2, 1, 0, 1, 1, 2, 0, 0]) With labels and no indices, non-zero elements are counted: >>> lbl, nlbl = ndimage.label(a) >>> ndimage.histogram(a, 0, 1, 10, lbl) array([0, 0, 2, 1, 0, 1, 1, 2, 0, 0]) Indices can be used to count only certain objects: >>> ndimage.histogram(a, 0, 1, 10, lbl, 2) array([0, 0, 1, 1, 0, 0, 1, 1, 0, 0]) r