Template

A Template is the reference image that defines (or is rigidly/affinely aligned to) a Coordinate Space. It serves as the anatomical backdrop for annotation, registration, and visualization.

See also

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

Directory Structure

templates/
  └── <template_name>/
      └── <version>/
          ├── data_description.json (REQUIRED)
          ├── manifest.json         (REQUIRED)
          ├── processing.json       (REQUIRED IF COMPUTED)
          ├── template.ome.zarr (REQUIRED)
          └── template_{resolution}.nii.gz   (OPTIONAL)

Naming Convention

<template_name> = <organization>-<age>-<species>-<modality>-<technique>-template

Examples:

  • allen-adult-mouse-spim-lca-template

  • allen-adult-mouse-stpt-template

Files

template.ome.zarr

  • OME-Zarr >= 0.5

  • Coordinate transformations + orientation present

  • Millimeter units

template.nii.gz

  • Millimeter units

  • Correct affine orientation (RAS recommended)

data_description.json

  • aind_data_schema >= 2.0

manifest.json

  • References the Coordinate Space this template defines or is aligned to. Minimal required keys (draft):

    • coordinate_space – object with name and version

    • alignment – this template’s relationship to the Coordinate Space: defining (the template defines the space) or aligned (rigidly/affinely aligned to it)

    • created – ISO 8601 date/time

    • schema_version – version of the manifest contract

processing.json

  • Averaging / registration methods; reference datasets

Validation Rules

  • OME-Zarr multiscales metadata valid and consistent (scale factors monotonic).

  • Anatomical orientation and coordinate transformations are defined and consistent across provided formats.

  • No missing scale levels referenced by transformations.

  • The Coordinate Space referenced in manifest.json (matching name and version) must exist.

Versioning

Increment version when any of:

  • Source cohort or specimens change

  • Registration pipeline changes materially

  • Spatial resolution or orientation/origin changes

  • Intensity normalization method changes (affecting comparability)

Define a new template when:

  • Species or age group changes

  • Imaging modality or technique changes