Amira is a 3d visualisation software. It has its quirks and is far from free, but provides good all round visualisation, mixing of fast volume rendering and surface rendered neurons and access to Felix Evers' semi-automated tracing plugin.
- Using ShowClones to switch between and colorize volume renderings of different stacks e.g. clones or any other masked image
- Using ResultViewer to examine affine registrations and fix bad ones with surface based affine registrations
