Use the website
Open BrainMaps. You do not need a local installation to browse the catalogue.
Browse and view
- Open Categories, then choose a species. Species with atlases lead to their atlas catalogue; other species lead to their brain list.
- Choose an atlas and, where available, a release and named variant. A species can have several atlases and an atlas can have several annotation sets or resolutions.
- Open its viewer, or select an individual brain. Sign in when a dataset requires access.
- Use 3D or Slices, then adjust the available image channels or anatomical layers. See viewer controls.
An atlas mesh is a surface representation. It does not imply that a template image, voxel segmentation or registered specimen is also available. Check the layers shown for that dataset.
Accounts and permissions
Creating an account signs you in. You can view scientific datasets and add species immediately. An administrator must approve your account before you upload data or run processing writes.
To add a missing species, use Add a species on Categories, or open the species form. Choose an existing category, enter the common and scientific names, and submit. Existing species and categories are curated by superadmins.
Account approval and a brain’s verification flag are different: approval controls contributions; verification describes a catalogue record. Verification is not the gate for signed-in viewing.
Add a brain
Choose the path that fits your data:
| Input | Workflow |
|---|---|
| Single NIfTI or TIFF file | Browser upload, confirm metadata, run a CLI worker |
| Large single-channel volume or TIFF slice folder | Convert and upload with brainmaps upload image |
| Existing multichannel OME-Zarr | Preserve the original dataset; use a compatible hosted Zarr source and check its metadata |
After uploading, open Uploads and use Finish setup to create the brain record, set its species and licence, and optionally associate an atlas. An atlas association alone does not register an image into atlas coordinates.
Read the upload guide before converting multichannel data: the current precomputed converter selects the first channel and can rescale intensities.
Account and processing tools
- Account: profile, password change and personal access tokens.
- Uploads: upload records, metadata review and brain setup.
- Jobs: processing progress and errors. A worker must be running for queued computation to execute.
- Atlas administration: available to the atlas creator and administrators that creator appoints.
Tokens, private saved viewer states and operational job queues retain their own access rules; the shared dataset policy does not make other users’ account credentials accessible.
Sharing and support
Share the brain or atlas page URL so the recipient has its metadata and attribution. Protected datasets require the recipient to sign in. Colour and contrast edits change the display, not the stored measurements.
Use the source publication and dataset-specific licence when citing or reusing data. For account access or missing data, use Contact.