img_src = cv2.imread('someimg.jpg')
h, w, c = img_src.shape
# an empty black image for saving pixels
img_dest = np.zeros((h, w, c), dtype=np.uint8)
for ixy in xy_list:
x, y = xy_list[ixy]
# copy pixels at given locations
img_dest[x, y, :] = img_src[x, y, :]
cv2.imwrite('output.jpg', img_dest)
Может ли это решить вашу проблему?