Aligning and Restoring Imperfect ssEM Images for Continuity Reconstruction

The serial section electron microscopy reconstruction method is commonly used in large volume reconstruction of biological tissue, but the inevitable section damage brings challenges to volume reconstruction. The section damage may result in imperfect section alignment and affect the subsequent neuron segmentation and data analysis. This paper proposes an aligning and restoring method for imperfect sections, which contributes to promoting the continuity reconstruction of biological tissues. To align imperfect sections, we improve the optical flow network to address the difficulties faced by traditional optical flow networks in handling issues related to discontinuous deformations and large displacements in the alignment of imperfect sections. Based on the deformations in different regions, the Guided Position of each coordinate point on the section is estimated to generate the Guided Field of the imperfect section. This Guided field aids the optical flow network in better handling the complex deformation and large displacement associated with the damaged area during alignment. Subsequently, the damaged region is predicted and seamlessly integrated into the aligned imperfect section images, ultimately obtaining aligned damage-free section images. Experimental results demonstrate that the proposed method effectively resolves the alignment and restoration issues of imperfect sections, achieving better alignment accuracy than existing methods and significantly improving neuron segmentation accuracy. Our code is available at https://github.com/lvyanan525/Aligning-and-Restoring-Imperfect-ssEM-images .