sparrow.io.merscope

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sparrow.io.merscope#

sparrow.io.merscope(path, to_coordinate_system='global', z_layers=3, backend=None, transcripts=True, mosaic_images=True, do_3D=False, z_projection=False, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}), filter_gene_names=None, output=None)#

Read MERSCOPE data from Vizgen.

Wrapper around spatialdata_io.merscope, but with support to read in the data as 3D (z,y,x) or perform a z-projection, and with support for reading multiple samples into one spatialdata object This function reads the following files:

  • {ms.TRANSCRIPTS_FILE!r}: Transcript file.

  • mosaic_**_z*.tif images inside the {ms.IMAGES_DIR!r} directory.

Parameters:

  • path (str | Path | list[str] | list[Path]) – Path to the region/root directory containing the Merscope files (e.g., detected_transcripts.csv). This can either be a single path or a list of paths, where each path corresponds to a different experiment/roi.

  • to_coordinate_system (str | list[str] (default: 'global')) – The coordinate system to which the elements will be added for each item in path. If provided as a list, its length should be equal to the number of paths specified in path.

  • 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).

  • 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.

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

  • do_3D (bool (default: False)) – Read the mosaic images and the transcripts as 3D.

  • z_projection (bool (default: False)) – Perform a z projection (maximum intensity along the z-stacks) on z-stacks of 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.

  • filter_gene_names (str | list[str] (default: None)) – Gene names that need to be filtered out (via str.contains), mostly control genes that were added, and which you don’t want to use. Filtering is case insensitive. Also see sparrow.read_transcripts.

  • output (str | Path | None (default: None)) – The path where the resulting SpatialData object will be backed. If None, it will not be backed to a zarr store.

Raises:

  • AssertionError – Raised when the number of elements in path and to_coordinate_system are not the same.

  • AssertionError – If elements in to_coordinate_system are not unique.

  • ValueError – If both do_3D as z_projection are set to True.

Return type:

SpatialData

Returns:

: A SpatialData object.

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