aind-zarr-utils

Utilities for working with AIND Zarr assets, metadata, Neuroglancer annotations, and SmartSPIM pipeline coordinate transforms.

The recommended API is asset-centric:

from aind_zarr_utils import Asset, Points, Space
from aind_s3_cache.json_utils import get_json

ng_state = get_json("s3://aind-open-data/dataset/neuroglancer_state.json")
asset = Asset.from_zarr("s3://aind-open-data/dataset/image.ome.zarr/0")

points = Points.from_neuroglancer(ng_state)
ccf_points = asset.transform(points, to=Space.CCF_MM)

Asset owns metadata discovery, Zarr opening, transform-chain resolution, and pipeline overlays. Points carries named (N, 3) arrays together with an explicit coordinate-space tag, so one asset.transform(...) call replaces the older family of *_to_ccf / ccf_to_* helper calls.

Key Features

  • Asset discovery: Build an Asset from a Zarr URI, asset root, or Neuroglancer state.

  • Image construction: Create SimpleITK or ANTs images through Asset.image(), with optional pipeline corrections.

  • Header-only stubs: Use Asset.stub() for coordinate operations without loading image pixels.

  • Point transforms: Move Points between Zarr indices, light-sheet anatomical space, pipeline-corrected anatomical space, and Allen CCF.

  • Legacy compatibility: Lower-level zarr, neuroglancer, and pipeline_transformed functions remain available for explicit workflows.

Contents

Indices and tables