I have managed to script Trackmate for my purposes (thank you @tinevez for the extensive documentation and examples!) and now would like to export the peaks or the spots detected as ImageJ ROIs.
I found the way to do this for 3D dataset here but my dataset is 2D + t. I tried to use the fact that the spots obtained via LogDetector is actually Trackmate
Spots and tried to obtain the
POSITION_T feature which returned
NONE. When I print the features I just get
RADIUS, QUALITY, POSITION_X, POSITION_Y, POSITION_Z. I then tried to loop through frames and compute spots at each time point and honestly this was not such a good idea.
Could someone point me to a correct way to export the peaks from 2D time-lapse to ImageJ Rois?
P.S On a side note, I also found that the
Spots Features mentions
POSITION_Z twice. I am not sure if it is a typo or it is intentional.