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I suppose that you wrote your quantization module yourself? In that case you could add your ROI mask as extra input argument and check for every pixel, if it should be taken into account for your quantization or not by looking up your ROI mask.

Otherwise there has to be some kind of definition in your quantization module, which pixels are to be processed (e.g. a key color or a 4th image channel or a float matrix with negative values for background pixels or ...).