Analyze Particles in Image Stack



I am a new user of ImageJ/Fiji and am having difficulties that I am unable to resolve. I created a stack of five images and applied thresholds of 64 and 246 to Brightness using Threshold Color (HSB). The threshold appears to be correctly applied to each image in the stack. The difficulty is when I then analyze the stack using Analyze Particles. Rather than getting the results for each image (slice), I get the results for the last slice repeated five times. If I split the stack into individual images and analyze them separately the results are fine What am I doing wrong with the analysis of the image stack?


I think your question slipped by. I don’t have an answer but I hope someone can help



How about scripting a little something to get things working…?? Here are a few helpful links to get you started on Scripting with ImageJ/Fiji:

To get you started… read through this older forum post to help solve this issue:

Is it a problem to process the images individually? As you can see in linked forum post - the code only works on individual images, not stacks. So you can write a script that 1) opens the stack, 2) converts them to individual images, 3) applies the Color Threshold to each image, and then 4) merges them back to a stack or so…



I was able to reproduce your problem and I think you might not be binarizing your stack before running the Analyze particles.

After you set your threshold values and hit the “Stack” button in the “Threshold Color” window, try this:

Process > Binary > Convert to mask

This step would change the stack appearance from white/red (as shown in your screenshot) to black/white. After that, Analyze particles… should give you the numbers for each slice.



Hi Ved,

Thank you very much for your reply. Process < Binary > Convert to mask fixed the problem.