A method and system for processing a 3D tissue sample is provided, comprising the steps of receiving a tube with an inner space and two open ends, wherein the tube is configured to retain the 3D tissue sample in the inner space, arranging the tube so that one of the two open ends of the tube is located at a fluid channel, and forcing or actively pressing a tissue processing agent through the fluid channel and into the tube so that the tissue processing agent passes through the tissue.
