Image

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.image.Image

Bases: BaseGroupv06[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], scales: Sequence[Sequence[float]], translations: Sequence[Sequence[float] | None], physical_coord_system: CoordinateSystem, name: str, multiscale_type: str | None = None, metadata: JsonValue | None = None, coord_transforms: Sequence[AnyTransform] = (), coord_systems: Sequence[CoordinateSystem] = ()) -> 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
`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
`physical_coord_system`	`CoordinateSystem`	The physical coordinate system after the scale and translations have been applied to each array.	required
`name`	`str`	A name for the multiscale image.	required
`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`
`coord_transforms`	`Sequence[AnyTransform]`	Additional coordinate transforms to add to this image.	`()`
`coord_systems`	`Sequence[CoordinateSystem]`	Additional coordinate systems to add to this image.	`()`

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.

transform_graph

transform_graph() -> TransformGraph

Create a coordinate transformation graph for this image.

ome_zarr_models.v06.image.ImageAttrs

Bases: BaseOMEAttrs

Metadata for OME-Zarr image groups.

Attributes:

Name	Type	Description
`version`	`Literal['0.6.dev4']`
`multiscales`	`list[Multiscale]`	The multiscale datasets for this image

transform_graph

transform_graph() -> TransformGraph

Create a coordinate transformation graph for these image attributes.

Multiscales metadata

ome_zarr_models.v06.multiscales.Dataset

Bases: BaseAttrs

An element of Multiscale.datasets.

Attributes:

Name	Type	Description
`path`	`str`
`coordinateTransformations`	`tuple[Scale \| Identity \| Sequence]`

build

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

Construct a Dataset.

Parameters:

Name	Type	Description	Default
`path`	`str`	Path to Zarr array.	required
`scale`	`Sequence[float]`	Scale factors for this Dataset. These should be set so the output voxel size matches the highest resolution dataset in the multiscales.	required
`translation`	`Sequence[float] \| None`	A translation to apply. This is applied after the scaling.	required
`coord_sys_output_name`	`str`	The name of the output coordinate system after this dataset is scaled and translated.	required

check_cs_input

check_cs_input() -> Self

Check the input of all multiscale transformations

check_cs_output

check_cs_output() -> Self

Check the output of all multiscale transformations

ome_zarr_models.v06.multiscales.Multiscale

Bases: BaseAttrs

An element of multiscales metadata.

Attributes:

Name	Type	Description
`coordinateSystems`	`tuple[CoordinateSystem, ...]`
`datasets`	`ForwardRef('tuple[Dataset, ...]')`
`coordinateTransformations`	`tuple[Identity \| MapAxis \| Translation \| Scale \| Affine \| Rotation \| Sequence \| Displacements \| Coordinates \| Bijection \| ByDimension, ...] \| None`
`metadata`	`TypeAliasType`
`name`	`TypeAliasType \| None`
`type`	`TypeAliasType`

intrinsic_coordinate_system

intrinsic_coordinate_system: CoordinateSystem

Physical coordinate system.

Should be used for viewing and processing unless a use case dictates otherwise. A representation of the image in its native physical coordinate system.

Notes

This is the coordinate system which is the output of all multiscale transformations defined in datasets.

ndim

ndim: int

Dimensionality of the data described by this multiscale metadata.

check_dataset_transform_output

check_dataset_transform_output() -> Self

Check the output of all transforms in 'datasets' are the same.

to_version

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

to_version(version: Literal['0.5']) -> Multiscale

to_version(version: Literal['0.4', '0.5']) -> Multiscale | Multiscale

Convert this Multiscale metadata to the specified version.

Currently supported conversions are

0.6 -> 0.5
0.6 -> 0.4

Parameters:

Name	Type	Description	Default
`version`	`Literal['0.4', '0.5']`	The version to convert to. Must be one of "0.4" or "0.5".	required