MaleCNS v1.0 — Male Fruit Fly Central Nervous System Connectome
Dataset Description
This repository mirrors the MaleCNS v1.0 connectome — the first complete wiring diagram of the central nervous system (brain + ventral nerve cord) of an adult male Drosophila melanogaster (fruit fly).
The original dataset was produced by a collaboration between:
- HHMI Janelia (FlyEM Project Team)
- University of Cambridge (Dept. of Zoology)
- MRC Laboratory of Molecular Biology
- Google Research
Original source: male-cns.janelia.org/download
License: CC-BY 4.0 — original license preserved.
What's in this repo
The flat connectome files from the Janelia GCS bucket (gs://flyem-male-cns/v1.0/connectome-data/flat-connectome/), including:
- Connectivity data — neuron-to-neuron synapse connections (from neuron, to neuron, connection weight)
- Neuron annotations — cell type labels, neurotransmitter predictions, soma locations
- Skeleton files — 3D morphology of individual neurons in SWC format
Dataset Statistics
| Property | Value |
|---|---|
| Neurons | ~166,700 |
| Synaptic connections | ~25 million |
| Coverage | Full CNS (brain + ventral nerve cord) |
| Resolution | 8nm isotropic EM |
| Release version | v1.0 (June 8, 2026) |
Intended Use
This mirror is being used as the data backbone for a personal AI assistant project (Jarvis) that:
- Runs the connectome as a live spiking neural network simulation (via Brian2)
- Feeds the simulation encoded representations of real task logs
- Applies Hebbian learning and neurogenesis rules on top of the static connectome
- Uses regions of network growth as signals for capability gaps in the AI system
This is an experimental research project. The connectome is not being modified — growth rules are applied in simulation only, on top of the original graph.
How the Simplified Activity Model Works
The simulation uses leaky integrate-and-fire (LIF) neurons — a simplified but biologically grounded model where:
- Each neuron accumulates charge from incoming synaptic signals
- When charge crosses a threshold, the neuron fires (emits a spike)
- Charge decays over time if threshold isn't reached
On top of the static MaleCNS topology, the following rules are applied:
- Hebbian strengthening — synaptic weights increase between neurons that fire together repeatedly
- Synaptic pruning — connections that never activate across N simulation steps are weakened and removed
- Neurogenesis trigger — when a neuron cluster consistently saturates (hits its firing ceiling), new nodes are spawned and attached to that region
Citation
If you use this data, please cite the original MaleCNS paper:
Schlegel et al. (2024). Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila. bioRxiv.
And link back to the original source: male-cns.janelia.org
Acknowledgements
All connectome data belongs to the original authors and is reproduced here under CC-BY 4.0. This repository does not claim ownership of the underlying biological data.
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