Splitting the colours channels and processing them independantly is certainly the way to go if you're going to stick with a 1-shot colour camera.
It's a technique I used when I was on the ToUcam as well, and describe at length in my article : Planetary Imaging and Image Processing. Of course it's over 14 months old now and techniques have changed a bit but for those still on the ToUcam or other 1-shot colour cameras, it's still useful.
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