A microscope system having a microscope forming an image of a specimen inserted onto an optical axis, an image-acquisition apparatus having an image-acquisition element which captures the image of the specimen, a purpose input unit with which an acquisition purpose of 3D image data is input, and a controller receiving the acquisition purpose, wherein the controller receives information about the numerical aperture of the microscope and information of a sampling pitch of the image-acquisition element, calculates a microscope resolution value and an image-acquisition-element resolution value on the basis of the received information, and sends at least one of the control signal for controlling the numeral aperture and the control signal for controlling the sampling pitch in response to the acquisition purpose to at least one of the microscope and the image-acquisition apparatus so that the calculated microscope resolution value and the calculated image-acquisition-element resolution value become the same.