Synapse Finder
This page includes an optimised version of a java program by Ding, Fan (fan at cs.wisc.edu) used for semi-automatically detecting outlines of synapses in EM images.
It uses a fast marching / level set algorithm, so the output is a slice through a 3D surface / height field rather than a vanilla line. J Sethian's web site at Berkeley has lots of material on the algorithms.
The original version is here - this version includes optimisations which allow the algorithms to run on medium sized EM images in reasonable time
The raw image...
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Links to an animation of the algorithm, some links, and a download page.