This document is the reference manual for the control program of the isocentric treatment unit of the Clinical Neutron Therapy System (CNTS) at the University of Washington Medical Center. It is intended primarily for cyclotron engineers and software developers, and may also be useful to technicians, physicists, and therapists. This manual describes the functions used to treat patients, perform calibrations, measure physics data, and troubleshoot the treatment equipment. It provides a comprehensive description of the CNTS user interface including the function of each key and dialog, and the meaning of each screen, indicator, and message. It describes program behavior that cannot be directly observed by the operator, including sequencing and communication with each of the attached device controllers. It describes the data files and their contents and explains when each file is read and written. This document is sufficiently thorough to serve as the specification for the control program of the isocentric unit.

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