the spot is filtered by a quality threshold

[asincerity]

I run the trackmate in the macro script as follow:
run('TrackMate', "use_gui=false "
+ "display_results=false "
+ "radius=2.5 "
+ "threshold=10 "
+ "subpixel=true "
+ "median=false "
+ "max_distance=2 "
+ "max_gap_distance=2 "
+ "max_frame_gap=2 "
+ "save_to=[" + path + File.separator + name +"spots.xml] ");
Then, I read the spot.xml in the matlab as follow:
[spotTable,~] = trackmateSpots(spotsPath, {'POSITION_X','POSITION_Y','POSITION_T','QUALITY' });
But I find the spots are filtered by a quality threshold. This value can be found in the .xml



So, how can i change the value in the run('Trackmate',...). What is the parameters that can be changed in the run('Trackmate',...).
Thank you for your patience

[tinevez]

Rmlml it looks like the macro reads and uses the last quality value defined as a threshold.
I can look into it to fix it, but I would be of the opinion of retiring the macro support. Thoughts?

[asincerity]

Rmlml it looks like the macro reads and uses the last quality value defined as a threshold. I can look into it to fix it, but I would be of the opinion of retiring the macro support. Thoughts?

When I use trackmate in macro, what are the parameters that I can specify in run() and where should I look for trackmate's support documentation for macro?

[tinevez]

In the code so far:
https://github.com/trackmate-sc/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/TrackMateRunner.java

But I see it does not work for you.
I can look into it and try to fix it, but I would be really in favor of retiring the macro support. It is really limited, does not let you configure a detector nor a specific tracker, has no filter, has no export. I strongly recommend instead using Jython scripting:
https://imagej.net/plugins/trackmate/scripting/scripting

[asincerity]

In the code so far: https://github.com/trackmate-sc/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/TrackMateRunner.java

But I see it does not work for you. I can look into it and try to fix it, but I would be really in favor of retiring the macro support. It is really limited, does not let you configure a detector nor a specific tracker, has no filter, has no export. I strongly recommend instead using Jython scripting: https://imagej.net/plugins/trackmate/scripting/scripting

Thank you for your reply.
I will try to use the Jython scripting.

[asincerity]

In the code so far: https://github.com/trackmate-sc/TrackMate/blob/master/src/main/java/fiji/plugin/trackmate/TrackMateRunner.java
But I see it does not work for you. I can look into it and try to fix it, but I would be really in favor of retiring the macro support. It is really limited, does not let you configure a detector nor a specific tracker, has no filter, has no export. I strongly recommend instead using Jython scripting: https://imagej.net/plugins/trackmate/scripting/scripting

Thank you for your reply. I will try to use the Jython scripting.

I am trying to use the jython code. How can I append code for save the whole trackmate work including setting parameters, spots and tracks. I think it is equal to the button in the GUI as following image:

I found a similar code
But I guess this one only saves tracks or points, not the whole job. And this still seems to be in java.

[tinevez]

Hello @asincerity

You can use the TmXmlWriter class. It does what the 'save' button does.

[asincerity]

thankyou vcery much.it really help me.