insitupy.read_xenium

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insitupy.read_xenium#

insitupy.read_xenium(path, nuclei_type='mip', load_cell_segmentation_images=True, verbose=True, transcript_mode='dask', restructure_transcripts=False)#

Reads Xenium In Situ data from the specified directory.

Parameters:

  • path (Union[str, os.PathLike, Path]) – Path to the Xenium data bundle.

  • nuclei_type (Literal["focus", "mip", ""], optional) – Type of nuclei image to load. Defaults to “mip”. If “mip” is unavailable, “focus” will be used as a fallback.

  • load_cell_segmentation_images (bool, optional) – Whether to load cell segmentation images. Defaults to True.

  • verbose (bool, optional) – Whether to print progress messages. Defaults to True.

  • transcript_mode (Literal["pandas", "dask"], optional) – Mode to load transcript data. Defaults to “dask”. - “pandas”: Loads the data into a pandas DataFrame. - “dask”: Loads the data into a Dask DataFrame for larger datasets.

  • restructure_transcripts (bool, optional) – Whether to restructure the transcript data. Defaults to False.

Returns:

An object containing the processed Xenium experiment data, including metadata, cells, images, and transcripts.

Return type:

InSituData

Raises:

  • InvalidXeniumDirectory – If the specified directory does not contain the required Xenium metadata file.

  • FileNotFoundError – If the specified directory does not exist.

  • ValueError – If an invalid value is provided for transcript_mode.

Notes

  • The function initializes an InSituData object with metadata and loads cell data, images, and transcripts.

  • For Xenium versions <2.0, the “mip” image is used if available; otherwise, the “focus” image is loaded.

  • Cell segmentation images are loaded if available and load_cell_segmentation_images is True.

  • Transcript data can be loaded using either pandas or Dask, depending on the transcript_mode parameter.

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