I'm currenlty analyzing receptor autoradiography images of human brain sections using MCID software.

I'm having some trouble understanding how properly analyzing the images, for example: what should I do when a specific slice (of a specific region) has an uneven signal (so for example, one part is darker than the other part)? Should I analyze only the darker part or do I measure the whole slice obtaining a mean value?

Or, how do I understand when it's better to exclude a specific slice (maybe because too damaged)?

So, in other words, I'm looking for a guide (possible a complete guide) that could assess all the possible problems encountered during these kinds of analysis.

Thank you in advance.