Morphological Filters Functional

remove_small_objects(np_mask, min_size=3000, avoid_overmask=True, overmask_thresh=95)[source]

Remove connected components which size is less than min_size.

is True, this function can recursively call itself with progressively to avoid removing too many objects in the mask.

Parameters
  • np_img (np.ndarray (arbitrary shape, int or bool type)) – Input mask

  • min_size (int, optional) – Minimum size of small object to remove. Default is 3000

  • avoid_overmask (bool, optional (default is True)) – If True, avoid masking above the overmask_thresh percentage.

  • overmask_thresh (int, optional (default is 95)) – If avoid_overmask is True, avoid masking above this threshold percentage value.

  • np_mask (numpy.ndarray) –

Returns

Mask with small objects filtered out

Return type

np.ndarray

watershed_segmentation(np_mask, region_shape=6)[source]

Segment and label an binary mask with Watershed segmentation 1

The watershed algorithm treats pixels values as a local topography (elevation).

Parameters
  • np_mask (np.ndarray) – Input mask

  • region_shape (int, optional) – The local region within which to search for image peaks is defined as a squared area region_shape x region_shape. Default is 6.

Returns

Labelled segmentation mask

Return type

np.ndarray

References

1

Watershed segmentation. https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_watershed.html