Luka there will not be any red pixels showing up if your shooting with say the Oiii filter and the camera is set to mono. The bayer matrix is a physical pixel mask so red ones will only be red. If your shooting in mono the camera simply outputs a mono file stripped of the colour information, try shooting a daytime shot to see what i mean. When you put a narrowband filter in front, it only passes that part of the spectrum, and regardless of whether you have it set for mono or colour, you will only get data from the pixels that can pick up that spectrum area. I only suggest using a mono setting because it mimics mono camera operation and will allow you to layer colour it as per standard mono camera practice.
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