A microscope system includes a microscope apparatus including a stage on which a sample is placed and an objective lens that collects laser light to the sample on the stage, a light source unit including a light source that emits the laser light, a scanning mechanism configured to guide the laser light from the light source unit and change a direction of the guided laser light to scan the sample on the stage, a photodetector configured to guide returned light from the objective lens of the microscope apparatus and convert the guided light into an electrical signal, a controller configured to control at least the scanning mechanism and generate image data from the electrical signal output from the photodetector, and a computer connected to the controller through a bus interface and configured to process the image data transferred from the controller through the bus interface.