One challenge I have encountered with microscope photography is the very limited depth of field. Only a very thin slice of the subject matter (whether that is coffee grinds or paramecium) can be in focus at a time.
For relatively still subjects, I have found photo stacking (sometimes called z-stacking or focus blending) can effectively increase the depth of field.
I downloaded a trial version of Photoshop and used the instructions found in the article “Focus Stacking comparing Photoshop, Helicon Focus and Zerene”. I took 9 photos of decaf coffee grinds taken at different focus depths, and blended them in Photoshop. Here is the result:
As a comparison, below is the first of the nine photos used. Only the highest part of the coffee grinds are in focus with everything below progressively blurred out.
This initial experiment used only 9 photos. I’ve seen examples online of dozens of images blended together to create incredible images.