So I found this:
When converting MATLAB code it might be necessary to first reshape a matrix to a linear sequence, perform some indexing operations
I was having a similar issue myself, as I am also trying to make the transition from MATLAB to Python. I was finally able to convert a numpy matrix, given in depth, row, col, format to a single sheet of column vectors (per image).
In MATLAB I would have done something like:
output = reshape(imStack,[row*col,depth])
In Python this seems to translate to:
import numpy as np
output=np.transpose(imStack)
output=output.reshape((row*col, depth), order='F')