Changelog

1.7

• Require pydantic < 2.13, due to new issues in model construction that are not yet resolved.
• Correctly allow colors metadata to be not set or null inside image-label metadata.

1.6

Require Python < 3.14. Due to issues with Python 3.14 and pydantic, ome-zarr-models is not yet compatible with Python 3.14.

New features

• ome_zarr_models.v04.Image and ome_zarr_models.v05.Image now have methods to convert between OME-Zarr 0.4 and 0.5 models.

Documentation improvements

• Improved the layout of metadata class API documentation by putting all attributes in a table.
• Added more descriptions to fields describing image-label metadata.
• Added documentation for the implementation of the next version of OME-Zarr. See the development groups API reference for more information.

1.5

bioformats2raw

ome-zarr-models now has support for bioformats2raw groups.

Documentation improvements

• Added ome_zarr_models.v05.plate.Plate to the API docs.

1.4

Fixing metadata

ome-zarr-models now has support for fixing common issues with OME-Zarr metadata when loading. See the metadata fixes page for more information.

Improvements

• Added a better error message when the 'ome' key is completely absent from Zarr group metadata.
• Fixed an import in the documentation examples
• Added search to the documentation

1.3

Bug fixes

• Fixed opening a HCS dataset with some well groups missing from the HCS Zarr group.

1.2

New Features

• ome_zarr_models.open_ome_zarr now accepts any store containing a group that can be opened with zarr.open_group.

Improvements

• Various optimisations have been made to reduce the number of file requests when creating a model class from an existing zarr.Group.
• ome_zarr_models.open_ome_zarr now includes the name of the group it was trying to validate alongside the validation error message.

Bug fixes

• Axes metadata for version 0.4 and 0.5 has been fixed to require the name field.

1.1

New Features

• Added a command line interface (CLI) for validating and viewing metadata of OME-Zarr groups. See the CLI docs page for more info.
• All models now support being created from Zarr groups in remote HTTP stores, and more generally from any groups stored in any unlistable store.
• ome_zarr_models.open_ome_zarr now has an optional version argument that can be used to specify the OME-Zarr version of the group you are trying to open.
• If ome_zarr_models.open_ome_zarr fails to load the Zarr group, validation error messages will now be printed to help with debugging why the Zarr group might not be valid OME-Zarr data.

Fixes

• Opening an OME-Zarr 0.5 Image group that had an integer data type with ome_zarr_models.open_ome_zarr previously identified the group as an ImageLabel group. Image groups are now always identified as image groups, unless they contain the "image-label" metadata field.

1.0

New Features

This is the first release to support OME-Zarr 0.5 🎉

Updated dependencies

To support OME-Zarr 0.5, minimum dependencies have been updated to:

• zarr 3.1.1
• pydantic 2.11.5
• pydantic-zarr 0.8.2

Breaking changes

• ome_zarr_models.common.image_label_types.Label has moved to ome_zarr_models.v04.image_label_types.Label.
• ome_zarr_models.common.validation.check_array_path now takes a mandatory expected_zarr_version keyword-only argument.
• ome_zarr_models.common.validation.check_group_spec and ome_zarr_models.common.validation.check_array_spec raise a ValueError instead of a RuntimeError.

0.1.10

Bug fixes

• Creating a HCS group with well paths that do not point to existing well Zarr groups no longer errors.

Breaking changes

• HCS.well_groups will now only return well groups that exist, instead of erroring out if a well group is defined in the HCS metadata but does not exist as a Zarr group.

0.1.9

Bug fixes

• Add a maximum pydantic requirement of version 2.11.4. This fixes issues using several classes in ome-zarr-models. We hope to fix and remove this pydantic pin in a new release shortly.

0.1.8

Bug fixes

• Fixed serialising models with model_dump(exclude_none=True). This (now fixed) bug was introduced in version 0.1.7.

0.1.7

Bug fixes

• The coordinateTransformations field of multiscales metadata is no longer seralised if it is None. This fix is to stay compliant with the OME-Zarr specification, that does not explicitly allow null for this field.

0.1.6

New features

• Added ome_zarr_models.v04.Image.datasets as a convenience property to get all the datasests in an image.

Minor improvements

• ome_zarr_models.v04.Image.new now checks that scales and translations are both the same length as paths, and raises an error if they are not.

0.1.5

New features

• Added a method to create new ome_zarr_models.v04.Image objects from scratch.

Minor improvements

• Improved the error message in ome_zarr_models.open_ome_zarr when a Zarr group can't be validated with any OME-Zarr groups.
• Simplified the class inheritance structure across the package.

Documentation improvements

• Added project governance to home page.

0.1.4

Documentation improvements

• Added a versioning policy to the documentation home page.
• Added some missing objects to the API documentation for v04.

0.1.3

Documentation improvements

• General minor improvements to the layout and look of the API docs.
• Added some notes on known issues that will be encountered with support for OME-Zarr 0.5 in the future.

New features

• The main OME-Zarr classes are now imported into the ome_zarr_models.v04 namespace, making them easier to import ( e.g., what was ome_zarr_models.v04.hcs.HCS can now just be ome_zarr_models.v04.HCS).

0.1.2

Documentation improvements

• Added a "How do I...?" page that explains how to do common tasks with ome-zarr-models.

New features

• Updated the return type on [ome_zarr_models.base.BaseGroup.ome_zarr_version] to allow "0.5" to be returned, in anticipation of upcoming support for OME-Zarr version 0.5.

Bug fixes

• Added ome_zarr_models.v04.image.Image to the __all__ of ome_zarr_models.v04.image
• Added ome_zarr_models.v04.well.Well to the __all__ of ome_zarr_models.v04.well

0.1.1

Bug fixes

• ome_zarr_models.v04.image_label.ImageLabel data is now correctly parsed. Previously the 'image-label' field was loaded, but not validated or parsed.

Documentation improvements

• Fixed the pip install command on the home page.
• Added a conda install command to the home page.

0.1

First ome-zarr-models release.