Presented with a problem like this, I'd get annoyed and then hit a C compiler ;-)
Assuming the scans are false colour, I'd assign a transparent colour.
I'd load each image in turn, pre-rotate it into a desired perspective (either using it as texture for an OpenGL quad, or perhaps some custom rendering routine) and stack them depth sorted (farthest away first) according to the current viewing direction.
It wouldn't give you a realtime view, of course (unless your machine has some real grunt) but it would give you a 3D reconstruction from the slices.