Registration is a important tool in image processing that is applied to match regions in two or more pictures. Virtually all large systems which evaluate images require the registration of images. In this thesis, image registration technique by maximization of mutual information was studied. The technique was applied to biological images of fly brains. Our experimental data supplied by Dr. Chiang’s laboratory of Tsing Hua University. By applying the registration technique, we identify the neuropils in the fly brain and the average locations of the neuropils were computed. In addition, we also analyze the size of Drosophila’s left and right brains.