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neuPrint

neuPrint (https://neuprint.janelia.org) hosts connectome datasets (neurons, synaptic connections,

For agents: neuPrint hosts connectome datasets (neurons, synapses) from Janelia, with a documented REST API, dataset metadata, and bulk downloads for neuroscience research.

connectomeneuroscience datasetsneuprintfruit fly brainrest api

Their llms.txt

The beginning of the file, from our validated copy saved 2026-10-26T13:10:56.813Z. Cached copy · Source on janelia.org

# neuPrint

> neuPrint (https://neuprint.janelia.org) hosts connectome datasets (neurons, synaptic connections,
> synapses, skeletons, and brain regions) for interactive exploration and targeted queries.
> It is a shared server with limited capacity; it is NOT intended for exporting whole datasets.

Choose the right tool for the job:

- **Targeted questions** (particular cell types, circuits, brain regions, a few thousand neurons):
  query the neuPrint API, preferably via the `neuprint-python` client.
- **Whole-connectome analysis** (all neurons, all connections, all synapses, graph statistics,
  simulation, machine learning): download the bulk exports listed below, if available.
  Do not page through the entire dataset via the API.

Please be considerate of other users: run queries sequentially or with very limited
parallelism, and cache results locally rather than re-fetching them.

Access to all datasets, even publicly released ones, requires a token.
API token is available from https://neuprint.janelia.org/account after logging in (with a Google account).

## Docs

- [neuprint-python documentation](https://connectome-neuprint.github.io/neuprint-python/docs/): Python client (`pip install neuprint-python`); the recommended way to query neuPrint.
- [Bulk downloads FAQ](https://connectome-neuprint.github.io/neuprint-python/docs/faq.html#bulk-downloads): where to find whole-dataset exports.
- [REST API reference](https://neuprint.janelia.org/api/help): Swagger documentation for the HTTP API.
- [Dataset list](https://neuprint.janelia.org/api/dbmeta/datasets): JSON metadata for all datasets on this server, including older versions not described below.
- [Release notes and errata](https://neuprint.janelia.org/releasenotes)

## Datasets

### male-cns:v1.0

The complete MaleCNS connectome from the Janelia FlyEM Team Project,
the Cambridge Drosophila Connectomics Group, and Google Connectomics.
Covers the brain and nerve cord; 167k neurons.

- [Project overview](https://www.janelia.org/project-team/flyem/male-cns-connectome)
- Companion sites:
    - [Male CNS Connectome Site](https://janelia-flyem.github.io/male-cns)
    - [Cell Type Explorer](https://reiserlab.github.io/celltype-explorer-drosophila-male-cns)
    - [Base neuroglancer scene](https://neuroglancer-demo.appspot.com/#!gs://flyem-male-cns/v1.0/male-cns-v1.0.json)
    - [Clio](https://clio.janelia.org/ws/annotate?dataset=male-cns:v1.0&tab=bodies)
- Notes:
    - Synapse coordinates are stored in voxel units (8nm).

- Bulk downloads: see the [male-cns download page](https://male-cns.janelia.org/download), or the bucket `gs://flyem-male-cns/v1.0/` (list without login: https://storage.googleapis.com/storage/v1/b/flyem-male-cns/o?prefix=v1.0/&delimiter=/)

### optic-lobe:v1.1

A reconstruction of the Drosophila optic lobe from the Janelia FlyEM Team Project and Google Connectomics.
This covers a subset of the MaleCNS sample (right optic lobe; 50k neurons).
This database is provided as a companion t
…

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