I’m very new to FIJI, and just finished the wonderful Neubias Academy macro course.
I want to count the intersection of a red threshold with a green threshold (i.e., count the number of red cells also expressing green). How to combine the two sets of binary images to only show overlap? I see the “And, Or, and XOr” in the ROI manager; how should I use these? What would the appropriate commands be in a script?
If you have the binary mask it would be faster to use boolean operations (AND, OR, XOR) within
Process>Image Calculator..., which may be recorded and included in a macro.
If you only have the ROIs, it is possible to obtain the corresponding binary mask from the ROI Manager:
ROI Manager > Deselect
ROI Manager > More > OR(Combine)
Edit > Selection > Create Mask
Hope it helps
Thank you Pau. I was thinking inside of the ROI manager, but your idea of using Image Calculator sounds better. I appreciate your comment.