import numpy as np
a = np.array([[0, 1, 2, 4, 5, 1, 2, 3], [4, 5, 6, 8, 9, 5, 6, 7], [8, 9, 10,
    12, 13, 9, 10, 11]])
from collections import Counter
Counter(map(tuple, a.T))
Подсчет вхождений столбцов в массиве numpy