Comparing IF signal intensity in different histological samples


I would like an help in measuring and comparing the signal intensities of Tight junctions expressed in mouse gastrointestinal tract between treatment and control.
Especially I’ve a doubt regarding how to choose the section under microscope because the structure is different between control and treatment.

I really appreciate if someone could explain me all steps that I’ve to do in image J.

Here just tried to attach an example of the tissue structure, in green -JAM-A one of tight junctions I want to measure the signal intensity, in blue dapi. merge jam-a 100.tif (9.2 MB)

Thank you very much!