The setup:
The first thing is to acquire the best image you can before you do any postprocessing. It’s easier to fix (or ignore) minor problems than to fix major ones. So, turn the major ones into minor ones with a good setup. That means using a good camera, light tube, and microscope. I have never been all that impressed with most of the built-in cameras I’ve seen sold with microscopes, but I haven’t been keeping up with them. They might be fine. My setup is a Nikon Z7 on a 40-year-old Olympus BH-2, with a halogen bulb. A lot of people swear by new scopes with LED illumination. We have some Zeiss scopes at work like that. I’m not such a big fan, but that’s a matter of taste. Things seem a bit over-refractive to me on them. I’m assuming that folk will be using a digital camera. I vaguely remember various filters and tricks for film when I was just a tyke, but I’ve forgotten it, and I don’t know anybody who uses film any more.
If you are building your own camera setup, you will likely have to buy a tube to put the camera on. Remember that these have lenses inside of them. If they are not good lenses, they can introduce distortion. I bought one for my first camera setup off of Ebay, and it was a problem. It worked, but it degraded the sharpness of my results no matter what I did. In addition, make sure that the tubes don’t magnify too much — which will limit your field of view in the image. For some reason I don’t understand, it seems to be hard to find a light tube that doesn’t at least give at least 2x magnification.
Once the system is set up, make sure that you have your focus the best it can be on the camera sensor. You can use the focus on the light tube to try to get the focus on the camera as close to the point of focus through the eyepieces. That makes things convenient, but not necessary. You will be focusing using a monitor attached to the camera.
I have the hdmi output from the camera attached to a high resolution monitor. I like to have the monitor at the highest resolution I can afford. If I’m catching a 8Kx4K image and viewing it on 1028×780 screen, then each pixel on the screen is the average of something like 40 camera pixels. That means you may not be able to see to focus as best you can. With a “4K” (3800×2480) screen, each pixel on the screen represents around 3 camera pixels. You can get around this a little by using the zoom function in your camera if you have it. This may not be as big a deal if you are going to scale everything down to 2Kx1K images for using on web pages and Powerpoint slides, but remember it’s always easy to degrade a good image, and hard to improve a bad one. It’s better to get the best image you can and degrade it for presentation on low-resolution media.