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A systematic approach to designing a controller for a scanning cytophotometer is described. The approach, applicable to most instrument control requirements, is used to ensure that the various instrument subunits will operate together as a reliable system and that the system itself will operate reliably with other external systems such as computers. The instrument functional objectives are developed through a series of steps into a logic diagram that is easily implemented in hardware. This approach is most suitable to instruments that must perform a sequence of automatic operations on command. It may be used independently or with a microprocessor to provide both fixed and programmable capability in instrument control.