Tracking overlay question

Posting for one of our students:
I have single molecule imaging data showing molecules on a membrane diffusing into and out of a region of interest. I am trying to make a figure and/or movie that highlights tracks that start outside the region and move in, or start inside and move out.

I have successfully tracked the molecules using TrackMate, but cannot figure out how to show all the tracks I am interested in simultaneously, i.e. tracks filtered by start/end point inside/outside ROI. Also, when I export an overlay of a single representative track, the line is too thin to be easily visible, and I can’t seem to change the line thickness.

Can anyone help me figure out how to solve these problems in Trackmate? Or can anyone suggest a tool that can take in my Trackmate XML data and output a movie or figure with the tracks of interest overlaid on the original images?

Thanks,

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@nicost

Hello!

So… I am not too familiar with selecting individual tracks to only display… but the Getting Started with Trackmate page on the ImageJ wiki contains some helpful information. For example, regarding the ‘Select a View’ choice: “The first one, HyperStack displayer, simply reuses ImageJ stack window and overlay the results non-destructively over the image.” This should be applicable to tracks as well as spots - but not sure about a subset of tracks.

But of course, @tinevez will know best!

eta :slight_smile:

I am afraid the filtering requested by @nicost does not exist in TrackMate.
You have to export the tracks elsewhere (MATLAB?) and display them as you wish.

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