This page is a collection of pointers to information that Russ Taylor found while looking for techniques on computational optical sectioning microscopy. A related page describing confocal microscopy visualization is found here.
It looks like there are a lot of groups doing this. Here are some examples.
The NIH National Research Resource at Washington University in St. Louis provides a package for doing this that they call XCOSM. This site includes a tutorial, a downloadable executable, and example images.
Takeo Kanade's group at CMU describes their 3D optical reconstruction of cell shape from optical sections using differential interference contrast (DIC) microscopy. They attempt to reconstruct both the 3D structure and the refractive index distribution throughout the specimen.
There is a good description with images at the Laboratory for Optical and Computational Instrumentation at the University of Wisconsin at Madison (they are an NCRR). They describe it as follows: Out-of-focus interference can be removed by computer deconvolution of the digitized image. This is an iterative computational technique in which a stack of focal sections is recorded and the contribution of out-of-focus signal to a given section from structures in other sections is computed and subtracted from that section. This has proved to be a powerful technique where the out-of-focus signal rejection required is not too great. However, it requires that high levels of registration is maintained as a focal series is being recorded. This requirement is often difficult to meet when recording images from living samples that display a high degree of motility. They have links to vendors of software to do this, including Vaytek and Scanalytics. Vaytek's web page describes how to get turnkey systems, including microscopes, stepper motors, cameras, and software to perform deconvolution and 3D imaging.
There is an online description of the deconvolution techniques that were used in the study of live cardiomyocytes by Donald Winelmann at the University of Medicine and Dentistry of New Jersey.