TrackMate Modification

I’m currently working on a project to track the growth of neurons using timelapse imaging, and I’m trying to develop a plugin that will allow me to generate data concerning the persistence of each dendrite over time, the number of new branches added or detracted, and similar geometric features of neurons.

I’m relatively unfamiliar with imaging processes and I recently picked up coding, and I was wondering if you had any advice on how to go about modifying or adapting TrackMate such that I could develop such a plugin. I currently use Analyze_Skeleton and Strahler Analysis to find the junction points and end points of skeletonized images of neurons, and I was thinking of using that as a starting point for finding spots for each frame of a timelapse. I’m just a bit overwhelmed by the sheer amount of code in TrackMate, and it’d be awesome to hear back from you on how to parse through it or where to start.

Hi @szhang

I think your approach is sensible and does not need changing TrackMate.

What I would do is to first generate the time-lapse image of the junction points only with a script. Then use this movie as input to TrackMate (single points over black background). You might have to blur them or enlarge them so that TrackMate can track them.

Then put back the results of the tracking on the source image by editing the XML TrackMate generates.

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