ColonSplat: Reconstruction of Peristaltic Motion in Colonoscopy with Dynamic Gaussian Splatting

3D reconstruction could improve colonoscopy by estimating mucosal coverage and alerting clinicians to missed regions during screening. However, algorithm development is limited as no current datasets provide both a realistic in vivo appearance and dense, time-resolved 3D ground truth, especially under non-rigid deformation. We present C3VD-DEFCOL, a framework and dataset for evaluating deformable colonoscopy reconstruction with paired geometry and realistic texture. Starting from C3VD/C3VDv2 colon meshes and camera trajectories, we generate controlled deformations of the colon surface, including peristaltic waves and centerline motion, and render per-frame depth, surface normals, optical flow, camera poses, and time-stamped 3D meshes. We then use the rendered geometry, primarily depth, to condition an LTX-2.3-based sim-to-real translation model that produces RGB clips with in vivo-like mucosal color, texture, vasculature, and specular appearance while preserving the underlying 3D scene structure. The resulting dataset contains 110 videos from 11 unique colon mesh geometries, with varying camera trajectories, appearances, and parameterized deformation regimes, including three peristaltic severity levels that serve as controlled evaluation axes. We evaluate the generated videos using appearance realism, geometric consistency, and temporal consistency metrics, and use the paired ground truth to benchmark the downstream task of pose estimation in deformable 3D reconstruction. Our experiments show how pose estimation error increases with increasing deformation severity, providing a controlled stress test that is not possible with existing in vivo datasets. Overall, C3VD-DEFCOL is designed as a reproducible, quantitative evaluation platform for testing deformable 3D reconstruction algorithms, with the goal of reducing the domain gap between synthetic datasets and in vivo colonoscopy.

Monocular colonoscopic 3D reconstruction is important for surgical robotic colonoscopy, but remains challenging due to weak texture, specular reflections, limited view overlap, and non-rigid tissue motion. Conventional multi-view 3D reconstruction methods rely on stable correspondences and approximate rigidity, which are often violated in colonoscopy. Existing endoscopic methods often rely on domain-specific supervision, whereas there are not enough in-vivo labeled data available to adapt geometry foundation models to clinical colonoscopy. We present Colon3R, a cross-domain semi-supervised framework built on pretrained VGGT that transfers coupled camera, depth, and pointmap geometry from labeled phantom and simulated data to unlabeled in-vivo colonoscopy without requiring target-domain geometric annotations. Unlike source-only fine-tuning, which learns only from phantom and simulated data, Colon3R directly exploits unlabeled in-vivo video through teacher-derived cross-view supervision. Our proposed hierarchical quasi-rigid reliability selects reliable supervision at the sequence, directed-pair, and pixel levels, while source-preserving adaptation retains the learned coupled geometry during target-domain adaptation. Extensive experiments demonstrate that our method achieves superior overall performance over state-of-the-art approaches in depth, pointmap, and camera pose estimation. Qualitative comparisons on real in-vivo colonoscopy further show substantially more complete and geometrically consistent reconstructions than competing methods under clinical domain shift. The code is publicly available at https://github.com/vglx/Colon3R.

Background and Objective: Colonoscopy recording practice preserves text reports and still photographs, while the spatial information already present in the recorded video - where the scope traveled, where a lesion was observed, and whether the same lesion was seen again - is discarded when the procedure ends. This study determines whether a lesion-centered spatial record can be assembled and validated without full-colon 3D reconstruction. Methods: A four-layer hierarchical pipeline was assembled - (1) a global topological map, (2) lesion-level spatio-temporal tracks, (3) on-demand local 3D reconstruction, and (4) persistent lesion identity across repeated observations - and ran end to end on four public videos (two C3VDv2 sequences with ground-truth depth and two full REAL-Colon procedures; 40,245 frames). All components are published, individually validated methods; the contribution is their lesion-centered assembly, linking rules, and evaluation. Results: Revisits, impossible under forward-only mapping by construction, were detected by entry-map Bayesian localization: 5,614 and 4,043 revisit events (56 and 68 distinct nodes) in the two full procedures. Lesion-identity merging at the adopted threshold 0.5 maintained ground-truth purity 1.0 while auto-merging 20 of 231 candidate pairs. The endoscopy-specific geometry engine outperformed a general-purpose foundation model on all metrics (overall absolute relative error (AbsRel) 0.2276 vs. 0.3523). Conclusions: The results are partial but establish a concrete near-term path: revisit detection, lesion identity, and local 3D each returned quantitative, reproducible output without waiting for complete geometric reconstruction; validating the record on clinical data is the next step.