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Batch process ROI between two sets of images

Posted by dc1312 on Aug 06, 2014; 2:55pm
URL: http://imagej.273.s1.nabble.com/Batch-process-ROI-between-two-sets-of-images-tp5009046.html

I'm afraid I am completely new to writing macros for ImageJ and so I'm struggling and would really appreciate any help.

How do use one set of images to mask out another set of images in a batch process? For example I have two sets of images; the first set contains images only with a mask, the second set contains cells with my "interesting" data in. So for one cell I do this:

1. Open "mask" image
2. Create selection
3. Save as ROI
4. Open "interesting" image
5. Apply ROI
6. Set selection to value="NaN"
7. Save new "interesting" image

I can't work out a way to batch process many images. The tricky bit is saving the ROI from the mask and applying it to the appropriate cell.

Thank you for any help!

David