# 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 to earlier publications. For new analyses, use the full MaleCNS connectome.

- [Project overview](https://www.janelia.org/project-team/flyem/optic-lobe)
- Companion sites:
    - [Optic Lobe Cell Type Explorer](https://reiserlab.github.io/male-drosophila-visual-system-connectome)
    - [Base neuroglancer scene](https://neuroglancer-demo.appspot.com/#!gs://flyem-optic-lobe/v1.1/optic-lobe-v1.1.json)
- Citation: [Nern et al. (2025)](https://doi.org/10.1038/s41586-025-08746-0)

- Bulk downloads: `gs://flyem-optic-lobe/v1.1/` (list without login: https://storage.googleapis.com/storage/v1/b/flyem-optic-lobe/o?prefix=v1.1/&delimiter=/).
  The male-cns dataset is a superset of this dataset (same fly), so prefer male-cns for new analyses.

### manc:v1.2.3

The MANC connectome from the Janelia FlyEM Team Project and the Cambridge Drosophila Connectomics Group, and Google Connectomics.
The male adult Drosophila nerve cord; 23k neurons.

- [Project overview](https://www.janelia.org/project-team/flyem/manc-connectome)
- Companion sites:
    - [Base neuroglancer scene](https://neuroglancer-demo.appspot.com/#!gs://manc-seg-v1p2/manc-v1.2.3-neuprint-layers.json)
    - [Clio](https://clio.janelia.org)
- Citations
    - [Takemura et al. (2024)](https://doi.org/10.7554/eLife.97769.1)
    - [Marin et al. (2024)](https://doi.org/10.7554/eLife.97766.1)
    - [Cheong et al. (2025)](https://doi.org/10.7554/eLife.96084.2)

- Bulk downloads: `gs://manc-seg-v1p2/` (list without login: https://storage.googleapis.com/storage/v1/b/manc-seg-v1p2/o?prefix=&delimiter=/)

### hemibrain:v1.2.1

A reconstructon of the female central complex and surrounding neuropils from the Janelia FlyEM Team Project and Google Connectomics.
Covers roughly half of the brain, with ~22k fully reconstructed neurons and ~76k truncated neurons.

- [Project overview](https://www.janelia.org/project-team/flyem/hemibrain)
- Companion sites:
    - [Base neuroglancer scene](https://neuroglancer-demo.appspot.com/#!gs://flyem-views/hemibrain/v1.2/base.json)
    - [Clio](https://clio.janelia.org)
- Citation: [Scheffer et al. (2020)](https://doi.org/10.7554/eLife.57443)

- Bulk downloads: `gs://hemibrain/v1.2/` (list without login: https://storage.googleapis.com/storage/v1/b/hemibrain/o?prefix=v1.2/&delimiter=/)