Image

ome_zarr_models.v05.image.Image

Bases: BaseGroupv05[ImageAttrs]

An OME-Zarr image dataset.

Attributes:

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

datasets

datasets: tuple[tuple[Dataset, ...], ...]

Get datasets stored in this image.

The first index is for the multiscales. The second index is for the dataset inside that multiscales.

labels

labels: Labels | None

Any labels datasets contained in this image group.

Returns None if no labels are present.

from_zarr

from_zarr(group: Group) -> Self

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

Parameters:

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

new

new(*, array_specs: Sequence[AnyArraySpec], paths: Sequence[str], axes: Sequence[Axis], scales: Sequence[Sequence[float]], translations: Sequence[Sequence[float] | None], name: str | None = None, multiscale_type: str | None = None, metadata: JsonValue | None = None, global_scale: Sequence[float] | None = None, global_translation: Sequence[float] | None = None) -> Image

Create a new Image from a sequence of multiscale arrays and spatial metadata.

Parameters:

Name	Type	Description	Default
`array_specs`	`Sequence[AnyArraySpec]`	A sequence of array specifications that collectively represent the same image at multiple levels of detail.	required
`paths`	`Sequence[str]`	The paths to the arrays within the new Zarr group.	required
`axes`	`Sequence[Axis]`	`Axis` objects describing the axes of the arrays.	required
`scales`	`Sequence[Sequence[float]]`	For each array, a scale value for each axis of the array.	required
`translations`	`Sequence[Sequence[float] \| None]`	For each array, a translation value for each axis the array.	required
`name`	`str \| None`	A name for the multiscale collection.	`None`
`multiscale_type`	`str \| None`	Type of downscaling method used to generate the multiscale image pyramid. Optional.	`None`
`metadata`	`JsonValue \| None`	Arbitrary metadata to store in the multiscales group.	`None`
`global_scale`	`Sequence[float] \| None`	A global scale value for each axis of every array.	`None`
`global_translation`	`Sequence[float] \| None`	A global translation value for each axis of every array.	`None`

Notes

This class does not store or copy any array data. To save array data, first write this class to a Zarr store, and then write data to the Zarr arrays in that store.

ome_zarr_models.v05.image.ImageAttrs

Bases: BaseOMEAttrs

Metadata for OME-Zarr image groups.

Attributes:

Name	Type	Description
`version`	`Literal['0.5']`
`multiscales`	`list[Multiscale]`	The multiscale datasets for this image

Multiscales metadata

ome_zarr_models.v05.multiscales.Dataset

Bases: BaseAttrs

An element of Multiscale.datasets.

Attributes:

Name	Type	Description
`path`	`str`
`coordinateTransformations`	`tuple[VectorScale \| PathScale] \| tuple[VectorScale \| PathScale, VectorTranslation \| PathTranslation]`

build

build(*, path: str, scale: Sequence[float], translation: Sequence[float] | None) -> Self

Construct a Dataset from a path, a scale, and a translation.

ome_zarr_models.v05.multiscales.Multiscale

Bases: BaseAttrs

An element of multiscales metadata.

Attributes:

Name	Type	Description
`axes`	`Sequence[Axis]`
`datasets`	`ForwardRef('tuple[Dataset, ...]')`
`coordinateTransformations`	`tuple[VectorScale \| PathScale] \| tuple[VectorScale \| PathScale, VectorTranslation \| PathTranslation] \| None`
`metadata`	`TypeAliasType`
`name`	`TypeAliasType \| None`
`type`	`TypeAliasType`

ndim

ndim: int

Dimensionality of the data described by this metadata.

Determined by the length of the axes attribute.

to_version

to_version(version: Literal['0.4']) -> Multiscale

Convert this Multiscale metadata to the specified version.

Currently supported conversions are - 0.5 -> 0.4

Coordinate transformation metadata

ome_zarr_models.v05.coordinate_transformations.Identity

Bases: Transform

Identity transformation.

Notes

Although defined in the specification, it is not allowed to be used anywhere.

Attributes:

Name	Type	Description
`type`	`Literal['identity']`

ome_zarr_models.v05.coordinate_transformations.PathScale

Bases: Transform

Scale transformation parametrized by a path.

Attributes:

Name	Type	Description
`type`	`Literal['scale']`
`path`	`str`

ome_zarr_models.v05.coordinate_transformations.PathTranslation

Bases: Transform

Translation transformation parametrized by a path.

Attributes:

Name	Type	Description
`type`	`Literal['translation']`
`translation`	`str`

ome_zarr_models.v05.coordinate_transformations.VectorScale

Bases: Transform

Scale transformation parametrized by a vector of numbers.

Attributes:

Name	Type	Description
`type`	`Literal['scale']`
`scale`	`list[float]`

ndim

ndim: int

Number of dimensions.

build

build(data: Iterable[float]) -> Self

Create a VectorScale from an iterable of floats.

ome_zarr_models.v05.coordinate_transformations.VectorTranslation

Bases: Transform

Translation transformation parametrized by a vector of numbers.

Attributes:

Name	Type	Description
`type`	`Literal['translation']`	Type
`translation`	`list[float]`

ndim

ndim: int

Number of dimensions.

build

build(data: Iterable[float]) -> Self

Create a VectorTranslation from an iterable of floats.

Axes metadata

ome_zarr_models.v05.axes.Axis

Bases: BaseAttrs

Model for an element of Multiscale.axes.

Attributes:

Name	Type	Description
`name`	`str \| None`
`type`	`str \| None`
`unit`	`str \| TypeAliasType \| None`