The CRCNS (Collaborative Research in Computational Neuroscience) project has developed a set of publically available tools to enable the large scale reconstruction of 2D mosaics and 3D volumes collected via electron and light microscopy. These tools were first used to reconstruct the rabbit retina and details of the methods used can be found in our PLoS Biology Paper:

J.R. Anderson, B.W. Jones, J-H Yang, M.V. Shaw, C.B. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U V, R. Whitaker, D. Mastronarde , T. Tasdizen, R.E. Marc. "A Computational Framework for Ultrastructural Mapping of Neural Circuitry" in PLoS Biology, March, vol. 7, no. 3, pp. e74, 2009.