Trackmate export hyperstack display to PNG in a Jython script

imagej
trackmate

#1

Hi @tinevez,

Hope you’re doing well!

With your kind help, we’ve been able to automate trackmate and its numeric output via scripting, which is working amazing for us, but would also like to have some visual record of segmentation/tracking process, along with the numeric output.

Can you please point us how to include functionality of hyperstack display -> PNG output of a few frames of our video, saved to harddrive, into a macro/script?

Thank you!


#2

Hi @l-jaye

The command that does that is based on ImageJ capture image. You can find the code here:

This is what you would have to call to capture a RGB capture of the movie.
Best
jy