A microscope system and method is described for determining a position of an area of an object within the complete object, wherein the image of the area of the object is contained within a field of view of a microscope. Image data representing a low magnification image of the complete object is available for use in the method, and may be acquired using a low magnification image data source such as a scanner. In a preferred embodiment, the method is implemented in the form of a computer program running on a workstation, which displays, on a display screen the field of view image, and the image of the complete object, in which the position of the area of the object in field of view is highlighted.