The present microscope system has: a microscope, which has a light source, an aperture stop, a condenser lens, and an objective lens; a camera, which has a microlens array and an image pickup element; and an image processing unit, which constitutes a computer. The image processing unit divides a plurality of pixels allocated to each of the microlenses into bright-field image detection regions to be used for detecting bright-field images, and dark-field image detection regions to be used for detecting darkfield images, in accordance with the size of an aperture of the aperture stop. The image processing unit generates bright-field image data of a sample and darkfield image data of the sample.