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It is a relatively difficult topic, but look at chapter 7 of Mastering OpenCV with Practical Computer Vision Projects code here. The tracking of eye contours is performed. You can use it as a first stage of your tracking, and after use a Kalman filter doc or the condensation algorithm (aka particle filter) to perform the tracking (I don't find the documentation anymore, but the principles are describe in the book Learning OpenCV: Computer Vision with the OpenCV Library).
