spatialdata_io.cosmx

spatialdata_io.cosmx(path, dataset_id=None, transcripts=True, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}))

Read Cosmx Nanostring data.

This function reads the following files:

• <dataset_id>_`'exprMat_file.csv'`: Counts matrix.

• <dataset_id>_`'metadata_file.csv'`: Metadata file.

• <dataset_id>_`'fov_positions_file.csv'`: Field of view file.

• 'CellComposite': Directory containing the images.

• 'CellLabels': Directory containing the labels.

See also

• Nanostring Spatial Molecular Imager.

Parameters:

• path (str | Path) – Path to the root directory containing Nanostring files.

• dataset_id (str | None (default: None)) – Name of the dataset.

• transcripts (bool (default: True)) – Whether to also read in transcripts information.

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

• image_models_kwargs (Mapping[str, Any] (default: mappingproxy({}))) – Keyword arguments passed to spatialdata.models.Image2DModel.

Return type:

SpatialData

Returns:

: spatialdata.SpatialData