1. A microscope system comprising: a microscope device for acquiring a plurality of observation images with different focal points, a 3D image data constructing unit for constructing 3D image data based on the observation images, a smoothing strength calculating unit for calculating smoothing strength for smoothing the 3D image data, based on optical information of the microscope device, and a smoothing unit for smoothing the 3D image data with the smoothing strength calculated in the smoothing strength calculating unit.