1. A microscope system for stitching element images to generate a stitched image, comprising: an element image obtaining unit configured to obtain the element image that constitutes the stitched image; a user image obtaining unit configured to capture a plurality of user-specified areas being an area of a sample specified by a user, and to obtain a plurality of user images; a rectangle area deciding unit configured to decide a rectangle area comprising the plurality of user-specified areas; a candidate area deciding unit configured to decide, as a candidate area being an area to be a candidate to obtain the element image, each of a plurality of areas having a size of a field of view of the element image obtaining unit arranged in a grid-like manner in the rectangle area so as to fill the rectangle area decided by the rectangle area deciding unit; and an element area selecting unit configured to select an element area to obtain the element image, from the plurality of candidate areas decided by the candidate area deciding unit.