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
|
|
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], 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]
|
|
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 image. |
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.
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 |
to_version(version: Literal['0.6'], *, default_cs_name: str = 'physical', output_cs_name: str = 'output') -> ImageAttrs
Convert these Image Attributes metadata to the specified version.
Currently supported conversions are - 0.5 -> 0.6
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
version
|
Literal['0.6']
|
The version to convert to. Must be "0.6". |
required |
default_cs_name
|
str
|
The name of the default coordinate system to use for the 0.5 -> 0.6 conversion. Defaults to "physical". |
'physical'
|
output_cs_name
|
str
|
The name of the output coordinate system to use
for the 0.5 -> 0.6 conversion. Defaults to "output".
Only used if |
'output'
|
Notes
If there is more than one multiscale, the same default coordinate system names are applied to each multiscale. If you need them to be different, edit them manually after the conversion.
Multiscales metadata
Bases: BaseAttrs
An element of Multiscale.datasets.
Attributes:
| Name | Type | Description |
|---|---|---|
path |
str
|
|
coordinateTransformations |
tuple[VectorScale | PathScale] | tuple[VectorScale | PathScale, VectorTranslation | PathTranslation]
|
|
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: int
Dimensionality of the data described by this metadata.
Determined by the length of the axes attribute.
to_version(version: Literal['0.4']) -> Multiscale
to_version(version: Literal['0.6'], *, default_cs_name: str = 'physical', output_cs_name: str = 'output') -> Multiscale
to_version(version: Literal['0.4', '0.6'], *, default_cs_name: str = 'physical', output_cs_name: str = 'output') -> Multiscale | Multiscale
Convert this Multiscale metadata to the specified version.
Currently supported conversions are - 0.5 -> 0.4 - 0.5 -> 0.6
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
version
|
Literal['0.4', '0.6']
|
The version to convert to. Must be one of "0.4" or "0.6". |
required |
default_cs_name
|
str
|
The name of the default coordinate system to use for the 0.5 -> 0.6 conversion. Defaults to "physical". |
'physical'
|
output_cs_name
|
str
|
The name of the output coordinate system to use
for the 0.5 -> 0.6 conversion. Defaults to "output".
Only used if |
'output'
|