Establish Better(?) XYZ tiling conventions

Working off the tigerbox, we've established a convention across machines to just start in a consistent corner, call it (0,0,0), and tile with increasing volume. This convention includes a quirk where the y direction increases down the sample.

As written, we need to do some transformation hacks to bring the files into viewers like Imaris.

It would be better to establish a better coordinate frame setup, so we don't need to bookkeep why we're sprinkling minus signs all over the code.