Color tracks by frame position

Dear users and developers of trackmate, dear @tinevez,

is there a way to color tracks according to their current-frame/(total track length)?
For example: using a lookuptable red-hot: the beginning of the track is more red and gets white till the end of the track.

This is similar how imaris is presenting the tracks and it summarizes the direction of movement quite nicely even without a video.

Yes you can. Let me check.
Just select the Time (mean) in ‘Set color by’ menu.

Thank you I was guessing that it was this. However for my data everything connected to velocity and time is infinity.

It has something to do with the metadata. In fact I uploaded through a script ROIs that have then been tracked. So I can’t go back and fix the metadata (I already did a lot of manual correction). I guess I could fix it in the xml file. Do you have a suggestion where should I do it?


I reedited the image and added in properties a non zero time interval (1s).
This had an effect but somehow the traces still do no show the full bandwidth of colors (it is only for the first time point). The range should be from 0 to 53 and shows instead from 0-77.5. Also the velocity still gives Infinity values.

Not sure what I am doing wrong. Here is the original image and the xml file

12-blastocyst.tif (8.1 MB)

12-blastocyst_nuc1.xml (197.1 KB)

Ok the issue is that the image must have a non zero time interval. When the time interval is set properly everything runs fine. Changing the xml file can be tedious. I guess it is the EDGE_TIME entry one would need to modify.

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Dear @tinevez ,
I have an additional question related to my previous question (thanks to your help I solved).
How do you change the thickness of the track lines?
And can we color the dots with filled colors?


How do you change the thickness of the track lines?

You cannot do that right now. In the future version of TrackMate (soooon, or ideally March) you will be able to do so.

And can we color the dots with filled colors?

This feature is not planned sorry.