Changelog

All notable changes to aind-zarr-utils will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Comprehensive documentation website with Sphinx

  • User guides for ZARR conversion, S3 integration, coordinate systems, and pipeline corrections

  • Complete API reference documentation with autosummary

  • Installation, quickstart, and examples guides

  • Development setup and testing procedures documentation

  • Bug reporting guidelines

Changed

  • Enhanced docstrings across all modules for better API documentation

  • Improved error messages with more specific guidance

Fixed

  • Documentation build warnings and missing cross-references

[0.1.0] - 2024-XX-XX

Added

  • Initial release of aind-zarr-utils

  • Core ZARR to SimpleITK/ANTs image conversion functionality

  • Neuroglancer annotation processing with coordinate transformations

  • Multi-source JSON loading (S3, HTTP, local files) with caching

  • Pipeline-specific domain corrections for SmartSPIM compatibility

  • S3 integration with anonymous access and ETag-based caching

  • URI manipulation utilities for cross-platform path handling

  • Point coordinate transformations from image to anatomical space

  • Pipeline transformation chains for CCF registration

Core Modules

  • zarr: ZARR file conversion to medical imaging formats

  • neuroglancer: Neuroglancer state processing and annotation extraction

  • annotations: Point transformation utilities

  • json_utils: Unified JSON loading with S3 support

  • pipeline_transformed: Pipeline-specific coordinate transformations

  • pipeline_domain_selector: Version-aware spatial domain corrections

  • s3_cache: Efficient S3 resource caching with ETag validation

  • uri_utils: Cross-platform URI and path manipulation

Features

  • Multi-resolution support: Process ZARR files at different resolution levels

  • Coordinate system standardization: All outputs in LPS (Left-Posterior-Superior) coordinates

  • Unit conversion: Automatic scaling between micrometers, millimeters, etc.

  • Pipeline compatibility: Reproduce spatial domains from any SmartSPIM pipeline version

  • Efficient caching: Reduce S3 transfer costs with intelligent local caching

  • Anonymous S3 access: No credentials needed for public AIND datasets

  • Memory optimization: Stub images for coordinate-only operations

Version Format

This project uses Semantic Versioning:

  • MAJOR.MINOR.PATCH (e.g., 1.2.3)

  • MAJOR: Incompatible API changes

  • MINOR: New functionality (backward compatible)

  • PATCH: Bug fixes (backward compatible)

Change Categories

Added

New features or functionality

Changed

Changes to existing functionality (non-breaking)

Deprecated

Features that will be removed in future versions

Removed

Features removed in this version

Fixed

Bug fixes

Security

Security vulnerability fixes

Release Process

  1. Version Bump: Update version in src/aind_zarr_utils/__init__.py

  2. Update Changelog: Document all changes since last release

  3. Tag Release: Create git tag with version number

  4. GitHub Release: Create GitHub release with changelog notes

  5. PyPI Upload: Automated upload to PyPI via GitHub Actions

Migration Guides

From 0.x.x to 1.0.0 (Future)

When version 1.0.0 is released, this section will contain:

  • Breaking changes and how to adapt code

  • Deprecated feature replacements

  • New recommended usage patterns

Notable Dependencies

Core Dependencies

  • numpy: Numerical computing foundation

  • ome-zarr: ZARR file format support

  • SimpleITK: Medical image processing

  • antspyx: Advanced normalization tools

  • boto3: AWS S3 integration

  • requests: HTTP client for URL fetching

Version Compatibility

aind-zarr-utils

Python

SimpleITK

ANTs

ome-zarr

0.1.x

3.10+

2.2+

0.3+

0.7+

1.x.x (future)

3.11+

2.3+

0.4+

0.8+

Contributing

See Development Setup for information about:

  • Setting up development environment

  • Running tests and quality checks

  • Submitting pull requests

  • Documentation contributions

Support

License

This project is licensed under the MIT License - see the LICENSE file for details.

This changelog is automatically updated with each release. For detailed commit history, see the GitHub commit log.