A microscope system includes an accommodation unit, a stage, an optical system, an image pickup unit, a movement mechanism, a control unit, an image processing unit, and a display unit. The accommodation unit is capable of accommodating a plurality of specimens. On the stage, each of the specimens loaded from the accommodation unit is placed. The optical system includes a lens for spherical aberration correction. The image pickup unit is capable of capturing a partial image of each of the specimens placed on the stage, via the optical system. The movement mechanism moves the lens for spherical aberration correction along an optical axis. The control unit controls movement of the lens for spherical aberration correction by the movement mechanism and correct spherical aberration. The image processing unit combines the partial images captured by the image pickup unit and generate a composite image. The display unit displays the generated composite image.