A microscope system comprising: objective lenses with a plurality of magnifications; a microscope body; imaging means connected to the microscope body and including an image sensor configured to capture a microscopic image, wherein the image sensor comprises a plurality of pixels arranged in a matrix; an XY stage configured to place a slide and move in an X direction and a Y direction, wherein the XY stage has a mark so as to be captured by the imaging means, wherein the mark has a pattern that provides information on a predetermined axial direction by including a plurality of pairs of X lines with the same width arranged to be symmetric with respect to a common X-axis center line serving as the axis of symmetry while changing the width, said center line extending in the X direction as a stage X-axis and each pair extending in the X-direction, wherein the width of the pair of X-lines corresponds to the objective lenses with the plurality of magnifications, and a plurality of pairs of Y lines with the same width arranged to be symmetric with respect to a common Y-axis center line serving as the axis of symmetry while changing the width, said center line extending in the Y direction as a stage Y-axis and each pair extending in the Y-direction, wherein the width of the pair of Y-lines corresponds to the objective lenses with the plurality of magnifications, wherein the mark is configured to indicate information in association with a barycentric position in each any one of the plurality of pairs of X lines and the plurality of pairs of Y lines; and changing means configured to change an arrangement of the image sensor with respect to the microscope body, based on an image obtained by capturing the mark using the imaging means, so as to cause a direction defined by a pixel arrangement of the image sensor to align with one of the X direction and the Y direction of the XY stage, wherein the changing means comprises detecting means configured to detect a direction represented by the pattern from an image obtained by capturing the pattern of the mark, and configured to change the arrangement of the image sensor based on the direction represented by the pattern detected by the detecting means, and wherein the changing means is configured to rotate the image sensor with respect to the XY stage so as to cause the direction detected by the detecting means to align with one of a row direction and a column direction of the pixel arrangement of the image sensor. objective lenses with a plurality of magnifications; a microscope body; imaging means connected to the microscope body and including an image sensor configured to capture a microscopic image, wherein the image sensor comprises a plurality of pixels arranged in a matrix; an XY stage configured to place a slide and move in an X direction and a Y direction, wherein the XY stage has a mark so as to be captured by the imaging means, wherein the mark has a pattern that provides information on a predetermined axial direction by including a plurality of pairs of X lines with the same width arranged to be symmetric with respect to a common X-axis center line serving as the axis of symmetry while changing the width, said center line extending in the X direction as a stage X-axis and each pair extending in the X-direction, wherein the width of the pair of X-lines corresponds to the objective lenses with the plurality of magnifications, and a plurality of pairs of Y lines with the same width arranged to be symmetric with respect to a common Y-axis center line serving as the axis of symmetry while changing the width, said center line extending in the Y direction as a stage Y-axis and each pair extending in the Y-direction, wherein the width of the pair of Y-lines corresponds to the objective lenses with the plurality of magnifications, wherein the mark is configured to indicate information in association with a barycentric position in each any one of the plurality of pairs of X lines and the plurality of pairs of Y lines; and changing means configured to change an arrangement of the image sensor with respect to the microscope body, based on an image obtained by capturing the mark using the imaging means, so as to cause a direction defined by a pixel arrangement of the image sensor to align with one of the X direction and the Y direction of the XY stage, wherein the changing means comprises detecting means configured to detect a direction represented by the pattern from an image obtained by capturing the pattern of the mark, and configured to change the arrangement of the image sensor based on the direction represented by the pattern detected by the detecting means, and wherein the changing means is configured to rotate the image sensor with respect to the XY stage so as to cause the direction detected by the detecting means to align with one of a row direction and a column direction of the pixel arrangement of the image sensor.