Scene

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.scene.BaseSceneAttrs

Bases: BaseOMEAttrs

Base metadata for OME-Zarr scene groups.

Attributes:

Name	Type	Description
`version`	`Literal['0.6.dev4']`
`scene`	`SceneAttrs`

ome_zarr_models.v06.scene.Scene

Bases: BaseGroupv06[BaseSceneAttrs]

An OME-Zarr container group.

This is a group that stores a series of other multiscale images, along with additional coordinate transformations and coordinate systems.

Attributes:

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

images

images: dict[str, Image]

Mapping from path to image.

from_zarr

from_zarr(group: Group) -> Self

Create an OME-Zarr scene from a zarr.Group.

Parameters:

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

new

new(*, images: dict[str, Image], coord_transforms: Sequence[AnyTransform] = (), coord_systems: Sequence[CoordinateSystem] = ()) -> Scene

Create a new Scene from a sequence of images and coordinate metadata.

Parameters:

Name	Type	Description	Default
`images`	`dict[str, Image]`	A dictionary mapping image names to Image objects. The keys are the paths to the images within the scene.	required
`coord_transforms`	`Sequence[AnyTransform]`	Coordinate transforms to add to this scene.	`()`
`coord_systems`	`Sequence[CoordinateSystem]`	Coordinate systems to add to this scene.	`()`

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.scene.SceneAttrs

Bases: BaseModel

Metadata for OME-Zarr scene groups.

Attributes:

Name	Type	Description
`coordinateTransformations`	`tuple[Identity \| MapAxis \| Translation \| Scale \| Affine \| Rotation \| Sequence \| Displacements \| Coordinates \| Bijection \| ByDimension, ...]`
`coordinateSystems`	`tuple[CoordinateSystem, ...] \| None`