To acheive automatic segmentation of 3D electron microscopic neuropil images, two major challenges must be met. (1) Accuracy must be high enough to eliminate human correction from the process. Massive datasets are needed to examine brain circuitry and the reconstruction is not feasible by hand. (2) Automatic segmentation techniques must recognize enough detail to create models of neural activity. Certainly this requires identifying all synapses, and it will require identifying other subcellular components also (because subcellular components tell us where the synapses are and they can affect the flow of ions).