pymif.microscope_manager.zeiss_manager

Classes

ZeissManager

A manager class for reading and handling .czi datasets.

Module Contents

class pymif.microscope_manager.zeiss_manager.ZeissManager(path, scene_index: int = 0, scene_name: str | None = '', chunks: Tuple[int, Ellipsis] = None)[source]

Bases: pymif.microscope_manager.microscope_manager.MicroscopeManager

A manager class for reading and handling .czi datasets.

This class lazily loads data into a dask array and parses associated .czi metadata.

path[source]

chunks = None[source]

read(scene_index: int = 0)[source]

Read the Zeiss dataset and populate self.data and self.metadata.

Returns

Tuple[List[da.Array], Dict[str, Any]]: A tuple containing: - A list with one dask array representing the image data. - A metadata dictionary with pixel sizes, units, axes, etc.

_parse_metadata() → Dict[str, Any][source]

Parse metadata from the .czi dataset.

Returns

Dict[str, Any]: A dictionary containing dataset shape, voxel sizes, channel info, and other metadata.