Wrinkle Image Registration for Serial Microscopy Sections

3D Reconstruction from the microscopy images of serial sections plays an important role in analysis structure of biological specimens, such as neuronal circuits in brain tissue. During specimen sectioning and collecting, it is very hard to prevent wrinkle from these sections, which introduce distortion when imaging in electron microscopy and cause failure of structure reconstruction. In this paper, we propose a pipeline for registration of serial sections with wrinkle. First, Scale Invariant Feature Transform (SIFT) is used to detect corresponding landmarks across adjacent sections. Second, wrinkle areas are labeled manually in microscopy images, which is easy to distinguish by eye. Finally, a modified Moving-Least-Square deformation algorithm is applied to register adjacent sections with wrinkle. The algorithm reflects the discontinuity around wrinkle areas while keeps the smoothness in other regions. Experimental results demonstrate the effectiveness of our method.