Manage brain records

A brain record is the catalogue entry for a specimen. Its file uploads and layers hold the imaging data. Uploading bytes and creating a brain record are separate steps.

List and inspect

brainmaps brain list
brainmaps brain list --species 1 --limit 20
brainmaps brain get 123 --json

Use numeric IDs from your installation. brain get uses the brain’s numeric API ID, not its UUID or readable ID. The --category list option is currently accepted by the CLI but ignored by the API; filter by species instead.

Create a record from an upload

First upload and prepare the data. Copy the returned file-upload UUID:

brainmaps brain create \
  --name "Specimen 001" \
  --species 1 \
  --from-upload UPLOAD_UUID \
  --description "Acquisition and preparation notes"

Alternatively, --file /path/to/scan.nii.gz uploads a file while creating the record. Supply exactly one of --file or --from-upload. Creating a record does not itself guarantee conversion into a viewer-ready volume; use the upload and metadata-review workflow for raw data.

Optional --atlas-id associates the specimen with an atlas. This does not register the specimen into that atlas’s coordinate system. Registration needs matching volumetric data and a computed transform; see registration.

--color sets a default visualisation colour. There is no --category option on brain create: species determine catalogue placement.

Edit, delete and download

The current CLI has no brain update, brain delete, or file download command. Use the available website controls or the API, subject to its permissions.

brainmaps file list
brainmaps file get UPLOAD_UUID --json

file get returns metadata, not the data bytes. The API download action is GET /api/file-uploads/UPLOAD_UUID/download/; for object-storage uploads it returns a download_url. Deleting a catalogue record must not be treated as a guarantee that all underlying storage objects have been erased.