1. A microscope device which obtains an image of a sample to be observed, comprising: a microscope information obtaining unit which obtains microscope information, which is information about each configuration unit which configures the microscope device; a controller which receives the microscope information, and which transmits control information for controlling an operation of the configuration unit; a main body side transmitting/receiving unit which transmits the microscope information to the controller, and which receives the control information from the controller; and a main body side controlling unit which controls the operation of the configuration unit based on the control information received by the main body side transmitting/receiving unit, wherein the controller comprises: a controller side transmitting/receiving unit which receives the microscope information transmitted from the main body side transmitting/receiving unit, and which transmits the control information to the main body side transmitting/receiving unit, a displaying unit which displays an operation screen on which an operation button display used to obtain an instruction for the operation of the configuration unit is arranged based on the microscope information received by the controller side transmitting/receiving unit, an instruction obtaining unit which obtains the instruction by using the operation button display, and a controller side controlling unit which controls the controller side transmitting/receiving unit to transmit the control information, which corresponds to the instruction obtained by the instruction obtaining unit.