vEMRec: High-Resolution Volume Electron Microscopy Reconstruction Based on Structure-Preserving and High-Fidelity 3D Alignment

Three-dimensional (3D) alignment is a key step in volume electron microscopy (vEM), aimed at addressing misalignment during data acquisition, thereby recovering the correct biological structures. However, automated 3D alignment has long been challenged by the dilemma between eliminating nonlinear distortions and capturing natural morphological variations inherent to biological specimens. Here, we present vEMRec, a paradigm-shifting, fully automated algorithm for vEM 3D alignment. vEMRec redefines the 3D alignment problem by decoupling it into high-frequency and low-frequency subproblems. In this framework, precision rigid alignment is applied to correct rigid distortions, while a Gaussian filter-driven elastic registration algorithm addresses nonlinear distortions, all the while faithfully preserving biologically plausible deformations. Extensive experiments demonstrate that vEMRec achieves a paradigm shift in 3D alignment. Serving as a critical preprocessing step, vEMRec enhances performance in downstream isotropic reconstruction and 3D segmentation tasks by improving axial continuity in anisotropic data while preserving the structural integrity of ultrastructural details. Moreover, vEMRec accomplishes this through efficient computation, enabling TB-scale specimen analysis with biologically relevant throughput. vEMRec successfully optimized six representative large-scale real-world datasets, demonstrating its applicability, accuracy, and robustness for large-scale data processing.