A microscope controller that performs an operation for controlling an operation of each motorized unit configuring a microscope system, comprising: a touch panel unit that accepts an input made with an external physical contact, and has a display function; a controlling unit for setting a display area as a functional area by assigning an image for operating the motorized unit to the certain display area of the touch panel unit, and for generating a control instruction signal for controlling the motorized unit in accordance with a contact operation performed for the motorized unit corresponding to the functional area upon detection of an input made in the functional area; and a communication controlling unit for transmitting the control instruction signal to an external device that controls an operation of the motorized unit, wherein the controlling unit successively sets one or more functional areas in a predetermined range along a periphery of the touch panel unit, and generates a control instruction signal according to a drag operation performed in the functional area, wherein the controlling unit assigns, to the one or more functional areas set along the periphery of the touch panel unit, at least any of a function of adjusting a coordinate of a motorized stage in an optical axis direction, a function of adjusting an amount of dimming of a light source unit (6, 13), a function of adjusting an optical magnification by switching among objective lenses attached to a revolver unit, a function of switching among optical elements (35a, 35b) included in an optical element turret unit, and a function of adjusting a zoom magnification of a zooming mechanism, wherein the microscope controller further comprises a positional marker part (209, 209a) that is a physical marker at a predetermined position on the touch panel unit, wherein the positional marker part is a frame-shaped convex part that has a predetermined height and is provided along a periphery of the touch panel unit, or a level difference formed between a flat surface of the touch panel unit when the touch panel unit is installed at a concave bottom provided on a predetermined surface of a housing of the microscope controller and the predetermined surface of the housing, and wherein one or more protrusions are formed on an inner wall side of the frame-shaped convex part, or on a side wall of the level difference. a touch panel unit that accepts an input made with an external physical contact, and has a display function; a controlling unit for setting a display area as a functional area by assigning an image for operating the motorized unit to the certain display area of the touch panel unit, and for generating a control instruction signal for controlling the motorized unit in accordance with a contact operation performed for the motorized unit corresponding to the functional area upon detection of an input made in the functional area; and a communication controlling unit for transmitting the control instruction signal to an external device that controls an operation of the motorized unit, wherein the controlling unit successively sets one or more functional areas in a predetermined range along a periphery of the touch panel unit, and generates a control instruction signal according to a drag operation performed in the functional area, wherein the controlling unit assigns, to the one or more functional areas set along the periphery of the touch panel unit, at least any of a function of adjusting a coordinate of a motorized stage in an optical axis direction, a function of adjusting an amount of dimming of a light source unit (6, 13), a function of adjusting an optical magnification by switching among objective lenses attached to a revolver unit, a function of switching among optical elements (35a, 35b) included in an optical element turret unit, and a function of adjusting a zoom magnification of a zooming mechanism, wherein the microscope controller further comprises a positional marker part (209, 209a) that is a physical marker at a predetermined position on the touch panel unit, wherein the positional marker part is a frame-shaped convex part that has a predetermined height and is provided along a periphery of the touch panel unit, or a level difference formed between a flat surface of the touch panel unit when the touch panel unit is installed at a concave bottom provided on a predetermined surface of a housing of the microscope controller and the predetermined surface of the housing, and wherein one or more protrusions are formed on an inner wall side of the frame-shaped convex part, or on a side wall of the level difference.