--orientation
flag. What follows must be a string in the bg-space "initials" form, to describe the origin voxel.stack[0, :, :]
with matplotlib or when you open the stack with ImageJ. First dimension is the one that you are slicing, the second the height of the image, and the third the width of the image.--voxel-sizes
or -v
flags. These voxel sizes are in microns, and come in the same order as your orientation definition.