Count how many particle moving

Hi everyone

I am analyzing data using Fiji and Icy, and I want to count how many spots in the first image of the tif file moving out of its position (You can find the image in the attachment). Does Fiji or Icy have any plugin to do that? I really appreciate your help.Substack (1-13).tif (2.8 MB)


To get you started - I would start looking into TrackMate… This way - you can easily link your spots and find out whether or not they move from the first frame onwards…

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I also try using Trackmate to detect the moving, but maybe I am a newbie of using Trackmate so I have some difficulties. Can you explain more details of using this plugin for me please? Thank you very much.

Hey @Quan_Nguyen ,

the Trackmate website @etadobson linked has a lot of tutorials explaining in detail how to use it properly.

If you still struggle, would you mind sharing what difficulties you have? We can then help you better :wink:


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In some cases, Trackmate is so sensitive since it can detect some not moving particles. I try to control the threshold to improve the result but it seems not to work well. Are there any tips to set up the condition for efficient detecting? Thank you for your help.

Hi @Quan_Nguyen

Normally, I would recommend TrackMate as have others here, but the problem here is that the crowded nature of your data means that linkage of tracks is non-trivial. The ‘simple’ solution of filtering on Track Displacement will be inaccurate if moving spots are linked with static ones, or (more likely) other moving spots.

If you’re only interested in moving spots, you may want to try using the Image Calculator to find the difference between the first two frames.

Lots of other choices would work (Divide, Subtract, XOR) and you can find details of the calculations in the link above.

This will give you an image showing only particles that are present in one frame but not the other (IE ones that are not static). You can then use the spot detector in trackmate, set a threshold and use Analyze Particles or find another way to count the spots (below is the Count Masks output after dilating and filtering small objects).


Hope that helps!