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It turns out that this camera wraps 12 bits of Bayered color information into each 16 bits and publishes this as "YUYV 4:2:2" via UVC. The normal OpenCV VideoCapture stack interprets that as YUYV and performs RGB/ BGR color conversion on it.
The workaround was to patch cap_libv4l to unwrap the "YUYV" (which isn't actually YUYV) and debayer/demosaic it.
