Trackmate for 2-color co-localizations and co-tracking

Dear @tinevez,
My name is Hiteshika Gosain and I’m doing my PhD from WWU Münster, Germany. The topic of my thesis is “Super-resolution analysis of the membrane domain formation during the neuronal Polarisation”.
We are focusing on the exocyst subunits and want to Analyse the spatial and temporal resolution of all these subunits. To do this we are using single-particle tracking using TIRF.
I was using the trackmate and @msdanalyser program designed by you, and I must thank you for writing such a wonderful program.
If you have some time, I would like to bother you with some questions.
By far, I have been using a single colour for tracking purposes but now I want to extend my research to analyse 2 colours/multicolour for co-localization and co-tracking.
This may help me to understand where in space and time do these subunits assemble near the plasma membrane.
Can you please guide me if there’s a method to do multicolour tracking for two different protein of interests in the trackmate or have you designed another program for the same? If I split the channels, and then evaluate the single channel, is there a possible way to combine them later to get co-tracks?
Is there a way to determine the cluster analysis in order to check how many protei of interests constitute a single bright spot? Can we do this by Spot analysis in the trackmate?

Kind regards,

Hello @Hiteshika and thank you for posting the discussion here (and again for your kind words).

I am afraid there is no direct way to do all you want in TrackMate. TrackMate will only manage one collection of tracks. So ultimately you will have to deal with one TrackMate file per channel in your subsequent analysis.

And also there is no clustering analysis ready-made in TrackMate sorry. Maybe you want to look at the creations of Florian Levet?

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Dear @tinevez,

Thank you for your reply. There is no problem in analysing two channels separately. I was wondering that if I use the option in trackmate “to merge trackmate” file for 2 channels, would it get me close to understanding the behaviour of particles as co-tracking? Or would it simply just add the tracks in total without getting me the overlay?


Nono it will import the two set of tracks as if they came from one session. You will get their display as well.

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