Nikon patent application US20130182173 "Solid-state imaging device and electronic camera" by Hironobu Murata proposes a nice idea to combine a dedicated AF sensor with an imaging sensor without losing any light (in theory). The idea is simple: RGB color filter array does not use roughly 2/3 of the light in each pixel, why not use the lost light by a complementary-colored organic AF sensor stacked on top on the regular Bayer-pattern sensor:
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