hest.autoalign_visium

hest.autoalign_visium(fullres_img: ndarray, save_dir: str = None, name='') → Dict

Automatically find the spot alignment based on an image with apparent Visium fiducials

Parameters:

• fullres_img (np.ndarray) – image with apparent Visium fiducials

• save_dir (str, optional) – directory where the alignment file will be saved. Defaults to None.

• name (str, optional) – name of the samples, will be concatenated to the alignment filename. Defaults to ‘’.

Raises:

Exception – if cannot find alignment

Returns:

spot alignment as a dictionary

Return type:

Dict