thor.pp.nuclei_segmentation

thor.pp.nuclei_segmentation(image_path, save_dir=None, tile_size=(1000, 1000), method='stardist', **segment_kwds)

Segment nuclei from H&E stained images using stardist, cellpose or histocartography. The segmentation mask is saved as a sparse matrix in .npz format.

Parameters:

• image_path (str) – Path to the full resolution image to segment.

• save_dir (str) – Path to the directory where to save the segmentation mask.

• tile_size (tuple) – Size of the tiles to use for stardist segmentation.

• method (str) – Segmentation method to use. Can be ‘stardist’, ‘cellpose’ or ‘histocartography’.

• segment_kwds (dict) – Keyword arguments to pass to the segmentation function.