Recent technological developments have renewed the interest in large-scale neural circuit reconstruction. To resolve the structure of entire circuits, thousands of neurons must be reconstructed and their synapses identified. Reconstruction techniques at the light microscopic level are capable of following sparsely labeled neurites over long distances, but fail with densely labeled neuropil. Electron microscopy provides the resolution required to resolve densely stained neuropil, but is challenged when data for volumes large enough to contain complete circuits need to be collected. Both photon-based and electron-based imaging methods will ultimately need highly automated data analysis, because the manual tracing of most networks of interest would require hundreds to tens of thousands of years in human labor.