ImageJ, or its full-featured version Fiji, makes it easy to create volumetric renderings and flythroughs using the 3D Viewer plugin. Plugins are installed by just copying the jar file into the plugins folder, found using locate on my system at ~/.imagej/plugins. Multi-layer tifs or gifs can be used as input. Gimp cannot create multilayer tifs, but it can create gif animations, which are sufficient. Open as layers in Gimp to select multiple layer files, save as animated gif, open in ImageJ.
Inside ImageJ, Image -> Scale allows setting of proper scale. Making one axis longer etc. The Image menu also has Crop, Duplicate, Transform and Zoom. Image -> Adjust has Threshold, Brightness/Contrast, etc. Then, Plugins -> 3D Viewer.
The 3D Viewer plugin has nice recording features, with a built-in 'Record 360 degree rotation' under its View menu. It opens another Movie window, which can then be exported using ImageJ's File -> Save as and choosing Gif.
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