I'm sure you are going to share every step of the way on this adventure...
DoF is going to be a real issue at those magnifications, so I suspect keeping whatever you are shooting flat and on the focal plane is going to be critical to getting a strong image.
My unsolicited suggestion is that you use a different shot as a base shot: one with a lot of in-focus detail, and ideally, as Manfred suggested, reasonably flat and parallel to the sensor. A shot of that sort will allow you to see detail that the microscope reveals.