A few months back a member of our bee association reported on a microscopy class she had taken. One of the tools they learned to use was an image stacker that corrected for the depth of field problem usually seen in microscopes.
One thing this would be great at is pictures of honeycomb. You could get the face of the comb in focus and also an egg or larvum at the bottom. I'll probably also use it for micrographs of pollen using my high power microscope.
The shots below were taken of a very dead bee: the subject must not move as several photos are taken. For this particular image stack I used ten frames, 3 of which are shown in cropped and compressed format below. I got shots with the paper the bee is sitting on in focus all the way up to the hair on its back in focus. The program sifts thru these and judges which sections are in focus by several methods. The simple version is to look for maximum contrast between adjacent pixels.
There are several packages out there but I like CombineZP because it is FREE. Its a little buggy. This particular set of pictures winds up with the program crashing when it is done, but by that time it has run 6 versions of the picture using different methods, and you get to chose the best. The website says it was intended for Windows XP and Vista. I'm running it on Windows 7, using The Mighty Teraquad, my video editing beast. The version is whatever the latest version was today when I downloaded it.
Microscope: Edmund 10x/30x trinocular
Camera: Nikon D5100, Manual mode, remote shutter release
Mount: Edmund adapter tube with a Nikon T-Mount adapter
Lighting: Two LED desk lamps
A sampling of the pictures from which the final was made. These are cropped and compressed from the ones I actually used.
CombineZPTest 003Compr.jpg CombineZPTest 007Compr.jpg CombineZPTest 011Compr.jpg
And the stacked final version (I chose the Do Soft composition). I've cropped and compressed it for web use ... you have to zoom in really tight to tell the difference, but the full res version is slightly sharper.
Do Soft Stack[1,0,1]Compr.jpg