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Metadata fixing

ome-zarr-models will attempt to fix metadata that is not technically compliant with the OME-Zarr specification, but can still be unambiguously interpreted and made compliant. In these cases a ValidationWarning will be emitted explaining the fix made. This provides a useful interface for software packages and users to read metadata with mistakes, but still access it from ome-zarr-models with those mistakes corrected.

ome-zarr-models will always write specification-compliant metadata. The ome-zarr-models validate command will always raise an error on invalid metadata, regardless of whether a fix is available or not.

If you have a suggestion for a fix we could add, please open an issue!

Implemented fixes

  • If the "version" field is not present in OME-Zarr 0.5 Plate metadata it is automatically set to "0.5".
  • If the order of transforms is incorrect in OME-Zarr 0.4 images, they are automatically swapped to be in the correct order.