Microscope system and method of controlling a microscope system

A microscope system, comprising:

• an accommodation unit capable of accommodating a plurality of specimens;
• a stage on which each of the specimens loaded from the accommodation unit is placed;
• an optical system including a lens for spherical aberration correction;
• an image pickup unit capable of capturing a partial image of each of the specimens placed on the stage, via the optical system;
• a movement mechanism to move the lens for spherical aberration correction along an optical axis;
• a control unit to control movement of the lens for spherical aberration correction by the movement mechanism and correct spherical aberration;
• an image processing unit to combine the partial images captured by the image pickup unit and generate a composite image;
• a display unit to display the generated composite image;
• a microscope tube including the optical system;
• a movement unit to move at least one of the microscope tube and the stage along the optical axis;
• and
• a distance measurement unit,
• wherein the control unit calculates a first distance between an upper surface of each of the specimens and a focus position of the optical system, and controls the movement mechanism to move the lens for spherical aberration correction in accordance with the first distance,
• wherein the distance measurement unit measures a second distance between a predetermined position on a microscope tube side and the upper surface of each of the specimens, and
• wherein the control unit executes focusing by controlling the movement unit and calculates the first distance based on information of the second distance obtained from the distance measurement unit at a time when focus is obtained.