I admire your attitude, but I think this is way too big of both a control and data acquisition project for an Arduino.
With things like a 2 megapixel color USB microscope camera going for under $35 ( AGPtek 2.0 MP 400x USB Digital Microscope ),
I'd look for the the Arduino to do a different part, like control the laser and/or move the stage while your PC then grabs the image
via USB.