A connectome is a complete mapping of all connections, including every individual synapse and gap junction, between all neurons in a model organism's brain. In other words, a comprehensive circuit diagram of the brain. Current approaches to mapping the connectomes of model organisms employ serial block face scanning electron microscopy (SBF-SEM) and transmission electron microscopy (TEM). The only connectome that has been mapped out to date has been from the flatworm, C. elegans, which has only around 300 neurons. Candidate future connectomes include the fly, with around 10,000 neurons, and the mouse brain, with 100 million neurons.
Slightly more modest than a connectome is a mapping of all inter-areal connections, at the single axon level, within an individual brain. This approach is more amenable to coarser imaging resolutions of 80 nm versus 20 nm (for a connectome), thereby affording a 64-fold (4^3) decrease in image data acquisition time, and will result in complete whole-brain inter-areal wiring diagrams for the mouse in the near future.
Next: Mapping the Whole Mouse Brain