Upload a brain

Sign in with an approved contributor account. Have the species, acquisition notes, physical voxel size and data licence ready.

Single-file browser upload

1. Open Upload.
2. Choose a single .nii, .nii.gz, .tif or .tiff file.
3. Wait for the direct upload to finish.
4. Review the detected metadata. Confirm voxel size as X,Y,Z in micrometres and the anatomical orientation; correct missing or incorrect header values.
5. Confirm the metadata to queue conversion.
6. Run an authenticated CLI worker on a machine with access to your data: brainmaps worker run.
7. Follow progress in Jobs. Then use Uploads → Finish setup to create the brain record and associate its species and optional atlas.

A completed upload means the bytes arrived. The viewer-ready volume is a separate conversion result. A queued job does not run until a suitable worker claims it; see compute jobs.

Folders and multichannel data

Use the CLI for Zarr directories, TIFF stacks and existing Neuroglancer precomputed datasets. The browser’s upload form accepts single files.

For multichannel OME-Zarr, preserve the existing dataset with brainmaps upload folder. The current TIFF/Zarr-to-precomputed conversion selects one channel, time point and sample where present. Do not run that conversion if you need to keep all channels.

What to provide

• Identity: specimen name, species and acquisition/preparation notes.
• Geometry: axis order, physical voxel sizes with units, orientation, and any origin or registration transform.
• Channel metadata: marker names, display colours and meaningful intensity ranges.
• Anatomy: segmentation IDs and their names/colours when you have labels; a mesh alone is not a voxel segmentation.
• Provenance: source, licence and processing history.

Adding an atlas association does not register the scan. Use registration when the specimen must align with an atlas.

Data access

All signed-in users can read scientific data registered on the platform. Account approval controls contributions, not read access. Some source/upload URLs may also be publicly reachable; upload only data you are authorised to share. Protected research storage is accessed through an authenticated viewer session.

See viewing brains after conversion or direct Zarr upload is complete.