neuroglancer module

Reading Neuroglancer annotation state.

The implementation now lives in aind_zarr_utils.formats.neuroglancer. This module is a re-export shim preserved so that from aind_zarr_utils.neuroglancer import … and existing test fixtures that monkey-patch aind_zarr_utils.neuroglancer.zarr_to_sitk_stub etc. continue to work. New code should import from aind_zarr_utils.formats.neuroglancer directly.

Overview

The neuroglancer module contains legacy readers and coordinate helpers for Neuroglancer annotation state. New code should usually use Points.from_neuroglancer and then transform through an Asset:

from aind_zarr_utils import Asset, Points, Space

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

Coordinate Notes

Neuroglancer annotation points are read as level-0 (z, y, x) Zarr indices. Physical outputs from Asset.transform use the destination Space tag.

Legacy Examples

Extract annotation points from Neuroglancer JSON:

from aind_zarr_utils.neuroglancer import neuroglancer_annotations_to_indices

annotations, descriptions = neuroglancer_annotations_to_indices(
    ng_state,
    layer_names=["my_annotations"],
    return_description=True,
)

Convert to raw anatomical coordinates with explicit metadata:

from aind_zarr_utils.neuroglancer import neuroglancer_annotations_to_anatomical

physical_points, descriptions = neuroglancer_annotations_to_anatomical(
    ng_state,
    zarr_uri,
    metadata,
    scale_unit="millimeter",
    layer_names=["region_annotations", "landmarks"],
)