Duotoner's key purpose is to convert a full-colour image into a 2-channel image, suitable for reproduction with black ink and a single spot colour. The resulting image is saved as a CMYK image; the idea is that whichever of the three colour channels, C, M or Y is "dominant" will carry the actual colour information, and when printing, you'll replace that plate with the spot ink. The two unused channels will nonetheless carry "plausible" colours, so the DuoTone image can be used for proofing.
If, for example, you're separating to black and red, the red information will end up in both the Magenta and Yellow channels. When doing the actual print run you'd only use one of these two plates, and replace the ink with spot red - but printing a proof on a CMYK printer will still give a plausi
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