If this 3840 x 2160 matrix is the only data in the file you could do
import numpy as np
Yd = np.fromfile('file_with_matrix.bin', dtype=np.uint16).reshape(2160,3840).T
Y[i] = Yd.T
Note that both the 2nd and 3rd lines have transposes (.T). The 2nd line compensates for MATLAB's column-major reading compared to NumPy's row-major. You could instead do
import numpy as np
Y[i] = np.fromfile('file_with_matrix.bin', dtype=np.uint16).reshape(3840,2160)
Yd = Y[i].T
and only tranpose once.
