Using Vaa3d for 3d image registration

[akatav]

Dataset consists of multichannel multiframe tiff files.Each frame is obtained at a deeper focal length of in-vivo tissue.We are looking to correct motion artifacts of brain images obtained by 2d photon microscopy on live mice at successive focal lengths along the axial plane. So, in summary, although we do not have a time scale right now(maybe in future),we are just looking to correct for motion artifacts within and between frames.
More formally,there are n tiff stacks. Each stack has Nimgs where each img is from a depth along the axial plane of the brain, n is the number of channels. Once motion corrected, we are looking to trace the dendrites belonging to a stack in 3d.
Can someone please advice how to use Vaa3d for this motion correction and image registration problem ?