bioformats2raw

Warning

The implementation of OME-Zarr 0.6 is not final, and subject to change. It is provided so users can test and evaluate ome-zarr-models and the specification before it becomes final. Please report issues and provide feedback!

ome_zarr_models.v06.bioformats2raw.BioFormats2Raw

Bases: BaseGroupv06[BioFormats2RawAttrs]

An OME-Zarr bioformats2raw dataset.

Warnings

It is not recommended to write new bioformats2raw groups. bioformats2raw is designed to support existing legacy data, and will be superseded by other OME-Zarr features in the future.

Notes

Currently this class does not offer a way to access OME-XML metadata. Please comment on issue #374 if you would find accessing OME-XML metadata useful.

Attributes:

Name	Type	Description
`zarr_format`	`Literal[3]`
`node_type`	`Literal['group']`
`attributes`	`BaseZarrAttrs[BioFormats2RawAttrs]`
`members`	`Mapping[str, GroupSpec \| ArraySpec] \| None`

image_paths

image_paths: list[str]

All paths to OME-Zarr images in this group.

images

images: dict[str, Image]

All images in this group.

Returns:

Type	Description
`images`	Mapping from image path to Image object.

from_zarr

from_zarr(group: Group) -> Self

Create an OME-Zarr BioFormats2Raw model from a zarr.Group.

Parameters:

Name	Type	Description	Default
`group`	`Group`	A Zarr group that has valid OME-Zarr bioformats2raw metadata.	required

ome_zarr_models.v06.bioformats2raw.BioFormats2RawAttrs

Bases: BaseOMEAttrs

A model of the attributes contained in a bioformats2raw zarr group.

Warnings

It is not recommended to write new bioformats2raw groups. bioformats2raw is designed to support existing legacy data, and will be superseded by other OME-Zarr features in the future.

Attributes:

Name	Type	Description
`version`	`Literal['0.6.dev4']`
`bioformats2raw_layout`	`Literal[3]`
`plate`	`Plate \| None`
`series`	`TypeAliasType \| None`