To provide a microscope system enabling the user to accurately observe the surface of the observing target in a short time. A sensitivity parameter for adjusting a value of the pixel data corresponding to a plurality of pixels is set. The pixel data is acquired with a first sensitivity value set as the sensitivity parameter, and the number of pixels in which the peak value of the pixel data is smaller than or equal to a threshold value is detected. A ratio of the detected number of pixels with respect to the total number of pixels region is calculated, where the pixel data is acquired by a second sensitivity value different from the first sensitivity value when the ratio is greater than or equal to a reference value, and the pixel data is not acquired by the second sensitivity value when the ratio is smaller than the reference value.