Image J Fluorescent Tissue Analysis for Morphology

I am quite new to this program and I encountered a problem. I have a precision-cut tissue slice lying on a fluorescent foil and I need to analyze the different signals coming from the tissue. I am hoping this analysis will help me to correlate morphology studies of the tissues with the fluorescent images, so I need to find low/high signals coming from the tissue.
I tried some features of the program but did not understand if I need to delete the background noise or the signal coming from the foil itself or if I can do something to see the signals coming from only the below /upper level I determined.

This is my first massage so I can not attach any pictures but the example picture can be found at the link:

The area on the upper side is my reference and the one at the bottom is my foil with the tissue slice. All the conditions are the same for both chambers.

Thank you in advance, any answer will be much appreciated.