Could you provide a bit more information? For example, what kind of data are you using as input for this problem? Are you planning on using raw sequence data and then simulating a Giemsa stain with based on G+C content and other factors? Or are you correlating images of stained chromosomes with sequence or some other kind of data?
To a me, this is a very cool project, I'd definitely like to hear more about it. No matter what sort of data you're using, I would thinkg about using bioperl, as it's very likely that they have a module for doing at least some of what you're interested in. I highly recommend the GD package for this sort of stuff, and the Tisdale articles mentioned above can be relevant if you're manipulating megabases of nucleotide data.

I wish you luck. :)