A chromatography column is normally filled with a slurry of media for operation. A piston normally compacts the slurry in the column. The piston moves through a cavity in communication with both a slurry inlet and slurry ports which are in communication with the interior of the chromatography column. A controller receiving inputs from at least one of position sensors and a pressure sensor directs movement of the plunger in an operational step selected from the group of a selected movement and up to a selected pressure.