Circuits: a repository of (neural) schematics

Thu 30 January 2014

As someone who has dabbled in computer architecture, I find computing circuits fascinating, and none are more fascinating than biological computing circuits. It surprise surprise my EE and computer architecture friends, but there are still tremendous gaps in our knowledge about the wiring of neural systems, especially at the level of individual computing units (neurons).

Researchers in the field of "connectomics" have recently been meeting with success in tracing the connections between every cell I've been building probabilistic models to understand this data with Konrad Kording at Northwestern. Often the released data was in a collection of annoying formats with metadata scattered throughout. I'm putting our cleaned-up and annotated sqlite databases on the web of two of the datasets I've been working with (and hopefully more, soon).

The datasets

You'll find the physical locations of the cells, their "known" cell types, and the graph of their interconnections here, in sqlite format.

Github repository of circuit schematics

Example Plots

The Mouse retina connectome adjacency matrix (size of point proportional to number of synapses):

The physical location of the cell bodies of each cell, colored by cell type, in x-y-z.

The connectivity of the worm, c. elegans -- blue are chemical synapses, red are electrical synapses.