Trackmate in a macro and extended option

[fallet]

Dear Jean-Yves,
I am using trackmate since one month (I find it very powerful and easy to use ) and would like to have some additional options on it :

1. See displacement vector of all tracks (unified or not), finally I did it with R but could be interesting to have directly on the image ?
2. Reconnect tracks which are segmented, I have tested the “linear motion lap tracker” on simulated timelapse image with dots with linear motion but was surprised to find quite difficult to have the entire tracks on one block so maybe reconnect tracks could be a solution to my problem ? I can send you my images to test.
3. Finally, the most important one, I would like to use trackmate in a macro to batch files with defined parameters on TrackMate (I dont’ think it is possible to call plugin from R directly ?). But I don’t find the complete description to do it and obtain my results, I need only (track_ID, X, Y).
   Thanks so much, Mathieu Fallet

[tinevez (Jean-Yves Tinevez)]

Hello @fallet

So:

Unfortunately there is nothing like this in TrackMate. Which means that if you want directly within TrackMate, you would have to code it yourself.

Did you try to play with the parameters? TrackMate score is not horrible with linear motion:
https://imagej.net/TrackMate_Accuracy#Microtubule_scenario.

I only play with Python, and put some scripts together here:

Scripting TrackMate

There is also a way to call some of its function from IJ1 language:

TrackMate improvements for calling from an IJ macro

In v3.2.0 release notes it became possible to call TrackMate from an IJ macro, the example was the following syntax: run('TrackMate', "use_gui=false " + "save_to=[/Users/tinevez/Desktop/TrackMateSaveTest.xml] " + "export_to=[/Users/tinevez/Desktop/TrackMateExportTest.xml] " + "display_results=true " + "radius=2.5 " + "threshold=50.1 " + "subpixel=false " + "median=false " + "channel=1 " + "max_frame_gap=0" ) Are these currently the only things that can be sp…

Finally I know that @imagejan managed to create a small ImageJ2 wrapper that makes TrackMate callable from a macro. But I could not find it again.

[imagejan (Jan Eglinger)]

Finally I know that @imagejan managed to create a small ImageJ2 wrapper that makes TrackMate callable from a macro.

You mean my script that you added to the Scripting TrackMate page?

Scripting TrackMate

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Note that I also put together a few wrapper plugins that allow using TrackMate – as a whole, or spot detection and tracking in separated units – from KNIME, available via the FMI KNIME plugins update site:

fmi-faim/fmi-ij2-plugins

@fallet If you aim for batch processing a larger number of movies with the same parameters, I warmly recommend having a look at #knime and these nodes. I can assemble an illustrative workflow to share if required.