Atlas

An Atlas release bundles specific versions of the component assets required to interpret anatomical annotations in a defined coordinate space. It references (does not duplicate) one Coordinate Space, one or more Templates, and one or more Annotation Sets — all anchored to that single Coordinate Space. Each referenced Annotation Set brings its own unique Terminology, so a single atlas can group annotations that use different terminologies as long as they share the coordinate space. The atlas itself is mostly metadata + a manifest tying these components together.

See also

https://brain-bican.github.io/models/ParcellationAtlas/

Directory Structure

Subset of the global layout:

atlases/
  └── <atlas_name>/
      └── <version>/
          ├── data_description.json   (REQUIRED)
          └── manifest.json           (REQUIRED)

Naming Convention

Pattern for <atlas_name>:

<organization>-<age>-<species>-atlas

Examples:

  • allen-adult-mouse-atlas

  • allen-dev-P4-mouse-atlas

Files

data_description.json

Must validate against aind_data_schema >= 2.0. Records provenance, creators, high-level description, citation.

manifest.json

Canonical reference list to component assets. Minimal required keys (draft):

  • coordinate_space – object with name and version

  • templates – list of objects, each with name and version

  • annotation_sets – list of objects, each with name and version (terminology is referenced by the annotation set itself)

  • created – ISO 8601 date/time of atlas release

  • schema_version – version of future atlas-schema manifest contract

Validation Rules

  • Each referenced component and version must exist.

  • Every referenced Template must be aligned to the manifest’s Coordinate Space (matching name and version).

  • Every referenced Annotation Set must be anchored in the manifest’s Coordinate Space (matching name and version).

  • Each Annotation Set’s own manifest declares its Terminology; different Annotation Sets in the same atlas may use different terminologies.

Versioning

An atlas version increments whenever any referenced component version changes or when manifest metadata (beyond purely descriptive fields) changes. If only the description or non-semantic metadata changes, prefer adding an errata note instead of re-versioning.