Changelog

This page tracks changes to the Atlas Asset Organization specification.

v0.2.2 — October 1, 2026 — HTML · GitHub

Added processing.json to the annotation set specification, required if the annotation set is computed (for example, annotations transformed from another coordinate space). It describes how the annotations were derived. As for templates and coordinate transformations, the validator reports W010 when it is absent, since whether an asset is computed cannot be determined structurally, and under --level full validates it against aind-data-schema.

Added an optional citation.cff file, in Citation File Format, to every asset type (#58). aind-data-schema has no structured field for a complete citation. citation.cff cites the asset itself and can redirect credit to a publication through preferred-citation. The atlas specification no longer states that data_description.json records the citation.

v0.2.1 — September 24, 2026 — HTML · GitHub

Removed spacing from the coordinate space manifest. Voxel spacing maps pixels to physical coordinates, so it belongs to the images expressed in a space, not to the space. Added an optional scales key, the list of available voxel spacings, to the template manifest, and made scales optional in the annotation set manifest; both keys now share one definition. The OME-Zarr multiscales metadata remains the authoritative record of spacing. scales is now the only term for voxel spacing.

Clarified that scales entries in template and annotation set manifests may be anisotropic: a number for isotropic spacing, or a list of per-axis spacings (e.g. for section-based atlases). OME-Zarr and NIfTI support anisotropic spacing natively.

Specified the coordinate space origin as an [x, y, z] position in physical coordinates, measured along the space’s axes from voxel [0, 0, 0] of the defining template. Under --level full the validator reports E104 when origin is not three numbers.

Clarified coordinate space versioning. A new species or age group requires a new space. A new version of the defining template, or a different template (for example, another imaging modality) becoming the defining template, produces a new version of the space while coordinates stay comparable. The template specification now states how each template change affects its coordinate space.

v0.2.0 — September 11, 2026 — HTML · GitHub

Required a described_by field in every manifest.json, holding the URL of the specification of that asset type. schema_version records which version of the manifest contract applies; described_by records where that contract is documented, so a manifest read outside its asset tree still points back to the specification.

The validator reports W041 when described_by is absent, like any other missing minimal manifest key. Under --level full it also reports E103 when the value is not an absolute http(s) URL and W042 when the URL does not point at the asset type’s specification page.

v0.1.6 — August 24, 2026 — HTML · GitHub

Scoped modalities to acquisitions. A modality records how a volume was imaged, so it belongs to templates and to the atlases that compose them. Annotation sets, terminologies, coordinate spaces and coordinate transformations are parcellations, vocabularies, mathematical spaces and mappings; their data_description.json must leave modalities empty.

The validator enforces this under --level full and reports E102 when a non-acquisition asset declares a modality.

v0.1.5 — July 23, 2026 — HTML · GitHub

Added content (“full”) validation to the validator (--level full): aind-data-schema metadata validation, manifest cross-reference resolution, terminology CSV integrity, and OME-Zarr metadata checks. Requires the validate extra and Python 3.11+.

Enumerated the manifest keys for the coordinate space (origin, spacing, template) and annotation set (coordinate_space, terminology, optional template, scales) specifications.

Removed the redundant alignment key from the template manifest; the relationship is conveyed by the coordinate_space reference.

Removed the redundant created key from the atlas and template manifests; the release timestamp is recorded in data_description.json.

v0.1.4 — July 23, 2026 — HTML · GitHub

Added an optional spec-compliance validator (atlas-assets-validate) that checks a local or cloud-stored asset tree and reports errors and warnings. See Validator.

Added the required manifest.json file to the terminology specification.

Added the optional annotations_compressed_{resolution}.nii.gz file to the annotation set specification.

Added the optional legacy_files/ directory to the terminology specification.

Clarified that naming conventions are recommended guidelines, not requirements.

Generalized storage wording from “S3 bucket” to “folder or cloud object storage”.

Linked each changelog release to its rendered documentation and GitHub tag.

v0.1.3 — July 21, 2026 — HTML · GitHub

Reconciled the File Organization layout with the per-asset pages: corrected the annotation set file list, added the required manifest.json to templates and annotation sets, and added the coordinate spaces directory.

Copy-edited the specification for clarity, grammar, and tone.

v0.1.2 — June 22, 2026 — HTML · GitHub

Added an optional <label> token to the atlas naming convention.

Required a manifest.json file for the template component.

Specified OME-Zarr 0.5 as the minimum version and recommended compression for annotation OME-Zarr files.

Codified the annotation_values array name in the annotation set specification.

v0.1.1 — June 15, 2026 — HTML · GitHub

Updated the specification status from DRAFT to Released.

Surfaced the project version in the documentation sidebar.

v0.1.0 — June 15, 2026 — GitHub

First tagged release of the specification.

Clarified that an atlas groups one or more annotation sets and templates, all anchored to a single coordinate space, with each annotation set carrying its own unique terminology.

Amplified the AtOM model framing with explicit citations and named the BICAN Anatomical Structure schema.

Renamed “coordinate transforms” to “coordinate transformations”.

August 29, 2025

Adopted AtOM model with simplified terms

August 12, 2025

Renamed “2p” -> “stpt” to be consistent with historical documents

Added support for ANTs transforms

August 6, 2025

Adding definition clarification based on feedback

General cleanup

July 25, 2025

Proposed names at the bottom of doc for review

An atlas can only have one space and one annotation

July 22, 2025

Added Anatomical Template concept

Removed Anatomical Space from file organization, replaced with Anatomical Template

Relaxed requirement that versioning be semantic