I know this is not a pure bioinformatics question but my lab has been researching methods of obtaining large amounts of image sets automatically in order to extract useful histological features out of them and correlate with sequencing data. You may find similar work there
Our main material is H&E stained slides obtained through multi layered TMA dissection from FFPE tumors. Problem is that we want to take many optical microscopy photos in different zoom levels with optimized brightness and focus. Do you know if that kind of technology is generally commercially available?
I am a cytotechnologist that is studying bioinformatics so I am very interested in doing something similar to you in the future... but with cytology specimens. I think "Whole Slide Imaging Tech" is what you are looking for. It is very time consuming, data intensive, and EXPENSIVE. I work in an academic medical center and we only do WSI for samples that we need to sacrifice for IHC/Molecular. They archive the image of the HE slide for future reference then scrape it/stain it. I think some of the larger instruments that can do a few hundred slides at once are a few hundred thousand dollars. There is nothing scalable yet to my knowledge which is why we rarely do this in pathology (at the moment). I just take pictures of cancer cells with a microscope and cell phone and they come out great-- I am sure you are trying to do something on a large scale though and as far as I know there is no easy solution for this...yet (unless you have really deep pockets).