spatialdata_io.codex

spatialdata_io.codex(path, fcs=True, imread_kwargs=mappingproxy({}))

Read CODEX formatted dataset.

This function reads the following files:

• <dataset_id>_`'.fcs'`: Counts and metadata file.

• <dataset_id>_`'.tif'`: High resolution tif image.

See also

• CODEX output.

Parameters:

• path (str | Path) – Path to the directory containing the data.

• fcs (bool (default: True)) – Whether a .fcs file is provided. If False, a .csv file is expected.

• imread_kwargs (Mapping[str, Any] (default: mappingproxy({}))) – Keyword arguments passed to dask_image.imread.imread().

Return type:

SpatialData

Returns:

: spatialdata.SpatialData