loki.preprocess.segment_patches

loki.preprocess.segment_patches(img_array, coord, patch_dir, height=20, width=20)

Extracts small image patches centered at specified coordinates and saves them as individual PNG files.

Parameters:

  • img_array (numpy.ndarray) – A NumPy array representing the full-resolution image. Shape is expected to be (H, W[, C]).

  • coord (pandas.DataFrame) – A pandas DataFrame containing patch center coordinates in columns “pixel_x” and “pixel_y”. The index corresponds to spot IDs. Example columns: [“pixel_x”, “pixel_y”].

  • patch_dir (str) – Directory path where the patch images will be saved.

  • height (int) – The patch’s height in pixels (distance in the y-direction).

  • width (int) – The patch’s width in pixels (distance in the x-direction).

Returns:

None. The function saves image patches to patch_dir but does not return anything.