Most cameras will give you the proper output with 6 bits of padding. I have come across one that rearranged the bits when using 10 bit. It was still padded properly, but the bits were out of order.
You should also be able to convert the 16 bit image to an array, which you could manipulate without the Vision toolkit. It is just a lot easier with the toolkit.
Bruce
Bruce Ammons
Ammons Engineering