My 3D animation workflow involves a variety of tools. I found NCO to be extremely useful if your preferred data format is NetCDF. I use Perl as a general purpose scripting language. All the rendering is done using VTK via ParaView. Finally I use MPI to speed up the rendering process.

More information about 3D data visualization with ParaView can be found at the Ocean Data Visualization Wiki. The Wiki is based on an informal seminar that Ryan Abernathey and I organized at Scripps during Winter quarter 2013.

Notes: (1) For optimal visualization change resolution to original (click settings/change quality on the YouTube menubar). (2) For animations in stereoscopic 3D a red/cyan glass is needed (see Anaglyph 3D).