Before extracting crystallographic information from an electron-microscopy image, you would first decide which portion in the image is to be processed.

1. Use one or more of the four buttons  to select the portion.
2. Click the 'Fill' button  and fill the selected area(s) as shown in green color on the upper part of the following figure.
3. Click the 'Clip' button . Then you will get what you want as shown on the lower part.