I am very new to QuPath scripting, so please forgive me for what I assume is quite a simple problem!
When I select an annotation and ‘Send Region to ImageJ’ I have the option of including the overlay, which is what I need for my analysis.
However, when I run this script: https://qupath.readthedocs.io/en/latest/docs/scripting/overview.html#working-with-imagej
I do get the same output in imageJ except the overlay with the cell detection is not there. So my question is what can I add to the script in order to take the overlay into the ImageJ export.
One other minor thing is that using the script the output file is the file name of the scan, but when I use the command in QuPath it is the name of the Annotation. How would this be handled in the script?