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I don't think so. The effect works on re-encoding the color channels whereas for polarized output you would have to reposition the pixels similar to interlacing so the individual phases coincide with the filtering grid. This is certainly more a matter of using other tools. Anyway, I'm probably not the most qualified person to answer this as I've never done it, really and with only 5 or so 3D enabled Cinemas in Germany, chances are slim that I ever will. ;-)
Unlike with red/green 3D, for polarized lenses to work the two separate images have to be projected through two separate polarizing filters, so there is no sense in compositing the two images together before displaying them.
Chromadepth apparently uses prismatic lenses to separate different wavelengths of light to create the illusion of depth. This means the location of an object's color on the spectrum will determine the depth of that object with, as Wikipedia tells me, red being near blue being distant (those of us who wear glasses can sometimes see a subtle example if this effect by turning our heads with respect to the computer screen). If this method works with RGB sub-pixel-based displays, recreating it in AE would have to involve a depth map of some sort, rather than separate images for the left and right eyes.
In any #d project, you must first decide how your audience will view the end result. Then you decide on how to get it done.
The 3D Glasses effect is an anaglyph illusion. Output for polarization and shuttered glasses is capable of displaying a true 3D space but you must have two cameras in your comp and render two separate movies.
I'd like to ask some questions on this thread that I think fits in.
How far apart in terms of pixels should two virtual cameras be if I am going to create an anaglyph animation? Does the distance between the cameras change depending on how deep you want the space the be?
I have googled a bit on the subject, and I simply don't know how to determine how far the cameras should be.
Does anybody have any thoughs?
There's no fixed number, since the scale of the 3D scene you are constructing is arbitrary. Rather, you need to figure out how many pixels in your composition's world space correspond to the distance between a typical viewer's eyes. And be sure to consider the difference between pixels as a measure in world space, and comp pixels, which are not the same.