Inputting hand-generated XML with detected spots for interfacing with TrackMate's linking algorithms


I have generated an XML file in a format resembling one generated by the TrackMate GUI with my own detection/filtering scripts that creates instances of spots throughout the frames of my movie. I was hoping to link this directly into TrackMate with a Python script. This would be analogous to loading an XML file into the GUI as an intermediate between filtering>detection and tracking. Is this possible and are the codes that exist to already achieve this? Thank you for looking at my question–I am excited to get this working!


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Welcome to the forum, @Cyna_Shirazinejad!

Did you already see this guide?

Hello @Cyna_Shirazinejad

We are working on an example script that does that with @philgi.
We are not done yet but it should happen soon.
Watch this post for news:
Trackmate with manual detection and automatic tracking in jython script