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Description
With pure anaglyph there is the issue of binocular rivalry that is noticable with certain colors. They appear to be shimmering. With red/cyan glasses, this can be seen with deep red colors, for instance. Shimmering negatively affects the 3D perception.
Methods have been developed for Anaglyph to reduce binocular rivalry and increase eye comfort.
For real-time applications, the Dubois filter and the more recent Rendepth filter might be a good fit. The latter takes on the ideas of the Dubois filter, which was originally developed for CRTs, transfers them to LCDs and adds gamma correction to improve color reproduction.
An explanation of how the Dubois filter works can be found here, albeit in French. Toward the end of the article you can see color diagrams showing what color space remains after applying the filter.
Seemingly more sophisticated filters have been developed as well, but I think they might be more complicated to implement and more expensive to compute, so perhaps not a good fit for real-time use.
Here is a comparison of several filter methods (use the browser's reader mode, should the site appear broken).
I suggest to implement an optional color filter for anaglyphic rendering to increase eyecomfort.
An implementation of the Rendepth filter for red/cyan glasses can, for example, can be found here.