Register brains and build atlas templates

Registration computes a transform between a moving specimen and a fixed reference volume. An atlas association in the catalogue is metadata; it does not perform registration.

Required data

You need a fixed intensity volume, a moving specimen volume, valid voxel sizes/orientation, and compatible anatomy or image contrast. Optional label volumes can be warped with label-preserving interpolation. A mesh-only atlas variant does not provide the fixed image required by this workflow.

Install the registration extra from the CLI checkout:

uv sync --extra registration --extra interactive

Run a local registration

From that checkout:

uv run brainmaps register run \
  --fixed reference.nii.gz \
  --moving specimen.nii.gz \
  --output-dir ./registration-output \
  --preset affine

Presets are rigid, affine and syn. Use --labels labels.nii.gz for an optional label volume. --dry-run prepares the workspace and manifest without running ANTs. --interactive opens the optional Textual wizard.

Inspect the resulting alignment and quality-control outputs before treating it as an anatomical correspondence.

Record the target on the platform

register run can create API metadata with --create-api-run, --source-brain-id, --atlas-release-id and --atlas-variant-id. Record the exact variant when a release has several resolutions or annotation sets.

register create creates a run record; it does not execute registration. register list, get, progress and artifact inspect or update the recorded workflow. Creating metadata is separate from publishing output files and making registered layers available in the viewer.

Consensus templates and publication

The CLI also provides:

Command	Role
`register group`	Run a local group-template workflow from repeated `--image` inputs
`register batch`	Plan a platform-backed batch from selected atlas/image layers; use `--plan-only` to avoid creating a draft release
`register batch-run`	Execute a saved batch plan
`register batch-publish`	Publish subject registration results from a completed batch stage
`register group-publish`	Publish a group-template manifest to an atlas release
`atlas publish-release`	Publish a prepared release through the API’s governance checks

Use each command’s --help for the required manifest and release arguments. Publication changes shared platform records and is separate from local computation. Atlas administration is limited to its creator and delegated administrators.

Workers and remote data

Local registration commands run on the machine where you invoke them. The generic worker registry currently handles conversion and export jobs; it has no generic registration job handler. Atlas build jobs use a separate queue handled by worker run.

Any machine doing registration must be able to read its input data. A CLI process does not automatically inherit the browser’s viewer-session cookies.

CLI Species Management Compute Jobs