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Automatic
If you use automatic tracking, SynthEyes will track both shots simultaneously and automatically link trackers between the two shots. For this to work well, your two shots need to be properly matched, both in overall geometric alignment, and in color and brightness grading. A quick fix, if needed, is to turn on high-pass filtering in the image preprocessor. Be sure to set the proper dominant camera before auto-tracking, as SynthEyes will examine that to determine in which direction to place the links (from secondary trackers to primary camera trackers, which can be left to right or right to left).
Tip : you can use the Copy Splines script to copy splines from one eye to the other, if you want to mask some things out in both eyes.
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