API Reference

Complete API documentation for aind-zarr-utils.

Quick Reference

Recommended API

aind_zarr_utils.Asset	A SmartSPIM acquisition with eager metadata and lazy Zarr/transform I/O.
aind_zarr_utils.Points	A set of named (N, 3) point arrays, all in the same coordinate space.
aind_zarr_utils.Space	Coordinate spaces a Points instance can live in.
aind_zarr_utils.Origin	LPS-origin specification for an anatomical image.

Legacy Core Functions

aind_zarr_utils.zarr.zarr_to_ants	Convert a ZARR file to an ANTs image.
aind_zarr_utils.zarr.zarr_to_sitk	Convert a ZARR file to a SimpleITK image.
aind_zarr_utils.zarr.zarr_to_sitk_stub	Create a stub SimpleITK image with the same metadata as the ZARR file.
aind_zarr_utils.neuroglancer.neuroglancer_annotations_to_anatomical	Transform Neuroglancer annotations into anatomical points.

Legacy Pipeline Functions

aind_zarr_utils.pipeline_transformed.mimic_pipeline_zarr_to_anatomical_stub	Construct a SimpleITK stub matching pipeline spatial corrections.
aind_zarr_utils.pipeline_transformed.neuroglancer_to_ccf	Convert Neuroglancer annotation JSON into CCF coordinates.
aind_zarr_utils.pipeline_domain_selector.estimate_pipeline_multiscale	Heuristically estimate the multiscale pyramid level used by the pipeline.

Module Documentation

• asset module
  • Overview
  • Examples
• points module
  • Overview
  • Examples
• origin module
  • Origin
  • Overview
  • Examples
• image module
  • apply_pipeline_overlays()
  • Overview
• zarr module
  • scaled_points_to_indices()
  • zarr_to_ants()
  • zarr_to_sitk()
  • zarr_to_sitk_stub()
  • Overview
  • Key Concepts
  • Examples
• neuroglancer module
  • Overview
  • Coordinate Notes
  • Legacy Examples
• annotations module
  • annotation_indices_to_anatomical()
  • annotations_and_descriptions_to_dict()
  • Overview
  • Coordinate Systems
  • Examples
• pipeline_domain_selector module
  • Overview
• pipeline_transformed module
  • base_and_pipeline_anatomical_stub()
  • mimic_pipeline_zarr_to_anatomical_stub()
  • apply_pipeline_overlays_to_sitk()
  • mimic_pipeline_zarr_to_sitk()
  • base_and_pipeline_zarr_to_sitk()
  • apply_pipeline_overlays_to_ants()
  • base_and_pipeline_zarr_to_ants()
  • mimic_pipeline_zarr_to_ants()
  • indices_to_ccf()
  • neuroglancer_to_ccf()
  • ccf_to_indices()
  • ccf_to_indices_auto_metadata()
  • neuroglancer_to_ccf_auto_metadata()
  • swc_data_to_zarr_indices()
  • swc_data_to_ccf()
  • swc_data_to_ccf_auto_metadata()
  • indices_to_ccf_auto_metadata()
  • Overview
  • Legacy Workflow
  • Legacy Examples

Module Overview

Module	Purpose	Key API
asset	Recommended asset-centric workflow	Asset.from_zarr, Asset.image, Asset.stub, Asset.transform
points	Coordinate-space tagged point arrays	Points, Space
origin	Explicit origin value type	Origin.default, Origin.at, Origin.at_corner
image	Shared image and pipeline-overlay internals	apply_pipeline_overlays
zarr	Legacy ZARR to image conversion	zarr_to_ants, zarr_to_sitk, zarr_to_sitk_stub
neuroglancer	Neuroglancer annotation processing	neuroglancer_annotations_to_anatomical
annotations	Point coordinate transformation	annotation_indices_to_anatomical
pipeline_domain_selector	Version-specific domain corrections	estimate_pipeline_multiscale, apply_overlays
pipeline_transformed	Legacy pipeline coordinate transformations	neuroglancer_to_ccf, indices_to_ccf