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TODO.md

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TODO List

High Priority

Zarr Backend Fallback

Currently, when xr.open_dataset(..., engine="ome-zarr") is called on a regular (non-OME-NGFF) zarr file, it will raise an error. We should detect this case and automatically fall back to xarray's native zarr backend.

Implementation notes:

  • The backend's open_dataset() and open_datatree() already check _detect_store_type()
  • They try to fall back when store_type == "unknown"
  • However, the fallback currently calls open_ome_dataset() which also checks and raises ValueError
  • Need to either:
    1. Catch ValueError in backend and retry with zarr engine
    2. Pass a flag to open_ome_dataset() to skip the check
    3. Restructure so backend does fallback before calling open_ome_dataset()

Related code:

  • xarray_ome/backend.py: Backend entry point with fallback logic
  • xarray_ome/reader.py: open_ome_dataset() and open_ome_datatree() with detection
  • xarray_ome/_store_utils.py: _detect_store_type() function

Medium Priority

Add working code example at docs homepage start

The docs homepage should have a concrete working example right at the start that users can copy-paste and run immediately.

HCS Plate Structure Support

Add support for High Content Screening (HCS) plate/well structures from OME-NGFF.

References:

Performance Optimizations

  • Benchmark and optimize coordinate transformation
  • Consider caching metadata parsing
  • Profile large file opening

Integration with Visualization Tools

  • Examples with matplotlib/napari
  • Helper functions for common viz patterns

Low Priority

Additional Metadata Validation Options

  • More granular validation controls
  • Custom validation rules
  • Better error messages for invalid metadata

Time Label Support

Infrastructure is ready in transforms_to_coords() with time_labels parameter, but OME-NGFF spec doesn't currently define standard time labels location (unlike channel labels in omero.channels[].label).

Wait for spec extension before implementing.