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 specified in TrackMate by an IJ macro? I was hoping to be able to also include linking_max_distance and gap_closing_max_distance, and then open the analysis and save some of the results windows (using IJ macro language).

This would save me from having to halt the macro for user input (e.g. inputting the correct linking_max_distance and gap_closing_max_distance values, then clicking analysis and resuming the macro).

TrackMate really is great, and I thank everyone for their development of it as a great plugin.

Best

1 Like

Thanks @7rebor!

Actually you can. I just realized it was not documented yet.
Right now, you can look at this place in the code to have the list of all supported command:

The commands you are looking for are

max_distance
max_gap_distance
1 Like

@tinevez - thanks, just what I needed

Hi,

Is there a way to control any other parameters from the IJ macro? for example using LAP tracker instead of the simple LAP tracker to enable splitting? Or is the only option to use something like this python script from this discussion?