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Doing the Stereo Tracking
Once you have created stereo pairs, you need to track both left and right trackers. If both camera views are open, tracking will proceed in both views simultaneously (on multiple cores, if available). To track only on the left or right eye, switch to a single-camera viewport configuration.
When tracking stereo pairs, you may find it helpful to use the Stereo SimulTrack viewport configuration (two camera views, two SimulTracks). It will allow you to adjust multiple trackers on each camera simultaneously. If you are tracking a few tracker pairs at a time, "Force row mode" in the SimulTracks may be helpful.
You can also use Pan To Follow; it will affect both camera views based on the selected or cross-selected trackers.
Note that the settings of the left and right trackers in a pair are independent once the pair has been created. You will need to adjust each separately, and that may well be necessary depending on the shot.
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