Altering TrackMate spot size for multi-channel intensity analysis

Tags: #<Tag:0x00007fb8836db508>


Hi all,

I am aware of TrackMate-extras and benoit lombardo’s multi-channel intensity analysis, which has been really useful for me. I am having a slight problem though; I would like to increase the size of the already detected spots to be used by the intensity analyzer. It appears that increasing the displayed spot radius ratio doesn’t actually change the spot size for the intensity analysis, it just changes the display. As far as I can see I get the same results no matter what the display radius is.

This is probably best directed @tinevez




Hi Rob,

I think this cannot be done simply in TrackMate.
As you guessed correctly, the display radius is just a display settings.

The shortest way I see to achieve this is do it in an unsubtle way:

  • Edit the TrackMate XML file with a good text editor.
  • Search and replace all the spot tags RADIUS="5" by something large RADIUS="10".
  • Reload the TrackMate file and use the Recompute all spot features action in the last panel.

Tell us if it works!


Thanks @tinevez, worked exactly as you expected.

Is it possible to script the ‘load a TrackMate file’ plugin and ‘recompute all spot features’ action in IJ macro language? Just wondering if I can script that bit so I don’t have to manually open the XML files, recompute spot features and save the results for each XML.


No IJ1 macro support sorry.
You have to go to a language like Python to do it all.


Is there anybody willing to share a Python or Java script that tracks cells using TrackMate, then transfer the spots to another channel and measure intensities??

I’ve been writing macros in FIJI for a long time, but never ventured into Python or Java scripts. I’m willing to learn, but not to start from “print (hello)”. Would like a script that’s already written that I can adjust and tweek, instead of building from the beginning.

Thanks in advance.