Connectome Atlas Console. Complete Nervous Systems, Neuron by Neuron

A connectome is the complete wiring diagram of a nervous system. This console tells that story in chapters, from the whole animal down to a single flash on the retina, on the real released data. The reference connectome is the male Drosophila central nervous system, MaleCNS v1.0, published by the FlyEM team at HHMI Janelia with Cambridge, the MRC Laboratory of Molecular Biology and Google Research, released 8 June 2026 under CC-BY 4.0.

Nothing on this page quotes a number we did not recompute from the released files. Every asset and every count is produced by a documented pipeline that reads only the released files: annotations, the connection table, the synapse table and the neurotransmitter predictions, all downloadable without credentials from male-cns.janelia.org. The steps are listed in The engine chapter below.

// shown in the engine chapter

def scan_weights(path, body_ids, ...):
    # 151,856,684 rows, streamed in 16 M row batches
    for batch in table.to_batches(max_chunksize=16_000_000):
        ...

def run_sim(graph, seeds, ...):
    # leaky integrate and fire on the signed graph
    for step in range(steps):
        inflow = graph.dot(spikes)
        v = leak * v + inflow + drive
        fired = v > threshold
        ...

What this is and what it is not

It is the real wiring of one male fly’s central nervous system, baked from the released data, plus our own simulation pass over that wiring. It is not a recording of a brain, and it is not a biophysical model.

The honest weak points, stated plainly:

• The simulation is a graph traversal with spike timing. Each neuron integrates signed input, leaks, fires past a threshold of 0.1 of its total input weight, and goes refractory. There are no ion channels, no dendrites, no voltage-gated dynamics. The latency numbers in chapter six are properties of that traversal on the released graph, not biological measurements.
• The point cloud is synapse locations, not morphology. One dot per 4 um cube of presynaptic sites. It looks like the animal because the synapses fill the neuropil. The skeletons behind it are in the released dataset and we do not yet ship them.
• The matrix chapter draws the strongest connections only. The full graph has 151.9 million edges above one contact. Shipping all of them to a browser would dominate the page weight, so the console draws the 1.1 million at or above twenty contacts and states the cut. The counts in the right panel are the full counts, recomputed.
• One animal, one sex. MaleCNS v1.0 is a male. The female brain (FlyWire) is a different dataset with different annotations.

Why it belongs here

The Neutral Core claims substrate independence: the same causal organisation can run on a different physical base. Connectomics is where that claim meets data. A complete nervous system is now small enough to download, and this page exists so the claim can be looked at directly, chapter by chapter, without a credential or a cluster.

The fly is the reference organism for this site’s emulation coverage. The FlyWire whole-brain connectome post covers the female brain. The Eon Systems fruit fly emulation post covers what happens when a connectome drives a simulated body. This console holds the male CNS data itself.

Sources

• MaleCNS v1.0, FlyEM Team, HHMI Janelia, released 8 June 2026, male-cns.janelia.org, CC-BY 4.0. Preprint: bioRxiv 2025.10.09.680999.
• C. elegans connectivity: White et al. 1986; Cook et al. 2019, wormwiring.org.
• MICrONS mm3: microns-explorer.org, The MICrONS Consortium, Nature 2025 collection.
• Human neuron count: Azevedo et al. 2009, “Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain”, J. Comp. Neurol.