Starting TrackScheme within script - How to display tracks with microscopy image

Hello @tinevez,

I used TrackMate within a script to detect spots on a z-stack (t=1,z-slices=31) resulting in a xml-file. I want to display the images/z-stack and the detected spots in TrackScheme so that I can compare the detection to the image and delete spots.

For that I used the script proposed by you in the Topic Starting trackscheme within script, doesn’t synchronize selections with hyperstackdisplayer. It starts TrackScheme and displays the spots contained in my xml-file.

But I have 2 questions:
a) The Spots are displayed in front of a black backround. How can I load the images (z-stack, tif-file) from the script into TrackScheme to compare the detection to?
b) Once I have deleted some wrongly detected spots, how can I save these changes to my xml-file?

Hello @kolmogorv

a.
You need to input the path to the _ImageJ TIFF file in the TrackMate xml file.
Check this
https://imagej.net/TrackMate_FAQ#Copying_TrackMate_tracking_data_to_another_image_file.

b.
In a script? You have to use this class

In a UI? You have to display the TrackMate controller, that has a save button.

Thank you very much for your fast reply.

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