TrackMate - Transferring Tracks

Dear Jean-Yves,

I was wondering if there is any possibility to transfer Tracks that where generated on one data-set onto another data-set? The goal behind this approach would be to use the already generated tracks and apply them to another signal, so we could measure change in intensity over time.

It is not possible to perform the Tracking on this signal directly, but we are tracking the nuclei instead and were now wondering if we could transfer these tracks to the signal that we are really interested in.

Best regards,

Christian Fischer

Yes you can.

There is basically two ways.

1.
Either you have the other channel on a separate file. Then you have to edit the TrackMate file to have it load the specified file, and recompute all the features using the so-named action in the last panel.

2.
Or you have all the channels on a single file.
Normally, TrackMate measures signal only on the tracked channel, but Benoit Lombardo wrote a TrackMate module that does so:

Just drop the jar of the extras in your Fiji plugins folder, and it will get the new features.

3 Likes

Dear Jean-Yves,

thank you very much for your advice. This is exactly what we have been looking for. I already was able to implicate the editing of the XML file, but copying the additional files from Benoit Lombardo does not seem to change any features of TrackMate? Does it have anything to do with the fact that these files are .java and not .jar files?

Yes exactly.
Take the jar there .

Stupid me. I just realized that there are no release so no jar.
Take this one in the meantime:
http://dl.pasteur.fr/fop/rAe4nMYE/TrackMate_extras-0.0.1.jar

Hi! I am just starting to do what the original user wanted to do.
Create tracks using one channel, but then measure the intensity at each spot of a different channel. I have all the channels together in a hyperstack.

I clicked on your latest link, and it has been taken down.
Can you bring it back up again? Or has there been a new solution since May?

Thank you!
Sho Fujisawa

It is also possible to edit the XML file in order for it to load a different channel and then recompute all features (see above post of @tinevez).

Can you possibly help me further than that?
At what point during the tracking do I save the xml file? At the very end?
And what exactly do I change within the xml file? There’s a lot of lines here…

Thank you and happy holidays.

OK So I managed to put the tracks on the correct channel that I want to measure intensity of. But when I hit analysis, I still get the intensity of the channel that I used to track the cells.

I had to change the name of the file analyzed in 3 places in the xml file. Does that sound right?