when you say that your mudstone and sandstone is easily distinguishable by photos, that means they have different colours etc. To my understanding CANUPO plugin classifies based on geometries not further attributes. Maybe try to use the intensity value of your TLS data to discriminate between lithologies - this might be much easier. The only problem there is that you might have to aply a correction for the distance to the scanned object. It wood be off course bloody brilliant if there would be a build in tool in CC to do so, but their ain't...
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