Everything done with the vegetation, animals, and machines were all 100% CGI. However, for the Na'vi people, James Cameron came up with a revolutionary technology he named "Motion Capture Filming." This technique involves getting the actors in suits with markers on them, so the cameras track their movements, including all of the tiny details, muscles, and skin movements of the face. So, while the final picture was made with CGI on a green screen, the movements made by the Na'vi including facial gestures were the direct motions of the actors. For a more in-depth look at the motion capture technology, go to http://www.youtube.com/watch?v=P2_vB7zx_SQ
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