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Especially in shots that contain green-screen elements, you may have already roto'd out actors. Those same actors are often the elements that occlude objects you are trying to track. You can save your roto mattes (from whatever application you are using to generate them) and use them in SynthEyes for the planar trackers.
You can store the alpha channel in the RGB(A) source imagery (be sure to turn on the Keep Alpha checkbox when opening the shot), or you can store the alpha channel data in a separate set of files in tandem with the RGB imagery. The file naming is controlled by a preference, by default for a shot with files shot38_0000.dpx you'd name them shot38_alpha_0000.png for the default preference setting. Support for gray- scale-only image formats is limited: use PNG or TIFF files for true gray-scale images.
The alpha polarity control says whether to include or exclude the selected pixels in the alpha mask, or to ignore any alpha channel.
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