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 coordinate space content (using the templates directory because the defining template typically lives there) and implicit reference from other assets:

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

Naming Convention¶

<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: aind_data_schema >= 2.0; documents administrative metadata
manifest.json: documents the origin, spacing (inc units), and defining anatomical template

Versioning¶

New space when:

Interpretation of coordinates in physical units changes - i.e. change in origin.

New version when:

Defining template image changes