The FlyWire connectome provides the complete synaptic wiring diagram: every connection between every neuron, annotated with neurotransmitter type and synapse count. This lesson turns that raw edge list into analysable connectivity matrices and pathway maps.

Lesson 08 — Connectivity

Starting from ~50 million synaptic connections:

  1. Edge list loading — parsing the FlyWire synapse table
  2. Neurotransmitter assignment — each synapse inherits its presynaptic neuron’s NT identity (ACh, GABA, Glu, 5-HT, DA, OA)
  3. Neuropil connectivity matrices — aggregating synapses by source/target neuropil to reveal the coarse wiring diagram
  4. Pathway analysis — tracing multi-hop paths between regions
  5. Motif analysis — identifying recurring circuit motifs (reciprocal, convergent, divergent)

The connectivity matrix is the skeleton on which all simulation and analysis hangs. Get this right, and the dynamics emerge from the wiring.

Source: domains/bravli/codev/08-connectivity.org (1,045 lines, ~39 KB)