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imagej / imagej2

Open scientific N-dimensional image processing :microscope: :sparkler:
https://imagej.net/
BSD 2-Clause "Simplified" License
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Shuffled Image overlay #190

Open RyanSMcCool opened 6 years ago

RyanSMcCool commented 6 years ago

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.

imagejan commented 6 years ago

From your description, I'd suppose that this an issue in the imagej1 legacy component. But really, in order to judge this, more information is required: what's the macro code you're running, which operating system, which Java version, etc.

Why don't you create a topic in the issues category on the forum and share your macro and possibly some sample images to reproduce the issue?

RyanSMcCool commented 6 years ago

I'm working on creating an account for the forum now. I am currently running java 8 update 161, so as far as I'm aware it is the most recent version. My legacy components seem to be up to date as well. I am running jars/imagej-legacy.jar and jars/legacy-imglib1.jar.

RyanSMcCool commented 6 years ago

Just as another note while I prep a minimal code to share, I noticed that if I have the file open where I save my overlaid images, I can visually see images 3a-3c be overlaid and saved, followed by 2a-2c, and finally 1a-1c. Not sure if this will help diagnose a problem.