I am using Magix Movie Edit Pro MX Plus for 3D video editing. When I am ready to encode my videos, I have been exporting them as MPEG4 video files. However, when I output red/cyan anaglyph for my own viewing (I do not have a 3D monitor), I have been disappointed in the compression quality.
This became readily apparent today on some test shots that included grass, bushes, tree leaves and other high detail objects that compressed very poorly.
A better solution is to just output using Windows Media exportt (File | Export movie | Windows Media export) and on the Advanced (Video) settings tab, make sure you have Windows Media Video 9, Variable bit rate-quality and and set the Bit-rate-quality setting to a high value (I’m using 90) for the video options.
This is producing a much cleaner video image with fewer compression artifacts. The regular MPEG4 video encoder seems to work well on normal 2D video but really chokes on anaglyph producing video with a great deal of compression artifacts.
I also found that exporting using the Quicktime option and the default Sorensen 3 codec worked well too, better than MPEG4 on the anaglyph format.