1. A microscope system comprising: a microscope device comprising an objective lens placed in a light path of observation light and configured to acquire a plurality of observation images with different focal points; a processor comprising hardware, wherein the processor is configured to: construct 3D image data based on the observation images, calculate smoothing strength for smoothing the 3D image data, based on optical information of the microscope device, and smooth the 3D image data with the calculated smoothing strength, wherein the smoothing strength is calculated by means of the following equation (1): 
 α=depth-of-field/field-of-view  (1) wherein α is smoothing strength, and wherein the depth-of-field (DOF) is a value calculated by the following equation (5): DOF = λ 2 ⁢ NA 2 ⁢ ( 5 ) wherein NA is a numerical aperture of the objective lens and λ is a wavelength of light.