A method and apparatus are provided for automatically separating radionuclides using a chromatographic separation process. The method includes the steps of displaying a first flow diagram on a display depicting flow of the radionuclides through a first set of separation elements of the plurality of separation processing elements, but only during a first step of the chromatographic separation process and displaying a second flow diagram on the display depicting flow of the radionuclides through a second set of separation elements of the plurality of separation processing elements, but only during a second step of the chromatographic separation process.