Skip to main content.

Synapse Finder

This page includes an optimised version of a java program by Ding, Fan (fan at 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...

Before After

Links to an animation of the algorithm, some links, and a download page.