The code perhaps works just for one image

[fokx]

Duplicates of #2 #5.
File "Skeletonization.py", line ..., in
fluxMap = flux(mir_delD_xn, mir_delD_yn)
File "skeleton2Graph.py", line 195, in flux
flux_x = Nx * delD_xn[pix[0] - 1:pix[0] + 2, pix[1] - 1:pix[1] + 2]
ValueError: operands could not be broadcast together with shapes (3,3) (0,0)
According to your instructions in #2, Igot
mir_delD_yn.shape: (284, 284)
the outputs of this line to be correct and non empty:
D,IDX = morph.distance_transform_edt(BW,return_distances=True, return_indices=True)

Help needed.

[Lehong-Wang]

I think I also came across the same issue. I could be wrong, but this is probably because you are using an image with black background with white pattern. It should be a white background image with black shape.