond those in the tutorial distributed on the CD. The site also has other updates, new plug-ins, bug fixes, and other information, all identical for both Mac and PC users. ------------------------------ Date: Mon, 1 Mar 1999 09:50:45 -0400 From: jjp3@po.cwru.edu (James Plantner) To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" UNSUBSCRIBE James J. Plantner, Ph.D. Center for Vision Research Case Western Reserve University Cleveland, OH 44106-5068 (216)844-3612; fax: (216)844-5297/3196 ------------------------------ Date: Mon, 01 Mar 1999 07:11:28 -0800 From: Jana Gut To: nih-image@io.ece.drexel.edu CC: nih-image-d@io.ece.drexel.edu Subject: unsubscribe Message-ID: <36DAADD9.3154AD90@ucdavis.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit unsubscribe ------------------------------ Date: Tue, 2 Mar 1999 12:19:01 +1100 From: GJOSS@rna.bio.mq.edu.au To: gary.chinga@pfi.no, nih-image@io.ece.drexel.edu Subject: Re: help! Message-ID: >From: Gary Chinga >To: "'GJOSS@rna.bio.mq.edu.au'" >Subject: help! >Date: Mon, 1 Mar 1999 10:05:26 +0100 > >hi! > >Thanks for your answer, but the following procedure > >vertical/horizontal line length = rLength[rCount]/2; >or = rArea[rCount]-1; > > >doesnt give the right length. I have measured two lines both manually >and with analyze particles, and if you see, dividing the perimeter by 2 >doesnt give the result i need. > > Area length {Measured with analyza particles} > 2.18 12.96 > 1.61 9.57 > > Area length {Measured manually} > 2.18 6.44 > 1.61 4.75 > >Gary. > I began my previous post with "Ah! an opportunity for me to also stumble "into the footprints of angels" :-)" in response to "Jared L. Rifkin" "at the risk of hopping on angels footprints->"; and stumble I did! :-) On checking, rather than off the top of my head, I find that analyzeParticles in Image returns the perimeter of the particle in the column labeled rLength and the perimeter counts around the outside of the vertical/horizontal line pixels counting corner pixels as sqrt(2) so that vertical/horizontal line length = rLength[rCount]/2-2*(sqrt(2)-1); or = rArea[rCount]-1; if length is measured between centres of end pixels; add 1 if length is to be measured between extremities of line. I should have emphasised however that the above works only on a pixel scale. analyzeParticles operates with scaled values {except in the case of analyzeParticles('rawXY');} so that the scalefactor is squared in the area measurement but not in the perimeter/length field. I expect this explains the above results. It usually seems easier to me to use getScale(scale,unit,AspectRatio); to retrieve scaling setScale(0,'pixel'); to disable scale prior to analyzeParticles in those cases where you need/want to play with integer pixel results. I suspect I am still floundering about. :-) 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, 02 Mar 1999 00:14:15 PST From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Problems with LG3 Message-ID: <19990302081417.22483.qmail@hotmail.com> Content-type: text/plain Dear Imagers I work with a JAI camera and frame grabber LG3, these work well when drived with the soft Scion Image, but if I'd like to acquire images with NIH-Image (or Image SXM), I have some problems when I start the command 'Start Camera'. The image is flashing between the 'real image' and a b/w grid (like 'chess game')... Someone can say me why? Thanks ....and sorry for my bad english. Enrico ************************************************************ Enrico BONINO, geologist University of Liege Dept. of Applied Geology Lab. MICA Geomaterials Characterization http://www.ulg.ac.be/mica Avenue des Tilleuls, 45 B-4000 LIEGE BELGIUM tel. 0032 (0)4 3669526 fax 0032 (0)4 3669520 E-mail: e_bonino@hotmail.com CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 ************************************************************ ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com -------------------------------- End of nih-image-d Digest V99 Issue #52 *************************************** From nih-image-request@io.ece.drexel.edu Tue Mar 2 09:23 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA13408; Tue, 2 Mar 1999 09:23:03 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 09:23:03 -0500 (EST) Message-ID: <36DBF035.C750834A@ucsd.edu> Date: Tue, 02 Mar 1999 06:05:41 -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, drjohnruss@aol.com Subject: Attn: John Russ re Photoshop plug-ins and 12 bit images References: <199903020831.DAA02953@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"E6fyv3.0.po2.s3_ss"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1039 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=us-ascii Content-Length: 1175 John, Have you developed a Photoshop filter for opening the variety of 12/16 bit images from confocal scopes? A number of confocal manufacturers now routinely generate 12 bits/channel images of both single images, 2 channel, 3 channel or 4 channels. They also generate extended Z-series of 1, 2, 3 or 4 channels. Photoshop simply can't handle any of these varieties other than a vanilla single gray scale 12/16 bit, or a 3 channel RGB version of the same. If there are only two channels (e.g. an FITC and a LRSC fluorophore, but no third channel) it tosses in the towel. I would be glad to send you sample files from the Olympus Fluoview confocal. This is stored as a Multi-TIFF 6.0 file, and includes tags for info on parameters of data collection. BioRad's new confocal also uses 12/16 bit images, though I believe that they are using their own proprietary format (BioRAD 4.2). 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 From nih-image-request@io.ece.drexel.edu Tue Mar 2 09:59 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA17978; Tue, 2 Mar 1999 09:59:04 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 09:59:04 -0500 (EST) Date: Tue, 02 Mar 1999 14:39:00 +0000 (GMT) From: Stamatis Pagakis Subject: Photoshop plug-ins and 12 bit images In-reply-to: <36DBF035.C750834A@ucsd.edu> X-Sender: spagaki@membo2.nimr.mrc.ac.uk To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"nleko.0.4n3.CX_ss"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1040 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1555 On Tue, 2 Mar 1999, Harvey J. Karten wrote: > John, > Have you developed a Photoshop filter for opening the variety of > 12/16 bit images from confocal scopes? A number of confocal > manufacturers now routinely generate 12 bits/channel images of both > single images, 2 channel, 3 channel or 4 channels. They also generate > extended Z-series of 1, 2, 3 or 4 channels. Photoshop simply can't > handle any of these varieties other than a vanilla single gray scale > 12/16 bit, or a 3 channel RGB version of the same. If there are only two > channels (e.g. an FITC and a LRSC fluorophore, but no third channel) it > tosses in the towel. > I would also like to express interest for such filters. We have a Leica TCS SP and routinely use Photoshop for our final image layout. However, we do need to open them first in NIH Image, due to the problems Harvey outlined. Making photoshop aware of multi_z-multi_channel tiff images will greatly simplify our work (and make us purchase the plug-ins of course...) Regards, *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Membrane Biology Mobile: 0370 654288 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < From nih-image-request@io.ece.drexel.edu Tue Mar 2 11:43 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA29594; Tue, 2 Mar 1999 11:43:01 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 11:43:01 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Tue, 2 Mar 1999 18:34:09 +0300 To: nih-image@io.ece.drexel.edu From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti) Resent-Message-ID: <"KH-xR3.0.6f6.Y31ts"@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/1041 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 200 Unsuscribe 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 Tue Mar 2 11:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA29843; Tue, 2 Mar 1999 11:44:08 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 11:44:08 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Tue, 2 Mar 1999 18:34:31 +0300 To: nih-image@io.ece.drexel.edu From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti) Subject: unsuscribe Resent-Message-ID: <"VsZ7K2.0.Ng6.t31ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1042 X-Loop: nih-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 Tue Mar 2 11:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA00306; Tue, 2 Mar 1999 11:45:52 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 11:45:52 -0500 (EST) From: Rainer Saffrich Date: Tue, 2 Mar 1999 17:30:46 +0100 (MET) Message-Id: <199903021630.RAA13402@anna.PI.EMBL-Heidelberg.DE> To: nih-image@io.ece.drexel.edu Subject: ARCHIVE egrep watershed latest/* Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: AAAAAAAAAAAAAAAAAAAAAA== Resent-Message-ID: <"nkogE1.0.Et6.IA1ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1044 X-Loop: nih-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 Tue Mar 2 11:48 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA00989; Tue, 2 Mar 1999 11:48:12 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 11:48:12 -0500 (EST) From: Rainer Saffrich Date: Tue, 2 Mar 1999 17:29:27 +0100 (MET) Message-Id: <199903021629.RAA13398@anna.PI.EMBL-Heidelberg.DE> To: nih-image@io.ece.drexel.edu Subject: ARCHIVE ls latest Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: AAAAAAAAAAAAAAAAAAAAAA== Resent-Message-ID: <"I7Jp52.0.hq6.891ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1043 X-Loop: nih-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 Tue Mar 2 14:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id OAA14865; Tue, 2 Mar 1999 14:09:14 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 14:09:14 -0500 (EST) From: DrJohnRuss@aol.com Message-ID: <175c97dc.36dc3338@aol.com> Date: Tue, 2 Mar 1999 13:51:36 EST To: hjkarten@ucsd.edu, nih-image@io.ece.drexel.edu Mime-Version: 1.0 Subject: Attn: Harvey Karten re Photoshop plug-ins and 12 bit images Content-transfer-encoding: 7bit X-Mailer: AOL for Macintosh sub 54 Resent-Message-ID: <"vJzN12.0.ZJ3.IH3ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1045 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset=US-ASCII Content-Length: 1102 In a message dated 3/2/99 2:08:52 PM, hjkarten@ucsd.edu writes: > Have you developed a Photoshop filter for opening the variety of >12/16 bit images from confocal scopes? Harvey: we have in development an expanded version of the tool kit which provides a variety of useful functions to process and measure 16 bit deep grey and 48 bit deep color images. Confocal microscopes are not the only important source of these (perhaps not the most important from market considerations) - scanners and digital cameras also produce deep images, and for densitometry on gels, astronomy, etc., the extra depth is vital. We hope to release the next version of the regular tool kit (3.0) within the next couple of months (it is still designed for 8 bit grey, 24 bit RGB). The deeper version (not part of the regular tool kit series, so it will have a somewhat higher price and smaller market) will come along after that - I can't promise a specific date right now. If there are particular functions that you are concerned about let me know what they are and I'll try to make sure they are covered. John Russ From nih-image-d-request@io.ece.drexel.edu Tue Mar 2 21:00 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA25815; Tue, 2 Mar 1999 21:00:56 -0500 (EST) Date: Tue, 2 Mar 1999 21:00:56 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903030200.VAA25815@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #53 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/53 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: 11243 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 53 Today's Topics: quantitation of neurite length [ David Wynick To: nih-image-d@io.ece.drexel.edu Subject: quantitation of neurite length Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hello we have just started to culture primary dorsal root ganglia. The outgrowth of a single neurite from the cell body is long and tortuous. we would like/need to be able to quantitate neurite length of many neurons from a single coverslip (in excess of 100/slide). As far as I can see a simple but laborious way is to capture the images open them in nih image and use the freehand tool to trace a single neuron then click on anlyse and then measure (after calibration). Then do the next neurite etc each value is then added to the total which can be viewed and then exported to excel for stats. One major problem that I cannot at present solve is there seems to be no way of definitaly showing which neurons have been quantitated ie to avoid accidentally counting the same one twice. It would be nice if one could somehow colour neurons all ready counted. Also, is there a quicker or better way to do this? I tried thresholding or density slicing in the hope that I could light up the neurites but unfortunately they just merge into the background. any advice and help greatfully accepted TIA David ---------------------- David Wynick Department of Medicine Bristol University Marlborough Street Bristol BS2 8HW, UK Tel: 44 (0)117 9283396 Fax: 44 (0)117 9283976 E-mail: d.wynick@bris.ac.uk ------------------------------ Date: Tue, 02 Mar 1999 06:05:41 -0800 From: "Harvey J. Karten" To: nih-image@io.ece.drexel.edu, drjohnruss@aol.com Subject: Attn: John Russ re Photoshop plug-ins and 12 bit images Message-ID: <36DBF035.C750834A@ucsd.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit John, Have you developed a Photoshop filter for opening the variety of 12/16 bit images from confocal scopes? A number of confocal manufacturers now routinely generate 12 bits/channel images of both single images, 2 channel, 3 channel or 4 channels. They also generate extended Z-series of 1, 2, 3 or 4 channels. Photoshop simply can't handle any of these varieties other than a vanilla single gray scale 12/16 bit, or a 3 channel RGB version of the same. If there are only two channels (e.g. an FITC and a LRSC fluorophore, but no third channel) it tosses in the towel. I would be glad to send you sample files from the Olympus Fluoview confocal. This is stored as a Multi-TIFF 6.0 file, and includes tags for info on parameters of data collection. BioRad's new confocal also uses 12/16 bit images, though I believe that they are using their own proprietary format (BioRAD 4.2). 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 ------------------------------ Date: Tue, 02 Mar 1999 14:39:00 +0000 (GMT) From: Stamatis Pagakis To: nih-image@io.ece.drexel.edu Subject: Photoshop plug-ins and 12 bit images Message-id: Content-type: TEXT/PLAIN; charset=US-ASCII On Tue, 2 Mar 1999, Harvey J. Karten wrote: > John, > Have you developed a Photoshop filter for opening the variety of > 12/16 bit images from confocal scopes? A number of confocal > manufacturers now routinely generate 12 bits/channel images of both > single images, 2 channel, 3 channel or 4 channels. They also generate > extended Z-series of 1, 2, 3 or 4 channels. Photoshop simply can't > handle any of these varieties other than a vanilla single gray scale > 12/16 bit, or a 3 channel RGB version of the same. If there are only two > channels (e.g. an FITC and a LRSC fluorophore, but no third channel) it > tosses in the towel. > I would also like to express interest for such filters. We have a Leica TCS SP and routinely use Photoshop for our final image layout. However, we do need to open them first in NIH Image, due to the problems Harvey outlined. Making photoshop aware of multi_z-multi_channel tiff images will greatly simplify our work (and make us purchase the plug-ins of course...) Regards, *-----------------*------------------*----------------------*---------------* >Dr Stamatis Pagakis spagaki@nimr.mrc.ac.uk < >Confocal and Image Analysis Laboratory Tel: +44 (0)181 913 8675 < >Membrane Biology Mobile: 0370 654288 < >National Institute for Medical Research Switchboard: 0181 9593666 x2621 < >The Ridgeway Message: x2219, x2622 < >Mill Hill, London NW7 1AA FAX: +44 (0)181 906 4477 < ------------------------------ Date: Tue, 2 Mar 1999 18:34:09 +0300 From: ippoliti@axrma.uniroma1.it (Rodolfo Ippoliti) To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" Unsuscribe 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: Tue, 2 Mar 1999 18:34:31 +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: Tue, 2 Mar 1999 17:29:27 +0100 (MET) From: Rainer Saffrich To: nih-image@io.ece.drexel.edu Subject: ARCHIVE ls latest Message-Id: <199903021629.RAA13398@anna.PI.EMBL-Heidelberg.DE> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: AAAAAAAAAAAAAAAAAAAAAA== ------------------------------ Date: Tue, 2 Mar 1999 17:30:46 +0100 (MET) From: Rainer Saffrich To: nih-image@io.ece.drexel.edu Subject: ARCHIVE egrep watershed latest/* Message-Id: <199903021630.RAA13402@anna.PI.EMBL-Heidelberg.DE> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: AAAAAAAAAAAAAAAAAAAAAA== ------------------------------ Date: Tue, 2 Mar 1999 13:51:36 EST From: DrJohnRuss@aol.com To: hjkarten@ucsd.edu, nih-image@io.ece.drexel.edu Subject: Attn: Harvey Karten re Photoshop plug-ins and 12 bit images Message-ID: <175c97dc.36dc3338@aol.com> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit In a message dated 3/2/99 2:08:52 PM, hjkarten@ucsd.edu writes: > Have you developed a Photoshop filter for opening the variety of >12/16 bit images from confocal scopes? Harvey: we have in development an expanded version of the tool kit which provides a variety of useful functions to process and measure 16 bit deep grey and 48 bit deep color images. Confocal microscopes are not the only important source of these (perhaps not the most important from market considerations) - scanners and digital cameras also produce deep images, and for densitometry on gels, astronomy, etc., the extra depth is vital. We hope to release the next version of the regular tool kit (3.0) within the next couple of months (it is still designed for 8 bit grey, 24 bit RGB). The deeper version (not part of the regular tool kit series, so it will have a somewhat higher price and smaller market) will come along after that - I can't promise a specific date right now. If there are particular functions that you are concerned about let me know what they are and I'll try to make sure they are covered. John Russ ------------------------------ Date: Wed, 3 Mar 1999 12:42:47 +1100 From: "Greg Joss" To: "Enrico BONINO" , nih-image@io.ece.drexel.edu Subject: Re: Problems with LG3 Message-ID: Date forwarded: Tue, 2 Mar 1999 03:24:44 -0500 (EST) From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Problems with LG3 Date sent: Tue, 02 Mar 1999 00:14:15 PST Forwarded by: nih-image@io.ece.drexel.edu Send reply to: nih-image@io.ece.drexel.edu > Dear Imagers > > I work with a JAI camera and frame grabber LG3, these work well when > drived with the soft Scion Image, but if I'd like to acquire images with > NIH-Image (or Image SXM), I have some problems when I start the command > 'Start Camera'. > The image is flashing between the 'real image' and a b/w grid (like > 'chess game')... > > Someone can say me why? > > Thanks ....and sorry for my bad english. > > Enrico > > ************************************************************ > Enrico BONINO, geologist > University of Liege > Dept. of Applied Geology > Lab. MICA Geomaterials Characterization > http://www.ulg.ac.be/mica > Avenue des Tilleuls, 45 > B-4000 LIEGE > BELGIUM > tel. 0032 (0)4 3669526 > fax 0032 (0)4 3669520 > E-mail: e_bonino@hotmail.com > CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 Hopefully you will get a more authoritive response direct from Scion, as I am not competant in electronics and hardware but in the meantime... Your symptoms are reminiscent of a problem that I once had with a particular camera (a JAVELIN I think) in which the voltage level of the video frame synchronising pulse was below the level required by the LG3. This was diagnosed for me by the university electronics workshop using an Osciloscope to display the video signal. Sounds like you are missing one of the two interlaced video fields per frame. 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 V99 Issue #53 *************************************** From nih-image-request@io.ece.drexel.edu Tue Mar 2 21:00 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA25765; Tue, 2 Mar 1999 21:00:42 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 21:00:42 -0500 (EST) From: "Greg Joss" Organization: Dept. of Biological Sciences To: "Enrico BONINO" , nih-image@io.ece.drexel.edu Date: Wed, 3 Mar 1999 12:42:47 +1100 Subject: Re: Problems with LG3 Priority: normal In-reply-to: <19990302081417.22483.qmail@hotmail.com> X-mailer: Pegasus Mail for Windows (v3.01b) Message-ID: Resent-Message-ID: <"d7gmx3.0.Do5.VF9ts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1046 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 1920 Date forwarded: Tue, 2 Mar 1999 03:24:44 -0500 (EST) From: "Enrico BONINO" To: nih-image@io.ece.drexel.edu Subject: Problems with LG3 Date sent: Tue, 02 Mar 1999 00:14:15 PST Forwarded by: nih-image@io.ece.drexel.edu Send reply to: nih-image@io.ece.drexel.edu > Dear Imagers > > I work with a JAI camera and frame grabber LG3, these work well when > drived with the soft Scion Image, but if I'd like to acquire images with > NIH-Image (or Image SXM), I have some problems when I start the command > 'Start Camera'. > The image is flashing between the 'real image' and a b/w grid (like > 'chess game')... > > Someone can say me why? > > Thanks ....and sorry for my bad english. > > Enrico > > ************************************************************ > Enrico BONINO, geologist > University of Liege > Dept. of Applied Geology > Lab. MICA Geomaterials Characterization > http://www.ulg.ac.be/mica > Avenue des Tilleuls, 45 > B-4000 LIEGE > BELGIUM > tel. 0032 (0)4 3669526 > fax 0032 (0)4 3669520 > E-mail: e_bonino@hotmail.com > CV-> http://ewse.ceo.org/anonymous/construct/build.pl/690804 Hopefully you will get a more authoritive response direct from Scion, as I am not competant in electronics and hardware but in the meantime... Your symptoms are reminiscent of a problem that I once had with a particular camera (a JAVELIN I think) in which the voltage level of the video frame synchronising pulse was below the level required by the LG3. This was diagnosed for me by the university electronics workshop using an Osciloscope to display the video signal. Sounds like you are missing one of the two interlaced video fields per frame. 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 Mar 2 23:37 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id XAA12828; Tue, 2 Mar 1999 23:36:59 -0500 (EST) Resent-Date: Tue, 2 Mar 1999 23:36:59 -0500 (EST) Date: Tue, 2 Mar 1999 18:21:35 -1000 From: Kathleen Annikki Moore X-Sender: moorekat@uhunix4 To: nih-image@io.ece.drexel.edu Subject: Can stitching be used for? Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"BP2w12.0.Hh2.jZBts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1047 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 437 Can one use an inexpensive quick stitch or video brush software to combine low resolution, microscopy video stills into larger, higher resolution images for measurement purposes? If you have a good microscope and magnification, will there be any problems or distortions in the stitched image taken from a low resolution video camera and/or a low resolution capture card (320x240) fed into laptop? Thank you for any answers. Kathy From nih-image-request@io.ece.drexel.edu Wed Mar 3 04:24 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id EAA13124; Wed, 3 Mar 1999 04:24:43 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 04:24:43 -0500 (EST) Date: Wed, 03 Mar 1999 10:09:29 +0100 From: Lucas Bickel Subject: Real images? X-Sender: lbickel@ubecx01.unibe.ch To: nih-image@io.ece.drexel.edu Message-id: MIME-version: 1.0 Resent-Message-ID: <"Oz8tX3.0.vn2.LnFts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1048 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 232 Hi While looking at NIH-image I'm always stumbling across a diference between real images and the rest of them. Now I'm wondering where the difference between those image types is? I hope someone can answer this question Lucas From nih-image-request@io.ece.drexel.edu Wed Mar 3 05:21 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA19277; Wed, 3 Mar 1999 05:21:12 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 05:21:12 -0500 (EST) Date: Wed, 3 Mar 1999 05:05:00 -0500 (EST) From: nih-image-owner@io.ece.drexel.edu Message-Id: <199903031005.FAA17356@io.ece.drexel.edu> To: nih-image@io.ece.drexel.edu Subject: ADMIN: list commands Resent-Message-ID: <"3gT6f1.0.MF4.EbGts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1049 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text Content-Length: 3727 NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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 Wed Mar 3 06:53 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA29393; Wed, 3 Mar 1999 06:53:51 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 06:53:51 -0500 (EST) From: Nicholas Price Sender: nprice@rpms.ac.uk Reply-To: n.price@rpms.ac.uk To: nih-image@io.ece.drexel.edu Message-ID: Date: Wed, 3 Mar 1999 11:38:27 +0000 (gmt) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1 X-Authentication: IMSP MIME-Version: 1.0 Resent-Message-ID: <"iiz1r2.0.XX6.esHts"@io> Resent-From: nih-image@io.ece.drexel.edu Subject: Unidentified subject! X-Mailing-List: archive/latest/1050 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 214 Unsubscribe ---------------------- Dr Nicholas Price, Medical Research Council Fellow, Department of Infectious Diseases, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, LONDON W12 ONN From nih-image-request@io.ece.drexel.edu Wed Mar 3 07:05 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id HAA00815; Wed, 3 Mar 1999 07:05:08 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 07:05:08 -0500 (EST) Message-Id: <3.0.5.32.19990303064456.0093d3a0@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: Wed, 03 Mar 1999 06:44:56 -0500 To: nih-image@io.ece.drexel.edu From: Wade & Cheryll Schuette Subject: Re: Can stitching be used for? In-Reply-To: Mime-Version: 1.0 Resent-Message-ID: <"eqdxZ2.0.Yy6.h4Its"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1051 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 1587 At 06:21 PM 3/2/99 -1000, you wrote: >Can one use an inexpensive quick stitch or video brush software to combine >low resolution, microscopy video stills into larger, higher resolution >images for measurement purposes? If you have a good microscope and >magnification, will there be any problems or distortions in the stitched >image taken from a low resolution video camera and/or a low resolution >capture card (320x240) fed into laptop? Thank you for any answers. > >Kathy Yes and yes. At least one person on this list has software out available to assist this process. (Mine's under conversion to Java, ETA another month). We used this technique extensively in a prior commercial research site. Images work best if flat-fielded (color-corrected with bright/dark images). Keeping away from image rotation really helps, but should be fairly easy with a good scope. 3x4 montages work pretty well. On larger ones, one problem is "getting lost" and missing a shot in the middle, with images of, say, blood vessel cross-sections. Immediate way to test it is grab a grid of 3x3 images, and assemble them in PhotoShop, which makes it easy to slide them across each other, assuming one can find fiducial (alignment) points by eye. I'll have an autocorrelation (fourier) aligner out soon that matches images that don't have obvious fiducial points, and that can deal with rotations and zooms. Overlap images about 15-20%, probably. Align working from center out. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 From nih-image-request@io.ece.drexel.edu Wed Mar 3 11:02 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA26770; Wed, 3 Mar 1999 11:02:24 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 11:02:24 -0500 (EST) X-Sender: jjp3@pop.cwru.edu Message-Id: Mime-Version: 1.0 Date: Wed, 3 Mar 1999 10:46:33 -0400 To: nih-image@io.ece.drexel.edu From: jjp3@po.cwru.edu (James Plantner) Subject: unsubscribe Resent-Message-ID: <"6W2TZ1.0.uy5.cZLts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1052 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3 From nih-image-request@io.ece.drexel.edu Wed Mar 3 12:44 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA07828; Wed, 3 Mar 1999 12:44:08 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 12:44:08 -0500 (EST) Date: Wed, 3 Mar 1999 09:27:26 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #53 In-Reply-To: <199903030201.VAA25899@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"Zw4XO1.0.xR1.44Nts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1053 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1035 Dear David, You can use the Draw Boundary command to draw a boundary around any ROI (marching ants) or use Fill to coloraa line selection. Rather than use many keystrokes, try the following little macro: Macro 'Measure Length [L]'; begin RequiresVersion(1.60); SetPalette(Grayscale,6); SetForeGroundColor(5); SetOptions('Length'); {choose length measurements} measure; Fill;{leave a permanent outline of areas measured} SelectTool('Freehand');{regains the tool, which is deselected upon measurement}; end; To threshold, try an axon specific stain such as antibodies to some of the neurofilaments. You might also be faster to use stereological methods by trying John Russ's Image Processing Toolkit or the Cavalieri3 macros available ty ftp from zippy.nimh.nih.gov/contrib. 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 Wed Mar 3 17:54 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA13686; Wed, 3 Mar 1999 17:54:53 -0500 (EST) Resent-Date: Wed, 3 Mar 1999 17:54:53 -0500 (EST) Date: Thu, 4 Mar 1999 09:42:21 +1100 (EST) Message-Id: <199903032242.JAA18786@rsphysse.anu.edu.au> X-Sender: njw109@rsphy1.anu.edu.au X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 To: nih-image@io.ece.drexel.edu From: Nicholas.Welham@anu.edu.au (Dr. Nicholas J. Welham) Subject: Ixmicro TV tuner cards Resent-Message-ID: <"gNROp3.0.Q-2.PhRts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1054 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 520 Has anyone tried using Image with one of these cards? Thanks Nick _______________________________________________________________ Dr. Nicholas Welham Applied Mathematics tel +61-2-6249-0520 Research School of Physical Sciences and Engineering fax +61-2-6249-0511 Australian National University http://rsphysse.anu.edu.au ACT 0200, Australia The opinions expressed here are not those of the University or Department - if they were I'd be paid considerably more than I am. From nih-image-d-request@io.ece.drexel.edu Wed Mar 3 17:55 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA13741; Wed, 3 Mar 1999 17:55:18 -0500 (EST) Date: Wed, 3 Mar 1999 17:55:18 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903032255.RAA13741@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #54 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/54 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: 12825 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 54 Today's Topics: Can stitching be used for? [ Kathleen Annikki Moore ] Re: Can stitching be used for? [ Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Can stitching be used for? Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Can one use an inexpensive quick stitch or video brush software to combine low resolution, microscopy video stills into larger, higher resolution images for measurement purposes? If you have a good microscope and magnification, will there be any problems or distortions in the stitched image taken from a low resolution video camera and/or a low resolution capture card (320x240) fed into laptop? Thank you for any answers. Kathy ------------------------------ Date: Wed, 03 Mar 1999 10:09:29 +0100 From: Lucas Bickel To: nih-image@io.ece.drexel.edu Subject: Real images? Message-id: Content-type: text/plain; charset="us-ascii" Hi While looking at NIH-image I'm always stumbling across a diference between real images and the rest of them. Now I'm wondering where the difference between those image types is? I hope someone can answer this question Lucas ------------------------------ Date: Wed, 3 Mar 1999 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: <199903031005.FAA17356@io.ece.drexel.edu> NIH-image Mailing List Help --------------------------- ********************************************************* * DO NOT SEND ADMINISTRATIVE COMMANDS TO THE LIST * ********************************************************* 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. Tips by Henry M. Thomas, 0) Remember that Archive is case-sensitive. 1) Use the proper address for the Archive nih-image-request@biomed.drexel.edu 2) title the Subject line of your email archive 3) turn off (or don't send) your email Signature if you have one 4) In the body of the email write ls latest 5) Send it. latest is a directory containing the latest 50 files. The ls command returns you a list of the filenumbers of the current 50 files. (currently in the 800's). so latest/862 is a filename. 6) Send a second email get latest/862 or whatever filenumber you need 7) But you probaly want a batch. If you want more than 16, start the body of the email with archive maxfiles 35 or however many you want then use Unix metacharacters to get more than one file. * matches any string. ? matches any single character. []'s matches any single character shown in the brackets. get latest/* all 50 get latest/8[3-6]? all from 830 to 869 8) To search for text (e.g. the word color) in all the files in the directory latest use egrep egrep color latest/* then use get to get the files you want. This archive server knows the following commands: 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 Lines starting with a '#' are ignored. Multiple commands per mail are allowed. Setting maxfiles to zero will remove the limit (to protect you against yourself no more than maxfiles files will be returned per request). Egrep supports most common flags. 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: Wed, 3 Mar 1999 11:38:27 +0000 (gmt) From: Nicholas Price To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Unsubscribe ---------------------- Dr Nicholas Price, Medical Research Council Fellow, Department of Infectious Diseases, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, LONDON W12 ONN ------------------------------ Date: Wed, 03 Mar 1999 06:44:56 -0500 From: Wade & Cheryll Schuette To: nih-image@io.ece.drexel.edu Subject: Re: Can stitching be used for? Message-Id: <3.0.5.32.19990303064456.0093d3a0@s.imap.itd.umich.edu> Content-Type: text/plain; charset="us-ascii" At 06:21 PM 3/2/99 -1000, you wrote: >Can one use an inexpensive quick stitch or video brush software to combine >low resolution, microscopy video stills into larger, higher resolution >images for measurement purposes? If you have a good microscope and >magnification, will there be any problems or distortions in the stitched >image taken from a low resolution video camera and/or a low resolution >capture card (320x240) fed into laptop? Thank you for any answers. > >Kathy Yes and yes. At least one person on this list has software out available to assist this process. (Mine's under conversion to Java, ETA another month). We used this technique extensively in a prior commercial research site. Images work best if flat-fielded (color-corrected with bright/dark images). Keeping away from image rotation really helps, but should be fairly easy with a good scope. 3x4 montages work pretty well. On larger ones, one problem is "getting lost" and missing a shot in the middle, with images of, say, blood vessel cross-sections. Immediate way to test it is grab a grid of 3x3 images, and assemble them in PhotoShop, which makes it easy to slide them across each other, assuming one can find fiducial (alignment) points by eye. I'll have an autocorrelation (fourier) aligner out soon that matches images that don't have obvious fiducial points, and that can deal with rotations and zooms. Overlap images about 15-20%, probably. Align working from center out. Wade Cheryll & Wade Schuette 2345 Stone Road Ann Arbor MI 48105 734-763-8278 ------------------------------ Date: Wed, 3 Mar 1999 10:46:33 -0400 From: jjp3@po.cwru.edu (James Plantner) To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-Id: Content-Type: text/plain; charset="us-ascii" ------------------------------ Date: Wed, 3 Mar 1999 17:48:50 +0100 From: "Andreas Becker" To: nih-image-d@io.ece.drexel.edu Subject: infarct volume Message-Id: <199903031648.RAA23374@Mailer.Uni-Marburg.DE> Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Is there a macro to measure infarct volumina in the brain by several brain slices? May be even semiautomatically. Thanks for your help Andreas Becker ---------------------------------------------------------------------- Andreas Becker Institut fuer Pharmakologie und Toxikologie Ketzerbach 63 35032 Marburg Tel: +49 6421 28 5820; privat +49 6421 47304 eMail: BeckerA@mailer.uni-marburg.de WWW : http://www.chemie.uni-marburg.de/~becker ------------------------------ Date: Wed, 3 Mar 1999 09:27:26 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: Re: nih-image-d Digest V99 #53 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Dear David, You can use the Draw Boundary command to draw a boundary around any ROI (marching ants) or use Fill to coloraa line selection. Rather than use many keystrokes, try the following little macro: Macro 'Measure Length [L]'; begin RequiresVersion(1.60); SetPalette(Grayscale,6); SetForeGroundColor(5); SetOptions('Length'); {choose length measurements} measure; Fill;{leave a permanent outline of areas measured} SelectTool('Freehand');{regains the tool, which is deselected upon measurement}; end; To threshold, try an axon specific stain such as antibodies to some of the neurofilaments. You might also be faster to use stereological methods by trying John Russ's Image Processing Toolkit or the Cavalieri3 macros available ty ftp from zippy.nimh.nih.gov/contrib. 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: Wed, 3 Mar 1999 17:26:32 +0000 (GMT Standard Time) From: David Wynick To: nih-image-d@io.ece.drexel.edu Subject: problems as a newby! Message-ID: Content-Type: TEXT/PLAIN; CHARSET=US-ASCII sorry to hassle you all but despite reading the manual we are having some problems measure neurite length of neuronal cultures. We have a graticule to calibrate and captured a picture of that and then used that to set scale. we cannot get the programme to remember that setting. When we then open all the pictures of the actual cells, we seem to have to go into set scale and type in the values for each image. Is there a way of saving the calibration for all images opened in a particular session? Best regards David ---------------------- David Wynick Department of Medicine Bristol University Marlborough Street Bristol BS2 8HW, UK Tel: 44 (0)117 9283396 Fax: 44 (0)117 9283976 E-mail: d.wynick@bris.ac.uk ------------------------------ Date: Thu, 4 Mar 1999 09:42:21 +1100 (EST) From: Nicholas.Welham@anu.edu.au (Dr. Nicholas J. Welham) To: nih-image@io.ece.drexel.edu Subject: Ixmicro TV tuner cards Message-Id: <199903032242.JAA18786@rsphysse.anu.edu.au> Content-Type: text/plain; charset="us-ascii" Has anyone tried using Image with one of these cards? Thanks Nick _______________________________________________________________ Dr. Nicholas Welham Applied Mathematics tel +61-2-6249-0520 Research School of Physical Sciences and Engineering fax +61-2-6249-0511 Australian National University http://rsphysse.anu.edu.au ACT 0200, Australia The opinions expressed here are not those of the University or Department - if they were I'd be paid considerably more than I am. -------------------------------- End of nih-image-d Digest V99 Issue #54 *************************************** From nih-image-request@io.ece.drexel.edu Thu Mar 4 08:11 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id IAA11086; Thu, 4 Mar 1999 08:11:33 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 08:11:33 -0500 (EST) Message-ID: <001501be6637$40ed98e0$9985e6d2@oemcomputer> From: "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?=" To: Subject: unsubscribe Date: Thu, 4 Mar 1999 21:05:06 +0900 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 Resent-Message-ID: <"gej8f1.0.Ww.MUdts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1055 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: 2 From nih-image-request@io.ece.drexel.edu Thu Mar 4 09:29 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA20465; Thu, 4 Mar 1999 09:29:53 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 09:29:53 -0500 (EST) Message-Id: In-Reply-To: <19990302081417.22483.qmail@hotmail.com> Mime-Version: 1.0 Date: Thu, 4 Mar 1999 10:14:45 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Problems with LG3 Resent-Message-ID: <"HL1yK2.0.FD4.LEfts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1056 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 509 >Dear Imagers > >I work with a JAI camera and frame grabber LG3, these work well when >drived with the soft Scion Image, but if I'd like to acquire images with >NIH-Image (or Image SXM), I have some problems when I start the command >'Start Camera'. >The image is flashing between the 'real image' and a b/w grid (like >'chess game')... Are you using a G3 Mac? The 1.62b30 version of NIH Image available from http://rsb.info.nih.gov/nih-image/ fixes a problem with Scion frame grabbers on G3 Macs. -wayne From nih-image-request@io.ece.drexel.edu Thu Mar 4 09:56 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA23561; Thu, 4 Mar 1999 09:56:07 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 09:56:07 -0500 (EST) Message-Id: In-Reply-To: Mime-Version: 1.0 Date: Thu, 4 Mar 1999 10:40:27 -0400 To: nih-image@io.ece.drexel.edu From: Wayne Rasband Subject: Re: Real images? Resent-Message-ID: <"85Mcj.0.c55.Ncfts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1057 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 504 >Hi > >While looking at NIH-image I'm always stumbling across a diference between >real images and the rest of them. Now I'm wondering where the difference >between those image types is? Images in NIH Image are 8-bits with a maximum of 256 gray values or colors except for very limited support for real (32-bit floating-point) images for use with the FFT and Image Math commands. My new ImageJ program at http://rsb.info.nih.gov/ij/ supports 8-bit, 16-bit, 32-bit real, and RGB data types. -wayne From nih-image-request@io.ece.drexel.edu Thu Mar 4 11:46 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id LAA04918; Thu, 4 Mar 1999 11:46:12 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 11:46:12 -0500 (EST) Date: Thu, 04 Mar 1999 10:28:28 -0600 (CST) From: Heidi Guetschow Subject: unsubscribe To: nih-image@io.ece.drexel.edu Message-id: <01J8FGJ9TSGI8YB8DE@carleton.edu> X-VMS-To: IN::"nih-image@io.ece.drexel.edu" MIME-version: 1.0 Resent-Message-ID: <"hdBMi3.0.Lm.LJhts"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1058 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu From nih-image-request@io.ece.drexel.edu Thu Mar 4 12:12 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id MAA08172; Thu, 4 Mar 1999 12:12:50 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 12:12:50 -0500 (EST) X-Sender: jjp3@pop.cwru.edu Message-Id: Mime-Version: 1.0 Date: Thu, 4 Mar 1999 11:55:20 -0400 To: nih-image@io.ece.drexel.edu From: jjp3@po.cwru.edu (James Plantner) Resent-Message-ID: <"LyYhd3.0.JM1.4ghts"@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/1059 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 14 unsubscribe From nih-image-request@io.ece.drexel.edu Thu Mar 4 16:52 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA09317; Thu, 4 Mar 1999 16:51:55 -0500 (EST) Resent-Date: Thu, 4 Mar 1999 16:51:55 -0500 (EST) Date: Thu, 04 Mar 1999 16:58:43 -0500 From: John Elsworth Subject: Frame Grabber for old Mac? To: NIH Image Reply-to: John.Elsworth@Yale.edu Message-id: <36DEFD53.61FC536D@Yale.edu> Organization: Yale University MIME-version: 1.0 X-Mailer: Mozilla 4.06 (Macintosh; I; 68K) Content-transfer-encoding: 7bit Resent-Message-ID: <"_rhFo3.0.dp1.9rlts"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1060 X-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: 498 I am looking for a frame grabber for a Mac 6100/60. This computer does not have PCI slots, but instead has (according to Apple) one 7 inch NuBus or PDS. Transilluminated images from X-ray film are to be captured via a monochrome CCD camera (CCIR format). Scion no longer produces a LG-3 for Nubus, so I was hoping someone out there could direct me to an alternative that is compatible with NIH Image (or maybe has an old LG-3 looking for a good home at a reasonable price!) Thanks John Elsworth From nih-image-d-request@io.ece.drexel.edu Fri Mar 5 06:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id GAA02300; Fri, 5 Mar 1999 06:13:14 -0500 (EST) Date: Fri, 5 Mar 1999 06:13:14 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903051113.GAA02300@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #55 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/55 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: 3961 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 55 Today's Topics: unsubscribe [ "=?iso-2022-jp?B?GyRCNGRFRDdyGyhC?= ] Re: Problems with LG3 [ Wayne Rasband ] Re: Real images? [ Wayne Rasband ] unsubscribe [ Heidi Guetschow To: Subject: unsubscribe Message-ID: <001501be6637$40ed98e0$9985e6d2@oemcomputer> Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit ------------------------------ Date: Thu, 4 Mar 1999 10:14:45 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Problems with LG3 Message-Id: Content-Type: text/plain; charset="us-ascii" >Dear Imagers > >I work with a JAI camera and frame grabber LG3, these work well when >drived with the soft Scion Image, but if I'd like to acquire images with >NIH-Image (or Image SXM), I have some problems when I start the command >'Start Camera'. >The image is flashing between the 'real image' and a b/w grid (like >'chess game')... Are you using a G3 Mac? The 1.62b30 version of NIH Image available from http://rsb.info.nih.gov/nih-image/ fixes a problem with Scion frame grabbers on G3 Macs. -wayne ------------------------------ Date: Thu, 4 Mar 1999 10:40:27 -0400 From: Wayne Rasband To: nih-image@io.ece.drexel.edu Subject: Re: Real images? Message-Id: Content-Type: text/plain; charset="us-ascii" >Hi > >While looking at NIH-image I'm always stumbling across a diference between >real images and the rest of them. Now I'm wondering where the difference >between those image types is? Images in NIH Image are 8-bits with a maximum of 256 gray values or colors except for very limited support for real (32-bit floating-point) images for use with the FFT and Image Math commands. My new ImageJ program at http://rsb.info.nih.gov/ij/ supports 8-bit, 16-bit, 32-bit real, and RGB data types. -wayne ------------------------------ Date: Thu, 04 Mar 1999 10:28:28 -0600 (CST) From: Heidi Guetschow To: nih-image@io.ece.drexel.edu Subject: unsubscribe Message-id: <01J8FGJ9TSGI8YB8DE@carleton.edu> ------------------------------ Date: Thu, 4 Mar 1999 11:55:20 -0400 From: jjp3@po.cwru.edu (James Plantner) To: nih-image@io.ece.drexel.edu Subject: Unidentified subject! Message-Id: Content-Type: text/plain; charset="us-ascii" unsubscribe ------------------------------ Date: Thu, 04 Mar 1999 16:58:43 -0500 From: John Elsworth To: NIH Image Subject: Frame Grabber for old Mac? Message-id: <36DEFD53.61FC536D@Yale.edu> Content-type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-transfer-encoding: 7bit I am looking for a frame grabber for a Mac 6100/60. This computer does not have PCI slots, but instead has (according to Apple) one 7 inch NuBus or PDS. Transilluminated images from X-ray film are to be captured via a monochrome CCD camera (CCIR format). Scion no longer produces a LG-3 for Nubus, so I was hoping someone out there could direct me to an alternative that is compatible with NIH Image (or maybe has an old LG-3 looking for a good home at a reasonable price!) Thanks John Elsworth -------------------------------- End of nih-image-d Digest V99 Issue #55 *************************************** From nih-image-request@io.ece.drexel.edu Fri Mar 5 16:33 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id QAA23773; Fri, 5 Mar 1999 16:33:01 -0500 (EST) Resent-Date: Fri, 5 Mar 1999 16:33:01 -0500 (EST) Date: Fri, 5 Mar 1999 16:14:21 -0500 (EST) From: Glenn C Yiu Sender: gcy3@columbia.edu To: nih-image@io.ece.drexel.edu Subject: Pausing Macros Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"nubaJ3.0.vP5.pa4us"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1061 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 346 Does anyone know how one can pause a macro such that the user can actually manipulate the image before moving onto the next step? It seems that the functions Wait and WaitForTrigger only stalls the macro and do not allow user input during the waiting time. I want to allow the user to select a ROI manually in between two steps of a macro. From nih-image-request@io.ece.drexel.edu Fri Mar 5 21:47 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id VAA17266; Fri, 5 Mar 1999 21:47:04 -0500 (EST) Resent-Date: Fri, 5 Mar 1999 21:47:04 -0500 (EST) Message-ID: <36E093D8.BEE13F6D@mpih-frankfurt.mpg.de> Date: Sat, 06 Mar 1999 03:32:57 +0100 From: Stanke Reply-To: stanke@mpih-frankfurt.mpg.de Organization: mpih-frankfurt X-Mailer: Mozilla 4.5 (Macintosh; I; PPC) X-Accept-Language: en MIME-Version: 1.0 To: "nih-image@io.ece.drexel.edu" Subject: unsubscribe Content-Transfer-Encoding: 7bit Resent-Message-ID: <"bdjZj1.0.ox3.BJ9us"@io> Resent-From: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1062 X-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: 2 From nih-image-d-request@io.ece.drexel.edu Sat Mar 6 22:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA28532; Sat, 6 Mar 1999 22:09:35 -0500 (EST) Date: Sat, 6 Mar 1999 22:09:35 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903070309.WAA28532@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #56 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/56 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: 2386 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 56 Today's Topics: Pausing Macros [ Glenn C Yiu ] unsubscribe [ Stanke To: nih-image@io.ece.drexel.edu Subject: Pausing Macros Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know how one can pause a macro such that the user can actually manipulate the image before moving onto the next step? It seems that the functions Wait and WaitForTrigger only stalls the macro and do not allow user input during the waiting time. I want to allow the user to select a ROI manually in between two steps of a macro. ------------------------------ Date: Sat, 06 Mar 1999 03:32:57 +0100 From: Stanke To: "nih-image@io.ece.drexel.edu" Subject: unsubscribe Message-ID: <36E093D8.BEE13F6D@mpih-frankfurt.mpg.de> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit ------------------------------ Date: Sat, 6 Mar 1999 21:57:57 -0500 From: hmthomas@mail.med.cornell.edu (Henry Thomas) To: nih-image@io.ece.drexel.edu Subject: Re: Pausing Macros Message-Id: Content-Type: text/plain; charset="us-ascii" Divide the macro into two macros. End the first part, draw the ROI, call the second part from the pulldown menu (or better, with a shortcut key). The pauses are "outside" the macros! The code may feel awkward, but the overall macro can work well and be very interactive >Does anyone know how one can pause a macro such that the user can actually >manipulate the image before moving onto the next step? It seems that the >functions Wait and WaitForTrigger only stalls the macro and do not allow >user input during the waiting time. I want to allow the user to select a >ROI manually in between two steps of a macro. -------------------------------- End of nih-image-d Digest V99 Issue #56 *************************************** From nih-image-request@io.ece.drexel.edu Sat Mar 6 22:09 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id WAA28566; Sat, 6 Mar 1999 22:09:43 -0500 (EST) Resent-Date: Sat, 6 Mar 1999 22:09:43 -0500 (EST) Message-Id: Mime-Version: 1.0 Date: Sat, 6 Mar 1999 21:57:57 -0500 To: nih-image@io.ece.drexel.edu From: hmthomas@mail.med.cornell.edu (Henry Thomas) Subject: Re: Pausing Macros Resent-Message-ID: <"S6MkJ2.0.HX6.8iUus"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1063 X-Loop: nih-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 Divide the macro into two macros. End the first part, draw the ROI, call the second part from the pulldown menu (or better, with a shortcut key). The pauses are "outside" the macros! The code may feel awkward, but the overall macro can work well and be very interactive >Does anyone know how one can pause a macro such that the user can actually >manipulate the image before moving onto the next step? It seems that the >functions Wait and WaitForTrigger only stalls the macro and do not allow >user input during the waiting time. I want to allow the user to select a >ROI manually in between two steps of a macro. From nih-image-request@io.ece.drexel.edu Tue Mar 9 09:45 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id JAA24804; Tue, 9 Mar 1999 09:45:17 -0500 (EST) Resent-Date: Tue, 9 Mar 1999 09:45:17 -0500 (EST) Date: Tue, 9 Mar 1999 15:14:00 +0100 (MET) From: Patrick Doyle To: nih-image@io.ece.drexel.edu Subject: Acquiring Images with Hamamatsu Argus 20 Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"1OTa53.0.1C5.koIvs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1064 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 502 I am interested in aquiring images from a Hamamatsu Argus 20. The Argus 20 can be connected to the SCSI port of a PC and so I `should' in principle be able to grab the images but have not been able to figure out how to do this with NIH Image. thanks for any info, Patrick Doyle _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ (=\ Dr. Patrick S. Doyle \=) Laboratoire Physico- Chimie / Institut Curie PCC / France _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ From nih-image-request@io.ece.drexel.edu Tue Mar 9 15:53 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id PAA28985; Tue, 9 Mar 1999 15:52:58 -0500 (EST) Resent-Date: Tue, 9 Mar 1999 15:52:58 -0500 (EST) Date: Tue, 9 Mar 1999 12:37:27 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: propagating cells through a stack In-Reply-To: <199809261014.GAA14217@io.ece.drexel.edu> Message-ID: MIME-Version: 1.0 Resent-Message-ID: <"eOH4-.0.Qd6.JQOvs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1065 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 756 I am trying Object-Image for the first time, with a time lapse stack and wish to measure intensities in cell regions over time. The cell regions are outlined as object clones (2 objects to identify 2 separate cell types) with the roi tool. Then ObjectToRoi is used in a macro to obtain the densities. How can the same objects be repeated through the stack to obtain intensities over time? Setting the 3D option during object definition would be a simple method, but that allows only non-area object types. Thanks, 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 Mar 9 17:25 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA09770; Tue, 9 Mar 1999 17:25:32 -0500 (EST) Resent-Date: Tue, 9 Mar 1999 17:25:32 -0500 (EST) Message-Id: In-Reply-To: References: <199809261014.GAA14217@io.ece.drexel.edu> Mime-Version: 1.0 Date: Tue, 9 Mar 1999 23:17:49 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: propagating cells through a stack Cc: vischer@bio.uva.nl Resent-Message-ID: <"q7eZx1.0.F02.ypPvs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1066 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 2292 >I am trying Object-Image for the first time, with a time lapse stack and >wish to measure intensities in cell regions over time. The cell regions >are outlined as object clones (2 objects to identify 2 separate cell >types) with the roi tool. Then ObjectToRoi is used in a macro to obtain >the densities. > > How can the same objects be repeated through the stack to obtain >intensities over time? Setting the 3D option during object definition >would be a simple method, but that allows only non-area object types. > >Glen MacDonald If I understand you right, you want to create identical roi objects in each slice. For clarity, I use here the term "color roi" for a permanent roi object, and "b/w roi" for the marching ant black and white roi as known from NIH Image. What you can do is simply take an existing b/w roi - be it by conversion or restoring-, select the desired slice, and convert the b/w roi back into a new color roi as highlighted in the sequence window. If you work with macros, use the command 'SwitchToObject' to select the right color. Below I list some conversion methods: Conversion from color to b/w roi can be done: - by macro command ObjectToRoi - or by clicking with the ObjectToRoi tool (extended tool window bottom left) onto the roi starting point - or by using RestoreRoi shortly after the previous roiobject was created Conversion from b/w to color roi can be done: - by macro command RoiToObject* - or by pointing onto a roi symbol in the sequence window while a roi exists and the object tool is selected (see how the cursor changes). Before converting a b/w roi into a permanent color roi, you have all the possibilities to move, add or subtract a piece ( control or option key), shrink or expand (InsetRoi) the roi until it has satisfactory form. *Note that RoiToObject(false) will keep the cell open for adding more clones. You also can re-open a cell later with the command OpenCell. 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 Mar 9 17:39 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id RAA11616; Tue, 9 Mar 1999 17:39:27 -0500 (EST) Resent-Date: Tue, 9 Mar 1999 17:39:27 -0500 (EST) Message-ID: <36E5A028.E45510F4@umich.edu> Date: Tue, 09 Mar 1999 17:26:50 -0500 From: Janet Szczesny X-Mailer: Mozilla 4.5 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: nih-image@io.ece.drexel.edu Subject: Stacks References: <199901270744.CAA00999@io.ece.drexel.edu> Content-Transfer-Encoding: 7bit Resent-Message-ID: <"j6BSs1.0.xQ2.i0Qvs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1067 X-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: 245 Hello- I was wondering if someone could explain -or direct me to a place where this is explained clearly- the process of stacking images. I have color images saved as TIFF. I have read the manual and was unenlightened. Thanks! Janet Szczesny From nih-image-request@io.ece.drexel.edu Wed Mar 10 05:13 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA05651; Wed, 10 Mar 1999 05:13:51 -0500 (EST) <199809261014.GAA14217@io.ece.drexel.edu> Resent-Date: Wed, 10 Mar 1999 05:13:51 -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: References: <199809261014.GAA14217@io.ece.drexel.edu> Mime-Version: 1.0 Date: Wed, 10 Mar 1999 10:59:01 +0100 To: nih-image@io.ece.drexel.edu From: Norbert Vischer Subject: Re: propagating cells through a stack Resent-Message-ID: <"pwXSA.0.Pj.o7avs"@io> Resent-From: nih-image@io.ece.drexel.edu Reply-To: nih-image@io.ece.drexel.edu X-Mailing-List: archive/latest/1068 X-Loop: nih-image@biomed.drexel.edu Precedence: list Resent-Sender: nih-image-request@io.ece.drexel.edu Content-Type: text/plain; charset="us-ascii" Content-Length: 3640 I respond here to a message of Greg Joss, which didn't appear on the list. Greg Joss wrote: >If I can interpose (or stick my head in :-), >I wouldn't be suprised if Glen MacDonald's cells are moving over time >so that Norbert's interpretation "If I understand you right, you want >to create identical roi objects in each slice." may not be true. >Glen may want to track roi's as the move through the timelapse stack. >In that case, Norbert has already given the key to the crux of the problem >in his note at the bottom but it may be a little obscure. >>*Note that RoiToObject(false) will keep the cell open for adding more >>clones. You also can re-open a cell later with the command OpenCell. >The point to note here is that each roi object can have a clone per slice >so that (up to the maximum clone count of 25) you could track an roiObject >over 25 positions. > >Design of object structure is the aspect of Object-Image which I find >most problematic because of limits set to counts. If the problem were >tracking (biol)cells or other objects over a timeslice stack, one would >like individual (biol)cells to have indentifying colours and to be able to >track further than 25 frames. >Perhaps Norbert could suggest a suitable Object-Image cell >structure/strategy in the case of many (biol)cells (ie 10's or 200<>300) >and many frames (>100). Greg, the limitations you mention are dominated by the way how are results stored in the built-in 'mini spreadsheet'. Spreadsheets use to grow vertically as more data of the same type are collected, and they grow horizontally as more categories are needed. The accumulation of large amouts of data should happen vertically. In Object-Image, clones can automatically create their result columns, which will expand the spreadsheet horizontally. Even with the current limit of 25 clones and 50 result columns, this can become impractical. Further, a cell should not become too complex due to the limited editing of individual objects within a cell. The number of cells (i.e. rows) is currently limited to 2500, I may increase this in future, when the new object result window (> 32k, better scrolling, sorting, statistics, hiding columns) is released. Possibly a part of the problem is the term 'cell' itself. In the old days, this was really a biological cell, but in fact it is just a general collection of graphical objects, which can be misleading. Going back to the problem of Glen to keep track of cell idendities through a stack, I have two suggestions: - use only a single cell type, and put a cell ID number into a separate dynamic column. The ID could be entered manually, or created automatically by evaluating x/y center, if the cell is traceable. After a cell is closed, you can add the ID with a statement like SetValue('ID', NewestCell, id); NewestCell is reliable even if the new cell has been inserted into an earlier image. - if there are only a few cells in a field (<= 8), you could mark each cell with a different object type: define several object types in the "Define Objects" dialog and switch to collect mode = single. The ID of a cell is now given by the object type (or color); same types appear in the same column. You also may use the shortcut key support to switch to an certain object type with a single key stroke. 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-d-request@io.ece.drexel.edu Wed Mar 10 05:14 EST 1999 Received: (from lists@localhost) by io.ece.drexel.edu (8.8.8/8.8.8) id FAA05730; Wed, 10 Mar 1999 05:14:14 -0500 (EST) Date: Wed, 10 Mar 1999 05:14:14 -0500 (EST) From: nih-image-d-request@io.ece.drexel.edu Message-Id: <199903101014.FAA05730@io.ece.drexel.edu> Subject: nih-image-d Digest V99 #57 X-Loop: nih-image-d@biomed.drexel.edu X-Mailing-List: archive/volume99/57 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: 9630 ------------------------------ Content-Type: text/plain nih-image-d Digest Volume 99 : Issue 57 Today's Topics: Acquiring Images with Hamamatsu Argu [ Patrick Doyle ] Re: propagating cells through a stac [ Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Acquiring Images with Hamamatsu Argus 20 Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am interested in aquiring images from a Hamamatsu Argus 20. The Argus 20 can be connected to the SCSI port of a PC and so I `should' in principle be able to grab the images but have not been able to figure out how to do this with NIH Image. thanks for any info, Patrick Doyle _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ (=\ Dr. Patrick S. Doyle \=) Laboratoire Physico- Chimie / Institut Curie PCC / France _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ _/ ------------------------------ Date: Tue, 9 Mar 1999 12:37:27 -0800 (PST) From: "G. Macdonald" To: nih-image@io.ece.drexel.edu Subject: propagating cells through a stack Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII I am trying Object-Image for the first time, with a time lapse stack and wish to measure intensities in cell regions over time. The cell regions are outlined as object clones (2 objects to identify 2 separate cell types) with the roi tool. Then ObjectToRoi is used in a macro to obtain the densities. How can the same objects be repeated through the stack to obtain intensities over time? Setting the 3D option during object definition would be a simple method, but that allows only non-area object types. Thanks, 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, 9 Mar 1999 23:17:49 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Cc: vischer@bio.uva.nl Subject: Re: propagating cells through a stack Message-Id: Content-Type: text/plain; charset="us-ascii" >I am trying Object-Image for the first time, with a time lapse stack and >wish to measure intensities in cell regions over time. The cell regions >are outlined as object clones (2 objects to identify 2 separate cell >types) with the roi tool. Then ObjectToRoi is used in a macro to obtain >the densities. > > How can the same objects be repeated through the stack to obtain >intensities over time? Setting the 3D option during object definition >would be a simple method, but that allows only non-area object types. > >Glen MacDonald If I understand you right, you want to create identical roi objects in each slice. For clarity, I use here the term "color roi" for a permanent roi object, and "b/w roi" for the marching ant black and white roi as known from NIH Image. What you can do is simply take an existing b/w roi - be it by conversion or restoring-, select the desired slice, and convert the b/w roi back into a new color roi as highlighted in the sequence window. If you work with macros, use the command 'SwitchToObject' to select the right color. Below I list some conversion methods: Conversion from color to b/w roi can be done: - by macro command ObjectToRoi - or by clicking with the ObjectToRoi tool (extended tool window bottom left) onto the roi starting point - or by using RestoreRoi shortly after the previous roiobject was created Conversion from b/w to color roi can be done: - by macro command RoiToObject* - or by pointing onto a roi symbol in the sequence window while a roi exists and the object tool is selected (see how the cursor changes). Before converting a b/w roi into a permanent color roi, you have all the possibilities to move, add or subtract a piece ( control or option key), shrink or expand (InsetRoi) the roi until it has satisfactory form. *Note that RoiToObject(false) will keep the cell open for adding more clones. You also can re-open a cell later with the command OpenCell. 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, 09 Mar 1999 17:26:50 -0500 From: Janet Szczesny To: nih-image@io.ece.drexel.edu Subject: Stacks Message-ID: <36E5A028.E45510F4@umich.edu> Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Hello- I was wondering if someone could explain -or direct me to a place where this is explained clearly- the process of stacking images. I have color images saved as TIFF. I have read the manual and was unenlightened. Thanks! Janet Szczesny ------------------------------ Date: Wed, 10 Mar 1999 10:59:01 +0100 From: Norbert Vischer To: nih-image@io.ece.drexel.edu Subject: Re: propagating cells through a stack Message-Id: Content-Type: text/plain; charset="us-ascii" I respond here to a message of Greg Joss, which didn't appear on the list. Greg Joss wrote: >If I can interpose (or stick my head in :-), >I wouldn't be suprised if Glen MacDonald's cells are moving over time >so that Norbert's interpretation "If I understand you right, you want >to create identical roi objects in each slice." may not be true. >Glen may want to track roi's as the move through the timelapse stack. >In that case, Norbert has already given the key to the crux of the problem >in his note at the bottom but it may be a little obscure. >>*Note that RoiToObject(false) will keep the cell open for adding more >>clones. You also can re-open a cell later with the command OpenCell. >The point to note here is that each roi object can have a clone per slice >so that (up to the maximum clone count of 25) you could track an roiObject >over 25 positions. > >Design of object structure is the aspect of Object-Image which I find >most problematic because of limits set to counts. If the problem were >tracking (biol)cells or other objects over a timeslice stack, one would >like individual (biol)cells to have indentifying colours and to be able to >track further than 25 frames. >Perhaps Norbert could suggest a suitable Object-Image cell >structure/strategy in the case of many (biol)cells (ie 10's or 200<>300) >and many frames (>100). Greg, the limitations you mention are dominated by the way how are results stored in the built-in 'mini spreadsheet'. Spreadsheets use to grow vertically as more data of the same type are collected, and they grow horizontally as more categories are needed. The accumulation of large amouts of data should happen vertically. In Object-Image, clones can automatically create their result columns, which will expand the spreadsheet horizontally. Even with the current limit of 25 clones and 50 result columns, this can become impractical. Further, a cell should not become too complex due to the limited editing of individual objects within a cell. The number of cells (i.e. rows) is currently limited to 2500, I may increase this in future, when the new object result window (> 32k, better scrolling, sorting, statistics, hiding columns) is released. Possibly a part of the problem is the term 'cell' itself. In the old days, this was really a biological cell, but in fact it is just a general collection of graphical objects, which can be misleading. Going back to the problem of Glen to keep track of cell idendities through a stack, I have two suggestions: - use only a single cell type, and put a cell ID number into a separate dynamic column. The ID could be entered manually, or created automatically by evaluating x/y center, if the cell is traceable. After a cell is closed, you can add the ID with a statement like SetValue('ID', NewestCell, id); NewestCell is reliable even if the new cell has been inserted into an earlier image. - if there are only a few cells in a field (<= 8), you could mark each cell with a different object type: define several object types in the "Define Objects" dialog and switch to collect mode = single. The ID of a cell is now given by the object type (or color); same types appear in the same column. You also may use the shortcut key support to switch to an certain object type with a single key stroke. 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 -------------------------------- End of nih-image-d Digest V99 Issue #57 ***************************************