Mean intensity of tracks using Trackmate

Hello folks,
I am looking for a way to estimate the mean intensity of each spot from every individual track identified with Trackmate. Is this possible?
Any tips would be appreciated.


I use this all the time. You need to install an extra jar and you can then filter on and record intensity in multiple channels. See:


B.R.I.A.L.L.I.A.N.T and thanks for the quick help!

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Hello everyone,
I am a novice to Trackmate. I am trying to average intensity of spot from each track. Would you explain how you did in your case.
example dataset:
Label id Track …Position_T Mean intensity
ID155461 155464 1 0 1160
ID156002 156002 1 179 1259
ID156008 156008 1 300 1200

I want to get mean of mean intensity from Track 1 and automate this process for all other tracks. Is there any plugin available?


Hi @John1 welcome to the forum. Usually best to start a new post if it’s a new question (to get better visibility) but I’ll do my best here.

If you have familiarity with R or MATLAB, this sort of summary statistic is fairly easy to do with the spots in tracks statistics.csv output. That said, you probably wouldn’t be asking if that were the case.

If you want to do this with a spreadsheet application you’re best to use Pivot Tables. I wrote a tutorial on this on my blog some time ago, check it out if you’re interested:

The basic idea is to select all of your data cells, then insert a Pivot Table.

Select the Track_ID as a row field and the MEAN_INTENSITY as a data field. Check the way the data are summarised and change to average if that’s what you want (you can do this in Excel or most open source implementations such as Libre office, shown here).

That should give you for each TRACK_ID, your summary statistic:


There is however an even easier way to do this. While trackmate doesn’t produce the mean track intensity by default in the tracks output, if you install the Trackmate Extension Trackmate-extras (direct link to jar) into your directory, it will output the mean mean track intensity in the “Track Statistics” output.


Hope that helps!


Hi @dnmason
Can I link this post from the TrackMate page? Because it’s awesome.

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Hi @tinevez, thanks for the comment! Please do!

Hi dnmason,
I really appreciate it. yes, that worked out well.



Hi there!
Here is my another query related to previous query.

Using Trackmate, I am working on measuring mean intensity of vesicles from each track. I am aware that Trackmate calculates mean intensity of each track using physical radius, R. But I want to estimate mean intensity based on estimated diameter which is calculated from contrast difference. To do this, I am now trying to write a script in MATLAB or Python. I was wondering if I can edit the Trackmate script to do this task or any other API would do. Any comments or suggestions would be helpful!

Thanks for your time! I am really grateful for your quick responses in my past queries!