Shuffled Image overlay

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I have been using macros for imageJ to perform image analysis for about a year now. After the last update, all of my codes that I had previously incorporated batch mode began shuffling up image orders when using the overlay command (i.e. Image 1a is suddenly being overlaid with Image 3c).

It seems to be systematically switching up files too so that if I run two different codes on the same sets of images the mismatch is maintained between codes. However, if I switch between sets of photos, the pattern by which the images are shuffled changes.

For example, I have images from 9Feb18. Images 1a through 1c overlay perfectly. However, at image 2a, image 3c is overlaid. Image 2b is then overlaid with 3b, 2c with 3a, 3a with 2c and so on. Meanwhile for 13Oct17 the image 1a is mismatched while 1B is matched properly.

Did some code change in the new batch mode? I technically have FIJI downloaded, but from my understanding FIJI is just ImageJ with extra features pre-installed.

No source file, test, or entry point is named. Begin by reproducing the mismatch in ImageJ's batch mode with the described image sets and compare behavior before and after the update; done means overlay pairing remains consistent.

Written by the indexing model from the issue text.