OMIO: A policy-driven Python library for reproducible microscopy image I/O

🚀 OMIO v0.2.1

May 13, 2026

This maintenance release restores compatibility with recent czifile, tifffile, and zarr/Dask dependency revisions and keeps OMIO's CZI, TIFF, conversion, and napari-cache workflows working across both legacy and current APIs.

📃 Changes

🧩 Fixed

• Restored CZI reader compatibility with czifile 2026.4.30 and newer.
• read_czi now resolves axes via scene metadata when CziFile.axes is no longer available.
• read_czi now retrieves structured CZI metadata via metadata(asdict=True) when the older metadata(raw=False) API is unavailable.
• Compatibility is implemented via feature detection instead of a hard dependency-version check, preserving support for older czifile releases.
• Restored TIFF axis handling for files where recent tifffile revisions collapse singleton dimensions in series[0].axes but still preserve the full shape in shaped_metadata.
• read_tif now uses shaped_metadata as a fallback axis source when tifffile drops singleton axes such as T=1 or Z=1.
• Restored compatibility with current dask.array.to_zarr / zarr behavior by switching napari-cache writes away from the deprecated zarr_read_kwargs path and to the current mode="w" API.

🧪 Testing and robustness

• Added regression tests covering both legacy and current czifile CZI-reader APIs.
• Added regression tests covering TIFF axis fallback from shaped_metadata when singleton dimensions are omitted from series[0].axes.
• Full pytest suite passes again under the current dependency set.

🎨 Project identity

• OMIO has its first own logo now! (December 30, 2025) That's cool, but does not affect functionality or justify a dedicated release on its own.