What would you need...

1. a cheap microscope - wouldn't need to be a good one because you'd only need to scan a very small area.
2. a cheap digital camera - cheap for the same reason.
3. a tracking mechanism - an old dot matrix printer should have most of what you'd need in the way of carriage and stepping motors.

Put it all together with some software. Shouldn't take reasonable programmer more than a month or two.