I was photographing a small beetle and ran into the problem that it was just 0.5 inches long, and the macro setting on my camera failed to produce a sufficiently detailed and crisp image. Therefore I placed the beetle under a 5× magnification microscope. However, the focal plane was not as thick as the beetle. Therefore, I could only have the feet or the head/top in focus but not both:
How can the beetle be photographed entirely in focus through the 5× scope?
You can use focus stacking. It is a way to combine similar pictures at lower DOF to create a picture of larger DOF. This video details the procedure.
The depth of field is a function of the relationship between the image magnification and the diaphragm opening (aperture).
You will have to reduce the aperture at that magnification or reduce the magnification at that aperture.
Changing the lens focal length to affect d.o.f. from a given subject-camera distance is changing the image magnification, in effect.
** One way to reduce the aperture, if the microscope has a fixed aperture, is to use a "field-stop."
To make a field stop, cut/or punch a clean circular hole in an opaque (black is better) stiff paper or thin card. You can use a sharpie, or india ink to make an index card black enough, too. Maybe you can find the right-sized metal or fibre washer in a hardware store or misc. parts you may already have around your studio, or lab, shop or house - paint it black to cut down flare. Tape it in place over the lens.
Place your aperture in front of the microscope lens centering the aperture. For some gross-specimen low-magnification 'scopes, this is relatively easy since the lens is quite large.
The field-stop acts as an outboard aperture to limit the light entering the lens to the centre. The effect is increased apparent depth due to the "stopping down" (reducing the aperture) of the lens.
Experiment to find the right aperture to achieve the depth of field you wish. The exposure will have to compensate for the reduction of light. There might be some vignetting, but c'est la vie.
The background could be a bit lighter, too, which might help the image detail rendition.
The depth of field is based on viewing distance and magnification. You can reduce the size of the aperture through which the light travels, but this would have to be done using different optics in the microscope itself. I don't think most microscopes have a depth of field adjustment available.
Focus stacking is the other option which basically works by taking multiple images and using the sharpest areas of each. It does require the subject to be stationary though so it won't work on live subjects.
There is an online microscopy depth of field calculator available here.
