A microscope system, comprising: an objective; a correction collar configured to move a lens in the objective and correct a spherical aberration; a controller configured such that, before a sample, that is an observation target, is observed, the controller: - obtains a plurality of inputs by an observer that specify relative positions of the objective with respect to the sample, and stores the relative positions in a memory of the controller; - sets a plurality of rotation angles of the correction collar; - makes an imaging apparatus obtain a plurality of pieces of image data of the sample, each corresponding to a rotation angle of the correction collar; calculates an evaluation value indicating a contrast of each image from each of the obtained pieces of image data, by a contrast evaluation method; determines, for each relative position, a rotation angle of the correction collar having a maximum evaluation value, and sets said angle having the maximum evaluation value as an optimum value, the optimum value corresponding to a state in which a spherical aberration caused in accordance with the relative position has been corrected; obtains a plurality of combinations that are each a combination of a respective one of the defined relative positions and a respective optimum value; and calculates a function expressing a relationship between the relative position and the optimum value on the basis of the obtained plurality of combinations by interpolation, the plurality of relative positions being positions arranged in an optical axis direction of the objective, wherein the controller is further configured to calculate, during observation of the sample, the optimum value according to an observation target surface of the sample, which is orthogonal to an optical axis of the objective, on the basis of the function calculated using the sample and the relative position which is determined from the observation target surface; and a correction collar driving mechanism configured to drive, during the observation of the sample, the correction collar in accordance with the optimum value, which is calculated by the controller. an objective; a correction collar configured to move a lens in the objective and correct a spherical aberration; a controller configured such that, before a sample, that is an observation target, is observed, the controller: - obtains a plurality of inputs by an observer that specify relative positions of the objective with respect to the sample, and stores the relative positions in a memory of the controller; - sets a plurality of rotation angles of the correction collar; - makes an imaging apparatus obtain a plurality of pieces of image data of the sample, each corresponding to a rotation angle of the correction collar; - obtains a plurality of inputs by an observer that specify relative positions of the objective with respect to the sample, and stores the relative positions in a memory of the controller; - sets a plurality of rotation angles of the correction collar; - makes an imaging apparatus obtain a plurality of pieces of image data of the sample, each corresponding to a rotation angle of the correction collar; calculates an evaluation value indicating a contrast of each image from each of the obtained pieces of image data, by a contrast evaluation method; determines, for each relative position, a rotation angle of the correction collar having a maximum evaluation value, and sets said angle having the maximum evaluation value as an optimum value, the optimum value corresponding to a state in which a spherical aberration caused in accordance with the relative position has been corrected; obtains a plurality of combinations that are each a combination of a respective one of the defined relative positions and a respective optimum value; and calculates a function expressing a relationship between the relative position and the optimum value on the basis of the obtained plurality of combinations by interpolation, the plurality of relative positions being positions arranged in an optical axis direction of the objective, wherein the controller is further configured to calculate, during observation of the sample, the optimum value according to an observation target surface of the sample, which is orthogonal to an optical axis of the objective, on the basis of the function calculated using the sample and the relative position which is determined from the observation target surface; and a correction collar driving mechanism configured to drive, during the observation of the sample, the correction collar in accordance with the optimum value, which is calculated by the controller.