Serial sections alignment

Hi, everybody!

The problem is how to align serial sections to make 3D-model of, for example, fish larvae skull. I use TrakEM2 plagin for manual images alignment and the VolumeViewer to control the results. The sections were cut in transverse plane, and my first task is to perfectly arrange the line of the cranial base (it is known from whole mount specimen). The Volume Viewer is very helpful since it allows to examine the stack in sagittal plane (see picture). Yet, the process is very time (and brain) consuming. So, the idea is straightforward: are there any tools which make it possible to move the individual transverse section up or down while viewing it (and the whole stack) in sagital plane?