A microscope system comprising: a microscope body; imaging means connected to the microscope body and including an image sensor configured to capture a microscopic image, the image sensor including plurality of pixels arranged in a matrix; a slide having an observation target region to be set for a tissue and an axis information mark (701, 703) including a plurality of pairs of X lines with the same width arranged to be symmetric 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 and each pair of X lines extending in the X direction, and a plurality of pairs of Y lines with the same width arranged to be symmetric 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 and each pair of Y-lines extending in the Y-direction, wherein the plurality of pairs of X lines and the plurality of pairs of Y lines are spaced apart from each other and located on the slide, wherein the X direction and the Y direction are orthogonal to each other, and wherein the axis information mark (701, 703) is configured to indicate information in association with a barycentric position in each of the plurality of pairs of X lines and the plurality of pairs of Y lines; a stage configured to place the slide as the observation target and move in the X direction and the Y direction; and detecting means configured to detect the direction indicated by the axis information mark (701, 703) from the image obtained by capturing the axis information mark (701, 703) by the imaging means and by utilizing the barycentric position, and changing means configured to change an arrangement of the placed slide with respect to the stage based on the direction detected by the detecting means so as to cause the direction indicated by the axis information mark (701, 703) to align with a direction of a pixel arrangement of the image sensor by rotating the slide. a microscope body; imaging means connected to the microscope body and including an image sensor configured to capture a microscopic image, the image sensor including plurality of pixels arranged in a matrix; a slide having an observation target region to be set for a tissue and an axis information mark (701, 703) including a plurality of pairs of X lines with the same width arranged to be symmetric 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 and each pair of X lines extending in the X direction, and a plurality of pairs of Y lines with the same width arranged to be symmetric 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 and each pair of Y-lines extending in the Y-direction, wherein the plurality of pairs of X lines and the plurality of pairs of Y lines are spaced apart from each other and located on the slide, wherein the X direction and the Y direction are orthogonal to each other, and wherein the axis information mark (701, 703) is configured to indicate information in association with a barycentric position in each of the plurality of pairs of X lines and the plurality of pairs of Y lines; a stage configured to place the slide as the observation target and move in the X direction and the Y direction; and detecting means configured to detect the direction indicated by the axis information mark (701, 703) from the image obtained by capturing the axis information mark (701, 703) by the imaging means and by utilizing the barycentric position, and changing means configured to change an arrangement of the placed slide with respect to the stage based on the direction detected by the detecting means so as to cause the direction indicated by the axis information mark (701, 703) to align with a direction of a pixel arrangement of the image sensor by rotating the slide.