The documentation on http://matplotlib.org/examples/mplot3d/hist3d_demo.html contains use of numpy.meshgrid, numpy.histogram2d and flatten. Meshgrid returns arrays of shape (ny, nx) while histogram2d returns arrays of shape (nx, ny). Thus, one or the other has to be transposed in order to use them all together after flatten (or flatten must be run with order='F' on one of the results)