Tree-Diffusion: Octree-Based Conditional Diffusion Model for Small Bowel Skeleton Generation with Geometric Direction Modeling

Accurate 3D reconstruction of the small bowel skeleton is vital for understanding intestinal morphology, de-tecting structural abnormalities, and supporting diagnosis, yet limited resolution, organ adhesion, complex anatomy, and scarce annotations make continuous skeleton extraction from masks challenging. Voxel-based methods often struggle with the sparse topology and geometric directionality inherent in the small bowel skeleton, leading to inefficiency and high memory cost. To address these limitations, we propose a novel octree-based conditional diffusion model (i.e., Tree-Diffusion) that generates anatomically consistent small bowel skeletons guided by 3D segmentation masks. Specifically, we introduce two modules that captures structural priors from masks and topology characteristics from skeletons, ensuring cross-domain alignment and high-quality skeleton generation. Besides, we design a synthesis strategy to generate anatomically plausible skeleton-mask pairs, serving as topological priors to guide the diffusion model toward realis-tic structure predictions. To efficiently represent the elongated skeleton, we adopt an octree- based spatial encoding of hierarchical geometric features. Compared with baselines, our model achieves superior performance in anatomical fidelity, directional consistency, and inference efficiency. The code is available at: https://github.com/Small-Bowel-Skeleton-GenerationlCode