A microscope system comprising: an observation optical system including an objective lens (126, 148); an imaging unit configured to capture an image of an observation object obtained by the observation optical system; a stage movable in an X-axis direction, a Y-axis direction, and a Z-axis direction, said stage is configured such that a slide of the observation object can be placed on it, said slide comprising a cover glass area and a focus reference mark (704, 705, 706) arranged around the cover glass area and a mark (701, 702, 703), wherein the stage comprises a first stage configured to move an XY plane including the X-axis direction and the Y-axis direction orthogonal to each other, on which the slide of the observation object is placed, and a second stage configured to move the first stage in the Z-axis direction aligned with an optical axis direction of an objective lens (126, 127) mounted in the observation optical system; first obtaining means (271, 272, 991) configured to obtain position information of the stage defined by the X-axis direction, the Y-axis direction, and the Z-axis direction, and to decide a position of the mark (701, 702, 703) in the X- and Y-axis directions obtained based on an image obtained by capturing the mark (701, 702, 703) provided on the slide placed on the first stage by the imaging unit and a position of the mark (701, 702, 703) in the Z-axis direction obtained based on a focus position of the image as slide reference positions, and to decide an observation position in the X-, Y-, and Z-axis directions based on the slide reference positions; measurement means configured to measure, using the imaging unit, focus positions at a plurality of points of the focus reference mark (704, 705, 706) arranged around the cover glass area of the slide; estimation means configured to estimate a distribution of positions of the upper surface of the slide in the Z-axis direction in the cover glass area based on the focus positions measured by the measurement means, wherein an observation position of a specimen on the slide in the Z-axis direction is managed based on the distribution estimated by the estimation means; and processing means configured to store the position information and the image of the observation object obtained by capturing the observation object by the imaging unit in storage means in association with each other. an observation optical system including an objective lens (126, 148); an imaging unit configured to capture an image of an observation object obtained by the observation optical system; a stage movable in an X-axis direction, a Y-axis direction, and a Z-axis direction, said stage is configured such that a slide of the observation object can be placed on it, said slide comprising a cover glass area and a focus reference mark (704, 705, 706) arranged around the cover glass area and a mark (701, 702, 703), wherein the stage comprises a first stage configured to move an XY plane including the X-axis direction and the Y-axis direction orthogonal to each other, on which the slide of the observation object is placed, and a second stage configured to move the first stage in the Z-axis direction aligned with an optical axis direction of an objective lens (126, 127) mounted in the observation optical system; first obtaining means (271, 272, 991) configured to obtain position information of the stage defined by the X-axis direction, the Y-axis direction, and the Z-axis direction, and to decide a position of the mark (701, 702, 703) in the X- and Y-axis directions obtained based on an image obtained by capturing the mark (701, 702, 703) provided on the slide placed on the first stage by the imaging unit and a position of the mark (701, 702, 703) in the Z-axis direction obtained based on a focus position of the image as slide reference positions, and to decide an observation position in the X-, Y-, and Z-axis directions based on the slide reference positions; measurement means configured to measure, using the imaging unit, focus positions at a plurality of points of the focus reference mark (704, 705, 706) arranged around the cover glass area of the slide; estimation means configured to estimate a distribution of positions of the upper surface of the slide in the Z-axis direction in the cover glass area based on the focus positions measured by the measurement means, wherein an observation position of a specimen on the slide in the Z-axis direction is managed based on the distribution estimated by the estimation means; and processing means configured to store the position information and the image of the observation object obtained by capturing the observation object by the imaging unit in storage means in association with each other.