BrainMaps documentation

BrainMaps is a catalogue and viewer for brain images, anatomical atlases and registration results. Use the website to explore data and the CLI to prepare, upload and process it.

These guides were checked against the platform and the CLI source checkout on 17 September 2026. The CLI source declares version 0.3.0; public package distribution is still pending. See installation before running CLI examples.

Start here

Use the website: browse categories, species, atlases and brains.
View brains and channels: 3D, slices, intensity controls and anatomical overlays.
Add data: choose browser upload or CLI processing.
Run registration and compute: local processing, registration records and atlas builds.
Use the API: authentication, catalogue records, layers and jobs.

Access

Every signed-in account can view the platform’s scientific datasets. Uploads and other processing writes require account approval. Signed-in users can add species; only superadmins can change categories or edit/delete existing species. See the access policy.

Some demos and source URLs are publicly accessible. Sign-in is not a promise that every underlying object-storage URL is private. Confirm the source’s licence and attribution before redistributing it.

Authentication