A microscope controller improves the operability in moving a stage when a stage moving operation is performed on a touch panel. The microscope controller for control of the operation of each electric unit configuring the microscope system solves problems by including: a touch panel unit having a display function and receiving an input by an external physical contact; a control unit for setting a display region as a function area by assigning an image for operation of the electric unit to a specified display region of the touch panel unit, and, when an input to the function area is detected, generating a control instruction signal for control of the electric unit depending on the contact operation to the electric unit corresponding to the function area, and a communication control unit for transmitting the control instruction signal to an external device for controlling the operation of the electric unit.