Deep Learning Based Correction Algorithms for 3D Medical Reconstruction in Computed Tomography and Macroscopic Imaging

This paper introduces a hybrid two-stage registration framework for reconstructing three-dimensional (3D) kidney anatomy from macroscopic slices, using CT-derived models as the geometric reference standard. The approach addresses the data-scarcity and high-distortion challenges typical of macroscopic imaging, where fully learning-based registration (e.g., VoxelMorph) often fails to generalize due to limited training diversity and large nonrigid deformations that exceed the capture range of unconstrained convolutional filters. In the proposed pipeline, the Optimal Cross-section Matching (OCM) algorithm first performs constrained global alignment—translation, rotation, and uniform scaling—to establish anatomically consistent slice initialization. Next, a lightweight deep-learning refinement network, inspired by VoxelMorph, predicts residual local deformations between consecutive slices. The core novelty of this architecture lies in its hierarchical decomposition of the registration manifold: the OCM acts as a deterministic geometric anchor that neutralizes high-amplitude variance, thereby constraining the learning task to a low-dimensional residual manifold. This hybrid OCM + DL design integrates explicit geometric priors with the flexible learning capacity of neural networks, ensuring stable optimization and plausible deformation fields even with few training examples. Experiments on an original dataset of 40 kidneys demonstrated that the OCM + DL method achieved the highest registration accuracy across all evaluated metrics: NCC = 0.91, SSIM = 0.81, Dice = 0.90, IoU = 0.81, HD95 = 1.9 mm, and volumetric agreement DCVol = 0.89. Compared to single-stage baselines, this represents an average improvement of approximately 17% over DL-only and 14% over OCM-only, validating the synergistic contribution of the proposed hybrid strategy over standalone iterative or data-driven methods. The pipeline maintains physical calibration via Hough-based grid detection and employs Bézier-based contour smoothing for robust meshing and volume estimation. Although validated on kidney data, the proposed framework generalizes to other soft-tissue organs reconstructed from optical or photographic cross-sections. By decoupling interpretable global optimization from data-efficient deep refinement, the method advances the precision, reproducibility, and anatomical realism of multimodal 3D reconstructions for surgical planning, morphological assessment, and medical education.