Coordinate Space¶

A Coordinate Space (anatomical space) defines the mathematical frame in which anatomical data are expressed: origin, axis directions/orientation, physical voxel spacing/units, and (optionally) an associated reference template image. Images are considered to reside in the same Coordinate Space when they are at least affine-aligned (same orientation, origin, and scaling) to the defining template/reference.

Directory Structure¶

Subset of the global layout showing only the coordinate space content:

coordinate-spaces/
  └── <coordinate_space_name>/
      └── <version>/
          ├── data_description.json (REQUIRED)
          └── manifest.json         (REQUIRED)

Naming Convention¶

Note

Naming conventions in this specification are recommended guidelines to encourage consistency, not requirements.

<coordinate_space_name> = <organization>-<age>-<species>-<label>-space

<label> is optional (e.g. ccf).

Examples:

allen-adult-mouse-ccf-space
allen-adult-mouse-space (no label)

Files¶

data_description.json

Must validate against aind_data_schema >= 2.0. Documents administrative metadata.

manifest.json

Documents the coordinate space. Minimal required keys (draft):

name – coordinate space name
version – coordinate space version
location – path to the asset
schema_version – version of the manifest contract
origin – anatomical origin of the coordinate system
spacing – physical voxel spacing, including units
template – object (name, version) identifying the template that defines the space

Versioning¶

New space when:

The interpretation of coordinates in physical units changes (for example, a change in origin).

New version when:

Defining template image changes