Abstract: A method and apparatus for aligning microscope images. Microscope images of the same or very similar subjects provided by different microscopes are aligned. The images from two types of microscope, such as a Virtual Microscope (VM) and a Light Microscope (LM) are used. An image produced by the virtual microscope is easily read by a viewer, as it represents a scan of a whole slide rather than individual high power fields of view. An area of the image can be selected for further examination or objective analysis by the LM microscope. The qualitative or quantitative information obtained from the Light microscope using the method described may then be located back into the virtual microscope image to provide understandable context.