Quick example of masking 0-count portions of a 2D histogram

masked_hist.py

import numpy as np
import matplotlib.pyplot as plt

x, y = np.random.normal(0, 1, (2, 1000))

counts, ybins, xbins = np.histogram2d(y, x, bins=30)
counts = np.ma.masked_equal(counts, 0)

fig, ax = plt.subplots()
ax.pcolormesh(xbins, ybins, counts)
plt.show()