The fine anatomical relationships between brain cells remain mostly unknown. This study examined the connectivity of a 1,500 μm3 volume of mouse neocortex. More than 2,000 29-nm coronal brain sections were generated with an automatic tape-collecting ultramicrotome and used in scanning electron microscopy, and the neocortical volume was reconstructed from the resulting images. 1,700 synapses were found in this volume, but there were many more incidences of axons touching spines without forming synapses, indicating that the close proximity of axons to spines does not predict connectivity.