I am taking a series of photos using a dSLR camera attached to a microscope that will be used in a stack to produce a single image with high depth of field. Can anyone recommend a level of resolution that I should use for each shot? The camera has a capacity of 18 megapixels, but I am concerned that if each picture is shot at such high resolution, I may introduce noise and the size of the final image will be huge. The software I am using does not address this. I expect to combine somewhere between 6 and 15 images.
Always use as much data as you can. It's actually easier to reduce noise when there's more information to begin with. (Reducing resolution is a brute-force noise removal tool, throwing away both noise and signal.)
If you're concerned about the size final image, reduce the resolution at that point.
I don't have too much to add, but I have some limited experience with focus stacking on microscopes that I can share.
I've done focus stacking on an SEM, the following image is a stack of only two images. I wish I had a third to fill in the blur in the middle.
Image of a flower I took with a scanning electron microscope. The near foreground and the 'sky' background are one image. The subject is a second exposure. I wanted to maximize blur of the background and maximize the clarity of the foreground.
Unless you are optically photographing a fixed subject, the subject will drift, so it is important to take the images quickly, and sequentially to minimize the impact. Frame a bit wider than normal so the final crop can be perfect.
mattdm has the answer you are looking for: Use full resolution as long as possible. Focus stacking will not reduce noise, it will improve image clarity by chooing regions that have better focus. Reducing noise would require a set of exposures at each focal distance to average out the noise- get more data for each pixel.