A photopheresis system (200) is disclosed, and that may be configured to execute one or more protocols. These protocols include: 1) protocols (400; 430; 460) for purging air out of a centrifuge bowl (210) used by the photopheresis system (200); 2) protocols (500; 510 550) for assessing the installation/operation of one or more pressure domes (330) used by the photopheresis system (200); and 3) protocols (580; 600; 660; 700; 740) for collecting buffy coat from blood processed by the photopheresis system (200).