1. A method for aligning microscope images comprising: providing a first image of a subject made up of biological tissue using a first microscope; providing a second image of the subject using a second microscope which is of a different type and different magnification than the first microscope, wherein the second image is of a selected part of the first image and wherein the first and second images are of the biological tissue stained with different stains; modifying the two images so that they have a similar appearance to facilitate a comparison of the images; and aligning the two images.