harpy.io.visium_hd

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harpy.io.visium_hd#

harpy.io.visium_hd(path, dataset_id=None, filtered_counts_file=True, bin_size=None, bins_as_squares=True, fullres_image_file=None, load_all_images=False, instance_key='cell_ID', region_key='fov_labels', output=None)#

Read 10x Genomics Visium HD formatted dataset.

Wrapper around spatialdata.io.readers.visium_hd.visium_hd, but with the resulting table annotated by a labels element.

Parameters:

  • path (str | Path) – Path to directory containing the 10x Genomics Visium HD output.

  • dataset_id (str | None (default: None)) – Unique identifier of the dataset. If None, it tries to infer it from the file name of the feature slice file.

  • filtered_counts_file (bool (default: True)) – Uses ‘filtered_feature_bc_matrix.h5’ (when True) or to ‘raw_feature_bc_matrix.h5’ (when False).

  • bin_size (int | list[int] | None (default: None)) – When specified, load the data of a specific bin size, or a list of bin sizes. By default, it loads all the available bin sizes.

  • bins_as_squares (bool (default: True)) – If True, the bins are represented as squares. If False, the bins are represented as circles. For a correct visualization one should use squares.

  • fullres_image_file (str | Path | None (default: None)) – Path to the full-resolution image.

  • load_all_images (bool (default: False)) – If False, load only the full resolution, high resolution and low resolution images. If True, also the following images: cytassist_image.tiff.

  • instance_key (str (default: 'cell_ID')) – Instance key. The name of the column in AnnData table .obs that will hold the instance ids.

  • region_key (str (default: 'fov_labels')) – Region key. The name of the column in AnnData table .obs that will hold the name of the elements that annotate the table.

  • 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.

Return type:

SpatialData

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