pymif.microscope_manager.zarr_manager

Classes

ZarrManager

A manager class for reading and handling OME-Zarr datasets.

Module Contents

class pymif.microscope_manager.zarr_manager.ZarrManager(path, chunks: Tuple[int, Ellipsis] = None)[source]

Bases: pymif.microscope_manager.microscope_manager.MicroscopeManager

A manager class for reading and handling OME-Zarr datasets.

This class reads NGFF-compliant multiscale image data along with metadata and optional label layers from a Zarr directory. It supports lazy loading with Dask, label layer detection, and integration with Napari for visualization.

Parameters

pathstr or Path: Path to the root directory of the OME-Zarr dataset.
chunksTuple[int, …], optional: Chunk size to apply when reading arrays. If None, native chunking in the Zarr arrays is used.

path[source]

chunks = None[source]

read() → Tuple[List[dask.array.Array], Dict[str, Any]][source]

Read an OME-Zarr dataset and extract both image data and metadata.

This method lazily loads the multiscale image pyramid and metadata from the root of the Zarr dataset. If /labels/ groups exist, they are also read into the self.labels attribute.

Returns

data_levelsList[dask.array.Array]: List of Dask arrays, one for each resolution level.
metadataDict[str, Any]: Dictionary containing image metadata such as axes, scales, sizes, channels, time increments, and units.

Raises

ValueError: If the dataset structure is invalid or lacks required metadata.

_load_labels() → Dict[str, List[dask.array.Array]][source]

Load label layers from the /labels/ group in the Zarr dataset.

Each label is stored as a multiscale pyramid similar to image data.

Returns

labelsDict[str, List[dask.array.Array]]: Dictionary mapping each label name to its list of pyramid levels.

add_label(label_levels: List[dask.array.Array], label_name: str = 'new_label', compressor: Any = None, compressor_level: Any = 3, parallelize: Any = False) → None[source]

Add a label layer to the Zarr dataset.

Parameters

label_levelsList[dask.array.Array]: A list of arrays representing a label image pyramid.
label_namestr, optional: Name of the label group (default is “new_label”).
compressorAny, optional: Compression method to use when writing labels.
compressor_levelAny, optional: Compression level to apply (default: 3).
parallelizebool, optional: If True, label data is written in parallel.

visualize_zarr(viewer: napari.Viewer | None = None) → napari.Viewer[source]

Visualize the OME-Zarr dataset using Napari’s napari-ome-zarr plugin.

Parameters

viewernapari.Viewer, optional: An existing viewer instance. If None, a new one will be created.

Returns

viewernapari.Viewer: A Napari viewer instance with the image loaded.