spatialdata_io.experimental.iss

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spatialdata_io.experimental.iss#

spatialdata_io.experimental.iss(path, raw_relative_path, labels_relative_path, h5ad_relative_path, instance_key=None, dataset_id='region', multiscale_image=True, multiscale_labels=True, imread_kwargs=mappingproxy({}), image_models_kwargs=mappingproxy({}), labels_models_kwargs=mappingproxy({}))#

Read Sanger ISS formatted dataset.

This function reads the following files:

  • <dataset_id>: Counts and metadata file.

  • <raw_relative_path>: Raw raster image.

  • <labels_relative_path>: Label image.

Parameters:

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

  • raw_relative_path (str | Path) – Relative path to the raw raster image file.

  • labels_relative_path (str | Path) – Relative path to the label image file.

  • h5ad_relative_path (str | Path) – Relative path to the counts and metadata file.

  • instance_key (str | None (default: None)) – Which column of the AnnData table (in the obs DataFrame) contains the instance identifiers (e.g. a 'cell_id' column); if not specified, such information is assumed to be contained in the index of the AnnData object.

  • dataset_id (str (default: 'region')) – Dataset identifier.

  • multiscale_image (bool (default: True)) – Whether to process the raw image into a multiscale image.

  • multiscale_labels (bool (default: True)) – Whether to process the label image into a multiscale image.

  • 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.

  • labels_models_kwargs (Mapping[str, Any] (default: mappingproxy({}))) – Keyword arguments passed to spatialdata.models.Labels2DModel.

Return type:

SpatialData

Returns:

: The spatial data object containing the ISS data.

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