aind-zarr-utils
Utilities for working with AIND Zarr assets, metadata, Neuroglancer annotations, and SmartSPIM pipeline coordinate transforms.
Recommended API
The primary entry point is Asset. It discovers an asset's alignment-channel
Zarr, loads metadata.nd.json and processing.json, opens the Zarr once, and
reuses that state for image, stub, and point-transform workflows.
from aind_zarr_utils import Asset, Points, Space
from aind_s3_cache.json_utils import get_json
zarr_uri = "s3://aind-open-data/dataset/image.ome.zarr/0"
ng_state = get_json("s3://aind-open-data/dataset/neuroglancer_state.json")
asset = Asset.from_zarr(zarr_uri)
points = Points.from_neuroglancer(ng_state)
ccf = asset.transform(points, to=Space.CCF_MM)
print(ccf.values)
If you already have metadata and processing dictionaries loaded, use the no-I/O
constructor. alignment_zarr_uri should be the Zarr used by the alignment
pipeline; source_zarr_uri is optional provenance for the Zarr you started
from.
from aind_zarr_utils import Asset
asset = Asset(
alignment_zarr_uri="s3://bucket/asset/alignment.ome.zarr/0",
metadata=metadata,
processing=processing,
source_zarr_uri="s3://bucket/asset/acquisition.ome.zarr/0",
)
Images And Stubs
Asset.image() returns a SimpleITK image by default and can also return an ANTs
image. Asset.stub() returns a header-only SimpleITK image for coordinate
operations without loading pixel data.
from aind_zarr_utils import Asset, Origin
asset = Asset.from_root("s3://aind-open-data/dataset")
sitk_img = asset.image(level=3)
ants_img = asset.image(level=3, library="ants")
stub, size_ijk = asset.stub(level=0)
pipeline_stub, native_size_ijk = asset.stub(pipeline=True)
anchored = asset.image(
level=3,
origin=Origin.at_corner("RAS", (0.0, 0.0, 0.0)),
)
origin is only accepted when pipeline=False. Pipeline images and stubs use
the pipeline-corrected origin from processing.json.
Coordinate Spaces
Points stores named (N, 3) arrays plus a Space tag. Constructors validate
shape and coerce arrays to floating point.
import numpy as np
from aind_zarr_utils import Asset, Points, Space
asset = Asset.from_zarr("s3://bucket/asset/image.ome.zarr/0")
indices = Points(
{"soma": np.array([[100, 200, 50], [120, 180, 60]])},
Space.ZARR_INDICES,
)
pipeline_mm = asset.transform(indices, to=Space.LS_PIPELINE_ANATOMICAL_MM)
ccf_mm = asset.transform(indices, to=Space.CCF_MM)
round_trip = asset.transform(ccf_mm, to=Space.ZARR_INDICES)
Supported spaces are:
Space.ZARR_INDICES: continuous level-0(z, y, x)Zarr indicesSpace.LS_SCALED_MM: spacing-scaled light-sheet coordinatesSpace.LS_ANATOMICAL_MM: raw Zarr anatomical LPS millimetersSpace.LS_PIPELINE_ANATOMICAL_MM: pipeline-corrected LPS millimetersSpace.CCF_MM: Allen CCF LPS millimeters
SWC coordinates can enter the same graph without opening image data first:
swc_points = Points.from_swc(swc_array, axis_order="zyx", units="micrometer")
ccf_points = asset.transform(swc_points, to=Space.CCF_MM)
Legacy Functions
The lower-level modules remain available for compatibility:
aind_zarr_utils.zarr:zarr_to_ants,zarr_to_sitk,zarr_to_sitk_stubaind_zarr_utils.neuroglancer: Neuroglancer annotation readersaind_zarr_utils.pipeline_transformed: explicit metadata transform helpers
The auto-metadata convenience helpers in pipeline_transformed are deprecated
in favor of Asset.from_zarr(...) / Asset.from_root(...) plus
Asset.transform(...).
Installation
pip install aind-zarr-utils
For development:
git clone https://github.com/AllenNeuralDynamics/aind-zarr-utils.git
cd aind-zarr-utils
uv sync
Development
Run the core checks with:
uv run ruff format
uv run ruff check
uv run mypy
uv run pytest
uv run --group docs sphinx-build docs/source docs/build/html -W --keep-going
Pull requests use Angular-style commit messages:
<type>(<scope>): <short summary>
1 maintainer
Metadata
1 maintainer
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