navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata

class navigate.model.metadata_sources.zarr_metadata.OMEZarrMetadata

Bases: Metadata

Class to generate OME-Zarr metadata.

__init__() → None

Metadata class

Store and convert internal representation of metadata (configuration, experiment, etc.) to alternative file types.

Note

Concept and some of the code borrowed from python-microscopy (https://github.com/python-microscopy/python-microscopy/).

Methods

__init__()	Metadata class
multiscales_dict(name, paths, resolutions[, ...])	Create a multiscale dictionary for the OME-Zarr metadata.
set_from_configuration_experiment()	Set from configuration experiment
set_from_dict(metadata_config)	Set from a dictionary
set_shape_from_configuration_experiment()	Set shape from configuration experiment
set_stack_order_from_configuration_experiment()	Set stack order from configuration experiment

Attributes

configuration	Return configuration dictionary
per_stack	Return per stack
shape	Return shape as XYCZT.
voxel_size	Return voxel size

multiscales_dict(name: str, paths: list, resolutions: Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]], List], view: Optional[Dict] = None) → Dict

Create a multiscale dictionary for the OME-Zarr metadata.

https://ngff.openmicroscopy.org/0.4/index.html#multiscale-md

Parameters:

• name (str) – The name of the dataset.

• paths (list) – The paths of the dataset.

• resolutions (List) – The resolutions of the dataset.

• view (Dict) – The view of the dataset.

Returns:

A dictionary containing the multiscale metadata.

Return type:

Dict

set_from_configuration_experiment() → None

Set from configuration experiment

set_from_dict(metadata_config: dict) → None

Set from a dictionary

Parameters:

metadata_config (dict) – dictionary of metadata: “c”, “z”, “t”, “p”, “is_dynamic”, “per_stack”

set_shape_from_configuration_experiment() → None

Set shape from configuration experiment

set_stack_order_from_configuration_experiment() → None

Set stack order from configuration experiment

active_microscope

Active microscope

Type:

str

property configuration: Optional[DictProxy]

Return configuration dictionary

Returns:

configuration – Configuration dictionary

Return type:

Optional[DictProxy]

dc

Step size between channels, should always be 1

Type:

int

dt

Time displacement (s)

Type:

float

dx

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

dy

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

dz

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

misc

misc notes

Type:

str

property per_stack: bool

Return per stack

Returns:

True if per stack, False otherwise

Return type:

bool

positions

Number of positions

Type:

int

property shape: tuple

Return shape as XYCZT.

Returns:

Shape as XYCZT

Return type:

tuple

shape_c

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_t

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_x

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_y

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_z

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

property voxel_size: tuple

Return voxel size

Returns:

Voxel size

Return type:

tuple