spatialdata_io.merscope

spatialdata_io.merscope(path, vpt_outputs=None, z_layers=3, region_name=None, slide_name=None, backend=None, transcripts=True, cells_boundaries=True, cells_table=True, mosaic_images=True, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}))

Read MERSCOPE data from Vizgen.

This function reads the following files:

• 'cell_by_gene.csv': Counts file.

• 'detected_transcripts.csv': Transcript file.

• 'cell_metadata.csv': Per-cell metadata file.

• 'cell_boundaries.parquet': Cell polygon boundaries.

• mosaic_**_z*.tif images inside the 'images' directory.

Parameters:

• path (str | Path) – Path to the region/root directory containing the Merscope files (e.g., detected_transcripts.csv).

• vpt_outputs (Path | str | dict[str, Any] | None (default: None)) –

  Optional arguments to indicate the output of the vizgen-postprocessing-tool (VPT), when used. If a folder path is provided, it looks inside the folder for the following files:

  • 'cell_by_gene.csv'

  • 'cell_metadata.csv'

  • 'cell_boundaries.parquet'

  If a dictionary, then the following keys should be provided with the desired path:

  • 'cell_by_gene'

  • 'cell_metadata'

  • 'cell_boundaries'

• z_layers (int | list[int] | None (default: 3)) – Indices of the z-layers to consider. Either one int index, or a list of int indices. If None, then no image is loaded. By default, only the middle layer is considered (that is, layer 3).

• region_name (str | None (default: None)) – Name of the region of interest, e.g., 'region_0'. If None then the name of the path directory is used.

• slide_name (str | None (default: None)) – Name of the slide/run. If None then the name of the parent directory of path is used (whose name starts with a date).

• backend (Optional[Literal['dask_image', 'rioxarray']] (default: None)) – Either "dask_image" or "rioxarray" (the latter uses less RAM, but requires rioxarray to be installed). By default, uses "rioxarray" if and only if the rioxarray library is installed.

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

• cells_boundaries (bool (default: True)) – Whether to read cell boundaries (polygons).

• cells_table (bool (default: True)) – Whether to read cells table.

• mosaic_images (bool (default: True)) – Whether to read the mosaic images.

• imread_kwargs (Mapping[str, Any] (default: mappingproxy({}))) – Keyword arguments to pass to the image reader.

• image_models_kwargs (Mapping[str, Any] (default: mappingproxy({}))) – Keyword arguments to pass to the image models.

Return type:

SpatialData

Returns:

: spatialdata.SpatialData