Abstract: To identify multi-protein complexes with high accuracy, Dr. Tessmer and her group from the University of Würzburg derived a system that uses fluorescence microscopy and atomic force microscopy (AFM) simultaneously on the same specimen. They overlaid images coming from the two different types of microscopes, and came up with a hybrid image that had more information about the specimen compared to the information gained from each microscope image alone. Localization of markers in AFM and fluorescence images and overlaying the images using the markers were all done manually in their work. In my work, I developed algorithms to automatically find the markers in both images and register images using the locations of the markers.