Microscopic image registration is a key component of the neural structure reconstruction with serial sections of neural
tissue. The goal of microscopic neural image registration is to recover the 3D continuity and geometrical properties of
specimen. During image registration, various distortions need to be corrected, including image rotation, translation,
tissue deformation et.al, which come from the procedure of sample cutting, staining and imaging. Furthermore, there is
only certain similarity between adjacent sections, and the degree of similarity depends on local structure of the tissue and
the thickness of the sections. These factors make the microscopic neural image registration a challenging problem.
To tackle the difficulty of corresponding landmarks extraction, we introduce a novel image registration method for
Scanning Electron Microscopy (SEM) images of serial neural tissue sections based on the structure of mitochondria. The
ellipsoidal shape of mitochondria ensures that the same mitochondria has similar shape between adjacent sections, and its
characteristic of broad distribution in the neural tissue guarantees that landmarks based on the mitochondria distributed
widely in the image. The proposed image registration method contains three parts: landmarks extraction between
adjacent sections, corresponding landmarks matching and image deformation based on the correspondences. We
demonstrate the performance of our method with SEM images of drosophila brain.