stereo.io.read_ann_h5ad

stereo.io.read_ann_h5ad(file_path, spatial_key='spatial', bin_type=None, bin_size=None, resolution=500)[source]

Read the H5ad file in Anndata format of Scanpy, and generate the StereoExpData object.

Parameters:

  • file_path (str) – the path to input H5ad file.

  • spatial_key (Optional[str]) – use .obsm['spatial_key'] as coordiante information.

  • bin_type (Optional[str]) – the bin type includes 'bins' or 'cell_bins', default to 'bins'.

  • bin_size (Optional[int]) – the size of bin to merge, when bin_type is set to 'bins'.

  • resolution (Optional[int]) – the resolution of chip, default 500nm.

Return type:

An object of StereoExpData.