![]() tiff is not working is because the first ‘analyze particles’ function was set up to reject objects less than 5000 units^2. Still not perfect but maybe something for you to work with. ![]() Run("Analyze Particles.", "size=0-Infinity show=Masks display exclude include summarize") Now that I’ve had a little more time, the following is an alternative thresholding approach that partially corrects the issue the previous macro encountered in one of the very dense cell clusters, whilst also cleaning up the workspace a bit by dumping some of the output masks into a new slice of the original image: setForegroundColor(255, 255, 255) Sorry, probably bad practice to reply to your own reply but I rushed the previous macro out as I was making myself late for an appointment. Run("Analyze Particles.", "size=0-Infinity show=Outlines display exclude include summarize") TRY LOOPING THROUGH THE ROI MANAGER HERE SELECT ORIGINAL OR BLACK-BACKGROUNDED IMAGE HERE Run("Analyze Particles.", "size=5000-Infinity show=Nothing exclude clear include summarize add") Run("Options.", "iterations=9 count=1 do=Dilate") HERE a good time to count groups of cells Run("Remove Outliers.", "radius=20 threshold=50 which=Bright") Run("Options.", "iterations=20 count=1 black do=Close") Run("Options.", "iterations=6 count=3 black do=Dilate") ImageCalculator("AND create", "Result of 0","2") Autogenerated macro, single images only! I’m not sure why I just spent 2 hours doing this but try this macro (It’s a bit clunky but does what you want I think): setForegroundColor(255, 255, 255)
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