Hi,

I don't know if in R there is a program that is useful for your question, but there is a imageJ. If I remember well this program perform the quantification of fluorescent intensity

In R, you can try the Bioconductor EBImage package. As already suggested, ImageJ is a favorite amongst biologists but there are plenty of image processing toolkits out there that can do what you want. Here is a non-exhaustive list trying to cover different programming environments: Octave's image package, vigra (C++ with python bindings), python's scikit-image, perl's IPA module and PDL image-related modules.