Introduction

I am working with (physical) array data, that is scanned in at 100 microns / pixel. The result of this is a tif image with many spots corresponding to the points of interest on the array, which each have varied intensities. I have already figured out how to split these tif images into smaller files so that each point of interest is its own file. Now I am trying to figure out the next step - that is, I want to analyze each one independently. Each spot essentially has a "background" and a "data" region, that I could specify roughly by pixel locations.
I should also mention that there will be many of these arrays as time goes on, so I am looking of course for a reproducible method that I can repeat for any number of arrays as time goes on.

Question

Can I take these files into perl, and then do a comparison of the color (in this case, the greyscale value) of pixel (A,B) in the image versus (C,D) in the same image?