OME-Zarr groups
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!
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 bioformats2raw is designed to support existing legacy data, and will be superseded by other OME-Zarr features in the future.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
|
|
Bases: BaseGroupv06[HCSAttrs]
An OME-Zarr high content screening (HCS) dataset.
Attributes:
| Name | Type | Description |
|---|---|---|
zarr_format |
Literal[3]
|
|
node_type |
Literal['group']
|
|
attributes |
BaseZarrAttrs[HCSAttrs]
|
|
members |
Mapping[str, GroupSpec | ArraySpec] | None
|
|
Well groups within this HCS group.
Notes
Only well groups that exist are returned. This can be less than the number of wells defined in the HCS metadata if some of the well Zarr groups don't exist.
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 |
Get a single well group.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
i
|
int
|
Index of well group. |
required |
Raises:
| Type | Description |
|---|---|
WellGroupNotFoundError
|
If no Zarr group is found at the well path. |
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
|
|
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 | None
Any labels datasets contained in this image group.
Returns None if no labels are present.
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(*, 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.
Bases: BaseGroupv06[ImageLabelAttrs]
An OME-Zarr image label dataset.
Attributes:
| Name | Type | Description |
|---|---|---|
zarr_format |
Literal[3]
|
|
node_type |
Literal['group']
|
|
attributes |
BaseZarrAttrs[ImageLabelAttrs]
|
|
members |
Mapping[str, GroupSpec | ArraySpec] | None
|
|
Bases: BaseGroupv06[LabelsAttrs]
An OME-Zarr labels dataset.
Attributes:
| Name | Type | Description |
|---|---|---|
zarr_format |
Literal[3]
|
|
node_type |
Literal['group']
|
|
attributes |
BaseZarrAttrs[LabelsAttrs]
|
|
members |
Mapping[str, GroupSpec | ArraySpec] | None
|
|
Create an OME-Zarr labels model from a zarr.Group.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
group
|
Group
|
A Zarr group that has valid OME-Zarr label metadata. |
required |
get_image_labels_group(path: str) -> ImageLabel
Get a image labels group at a given path.
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
|
|
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(*, 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.