thor.analy.read_polygon_ROI

thor.analy.read_polygon_ROI(json_path, adata, img_key=None)

Read polygon ROI from json file.

Parameters:

• json_path (str) – Path to json file.

• adata (AnnData) – Annotated data matrix.

• img_key (str, optional (default: None)) – Key for image in adata.uns[‘spatial’] where the ROI was drawn. None for full-resolution image. Valid keys are: ‘hires’, ‘lowres’, ‘fullres’

Returns:

roi_shape – Numpy array of shape (n_vertices, 2) containing the coordinates of the ROI polygon.

Return type:

np.ndarray