Last updated: 2026-09-16
MaleCNS is the first complete connectome of an adult male Drosophila central nervous system, mapping over 166,000 neurons, 125 million synapses, and 11,691 cell types across the central brain, optic lobes, and ventral nerve cord. Released 8 June 2026 by HHMI Janelia, Cambridge, MRC LMB, and Google Research.
About MaleCNS Connectome
MaleCNS is Janelia's finished map of the wiring inside an adult male Drosophila melanogaster's brain and nerve cord, built by the FlyEM project team at Howard Hughes Medical Institute's Janelia Research Campus (opened 2006) together with the University of Cambridge's Drosophila Connectomics Group, the UK Medical Research Council's Laboratory of Molecular Biology, and Google Research. Connectomics work at Janelia began around 2008; head of biology Gerry Rubin has said the original estimate under 2008-era technology was roughly 500 people working for 10 years, a scale the team only closed by betting that automated reconstruction could improve efficiency more than 1,000-fold. Funding came from HHMI's core budget, the Wellcome Trust, and MRC core funding to the Laboratory of Molecular Biology. Version 0.9 shipped 3 October 2025, version 1.0 on 8 June 2026, and the companion paper in Cell followed on 3 September 2026.
The nervous system was imaged whole with electron microscopy, then reconstructed with Google's PATHFINDER system, a flood-filling-network pipeline of convolutional neural networks that starts at a single pixel and traces every other pixel belonging to the same neuron through the 3D image volume. A later refinement added synthetic neurons to PATHFINDER's training data to raise segmentation accuracy without more hand-labeled examples. Every reconstructed neuron and synaptic connection was proofread and classified by cell type with a predicted neurotransmitter identity, and the team separately catalogued a set of sex-specific and sexually dimorphic cell types not distinguished in earlier connectomes. Unlike the brain-only hemibrain (25,000 neurons, 21 million connections) or FlyWire connectomes, MaleCNS is the only one of the three to include the full central nervous system in one specimen, so a signal can be traced from a sensory neuron straight through to a motor output in one dataset.
MaleCNS is built for Drosophila neuroscientists and computational connectomics researchers, not general software developers; there is no chat interface, REST API, or SDK aimed at building consumer products. Typical uses are tracing sensory-to-behavior circuits and comparing male-specific and sexually dimorphic wiring against earlier connectomes to study mating and aggression behavior. Community projects have also started treating the wiring diagram itself as a substrate for AI research, wiring MaleCNS into recurrent neural networks that play reinforcement-learning environments and into embodied sensorimotor-control experiments.
The full dataset is free to use, with the underlying files downloadable directly and no account required (see the pricing FAQ for license terms). Access otherwise runs through a handful of free browser-based and programmatic tools built for querying, visualizing, and scripting against the connectivity data, with no dedicated desktop or mobile client.
Pricing
0 license. No paid tier, subscription, or per-query fee; all data downloads and all browser tools (NeuPrint, Neuroglancer, Cell Type Explorer) are open access, attribution required.
Key Features
- Whole-CNS reconstruction: Covers the entire central nervous system, brain, optic lobes, and ventral nerve cord, of one animal with the neck connective intact; competing Drosophila connectomes cover only part of it.
- 11,691 annotated cell types: Every neuron is proofread and classified into one of 11,691 named cell types, each carrying a predicted neurotransmitter identity.
- PATHFINDER AI reconstruction: Google's flood-filling-network segmentation pipeline, refined with synthetic training neurons, converted serial electron-microscopy images into 3D neuron reconstructions.
- Sex-specific circuit mapping: Identifies 262 sex-specific and 114 sexually dimorphic cell types, about 4.8% of the central brain, browsable in the Dimorphism Explorer.
- Multiple free query tools: NeuPrint for connectivity queries, Neuroglancer for 3D visualization, Cell Type Explorer for browsing, Clio for annotation, and neuprint-python or natverse for programmatic access.
- Direct data downloads: Raw EM volumes, segmentations, synapse tables, skeletons, and a full neo4j connectivity database are downloadable without an account.
Pros
- The only published connectome covering an entire central nervous system in one animal rather than brain or nerve cord alone, useful for tracing signals end to end.
- Free with no paid tier, unlike most commercial neuroscience data platforms; the whole dataset, not a sample, downloads directly with no account needed.
- Reconstruction leaned on Google's PATHFINDER AI pipeline rather than manual tracing alone, which is why a whole-CNS map exists within one research programme's lifetime; earlier fly connectomes stayed brain-only to remain tractable.
- Pairs directly with the earlier, brain-only hemibrain and FlyWire datasets, letting researchers pinpoint newly identified sex-specific and sexually dimorphic circuits that neither of those datasets could show.
Cons
- No single bulk download: the dataset's annotation, connectivity, and skeleton files are split across many separate downloads in different formats (Feather, CSV, SWC, neo4j) that researchers must assemble themselves.
- Cross-dataset comparisons are noisy: independent analysis found that roughly a third of hemibrain cell types could not be reliably re-identified in FlyWire, and connection weights vary across specimens and datasets even within one species.
- Built for connectomics researchers, not general AI builders: there is no REST API, SDK, or chat interface, only query tools (NeuPrint) and programmatic libraries (neuprint-python, natverse) aimed at people who already work with EM connectivity data.
Frequently Asked Questions
How much do you pay for MaleCNS Connectome?
Nothing. The dataset and every companion tool are released free under a CC-BY 4.0 license, with no paid tier, subscription, or usage cap. Reusing the data or figures just requires attribution to the FlyEM, Cambridge, and Google Research collaboration.
Is MaleCNS Connectome free to use?
Yes, the entire connectome is free, not a limited trial or sample. Every file on the download page and every browser-based query tool is open to use at no cost; the only condition is the attribution covered in the pricing question above.
What should you use instead of MaleCNS Connectome?
For a brain-only view, the FlyWire and original hemibrain connectomes cover the Drosophila brain but not the ventral nerve cord. For nerve-cord-only circuitry, Janelia's earlier MANC dataset is narrower but was published sooner. Choose MaleCNS specifically when a project needs the intact brain-to-body pathway, sex-specific circuits, or the largest published single-animal neuron count to date.
Is MaleCNS Connectome better than FlyWire?
Neither replaces the other: FlyWire is a community-proofread map of the whole brain only, while MaleCNS also includes the optic lobes and ventral nerve cord, so it is the one to reach for when tracing a full sensory-to-motor pathway. FlyWire remains the deeper resource for brain-only circuit work, since its community has spent longer proofreading that single region.
How long does it take to get going with MaleCNS Connectome?
Browsing takes minutes: the MaleCNS Cell Type Explorer and Neuroglancer viewer open in a browser with no signup or install. Running real queries takes longer, since NeuPrint's Python client or the R-based natverse package needs a working Python or R environment, and downloading the full annotation and synapse tables takes longer still.