Image Focus Stacking
Focus stacking is a process by which images with very shallow depth of field can be combined such that the final image is a composite of a series of images, where the final image only contains sections that are in focus for each of the source images.
A good tutorial on implementing focus stacking in linux is given in this blog post; http://blog.patdavid.net/2013/01/focus-stacking-macro-photos-enfuse.html
There is a wikipedia article on focus stacking; http://en.wikipedia.org/wiki/Focus_stacking
It's possible to stack images from microscopes taken by adjusting the platform height, and moving different parts of the sample into the focal plane. This is called z-stacking.
I am looking to create a platform, using parts from a 3d printer, to automate creating z-stacked photomicrographs using a cheap ole' researcher microscope.