1. A microscope system for stitching a plurality of element images to generate a stitched image, the system comprising: at least one optical system via which a sample can be imaged; and a computer which is configured to function as: an element image obtaining unit configured to obtain, via the at least one optical system, each of the plurality of element images that constitutes the stitched image; a user image obtaining unit configured to move, according to an instruction from a user, a field of view of the user image obtaining unit to a plurality of positions on the sample corresponding, respectively, to a plurality of user-specified areas on the sample which are specified by the user, each user-specified area corresponding to a current field of view of the user image obtaining unit, and capture, via the at least one optical system, a plurality of user images of the respective user-specified areas on the sample; a rectangle area deciding unit configured to decide a minimum rectangle area comprising all of the plurality of user images of the plurality of user-specified areas obtained by the user image obtaining unit; a candidate area deciding unit configured to decide a plurality of candidate areas for obtaining respective ones of the plurality of element images, each of the plurality of candidate areas having a size of a field of view of the element image obtaining unit and being arranged in a grid-like manner in the rectangle area so as to fill the rectangle area decided by the rectangle area deciding unit; an element area selecting unit configured to select a plurality of element areas for respectively obtaining the plurality of element images, from among the plurality of candidate areas decided by the candidate area deciding unit, wherein the element image obtaining unit obtains, via the at least one optical system, the plurality of element images in the plurality of element areas selected by the element area selecting unit, and a stitched image generation unit configured to generate the stitched image by stitching the plurality of element images obtained by the element image obtaining unit, wherein: the at least one optical system comprises a first optical system and a second optical system; the first optical system includes a laser light source, a two-dimensional scanning unit configured to scan the sample by laser light emitted from the laser light source, a pinhole plate in which a pinhole is formed on an optically conjugated position with a light-collecting point of the laser light, and a photodetector configured to detect light that has passed through the pinhole plate; the element image obtaining unit obtains the plurality of element images via the first optical system, the element images being confocal images of the sample each generated from a detection signal output from the photodetector and information of a scanning position from the two-dimensional scanning unit; the second optical system comprises a light source, an objective lens configured to cast light from the light source on the sample, and a CCD camera comprising a light-receiving plane on an optically conjugated position with a focal plane of the objective lens; and the user image obtaining unit obtains the plurality of user images via the second optical system, the user images being non-confocal images of the sample generated by the CCD camera.