Lesion-centered 3D mapping of colonoscopy procedures: validation of a hierarchical ensemble pipeline on public benchmark videos

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.

Early screening via colonoscopy is critical for colon cancer prevention, yet developing robust AI systems for this domain is hindered by the lack of densely annotated, long-sequence video datasets. Existing datasets predominantly focus on single-class polyp detection and lack the rich spatial, temporal, and linguistic annotations required to evaluate modern Multimodal Large Language Models (MLLMs). To address this critical gap, we introduce Colon-Bench, generated via a novel multi-stage agentic workflow. Our pipeline seamlessly integrates temporal proposals, bounding-box tracking, AI-driven visual confirmation, and human-in-the-loop review to scalably annotate full-procedure videos. The resulting verified benchmark is unprecedented in scope, encompassing 528 videos, 14 distinct lesion categories (including polyps, ulcers, and bleeding), over 300,000 bounding boxes, 213,000 segmentation masks, and 133,000 words of clinical descriptions. We utilize Colon-Bench to rigorously evaluate state-of-the-art MLLMs across lesion classification, Open-Vocabulary Video Object Segmentation (OV-VOS), and video Visual Question Answering (VQA). The MLLM results demonstrate surprisingly high localization performance in medical domains compared to SAM-3. Finally, we analyze common VQA errors from MLLMs to introduce a novel "colon-skill" prompting strategy, improving zero-shot MLLM performance by up to 9.7% across most MLLMs. The dataset and the code are available at https://abdullahamdi.com/colon-bench .

Because dense frame-level annotation of colonoscopy videos is costly, we propose WSPolypNet, a weakly supervised framework for polyp localization using only video-level labels. WSPolypNet employs a 3D convolutional neural network trained with video-level supervision to generate class activation maps (CAMs), which identify candidate polyp regions without requiring frame-level spatial annotations. The CAM-derived localization cues are further enhanced using a multi-view strategy and provided to MedSAM2 as point prompts. MedSAM2 then propagates segmentation masks across the video, refining the coarse localization cues according to polyp boundaries. WSPolypNet achieved CorLoc scores of 47.80%, 43.68%, and 35.01% at IoU thresholds of 0.3, 0.5, and 0.7, respectively, compared with 36.87%, 33.72%, and 27.94% in the single-view setting. For small polyps, the multi-view strategy improved CorLoc@0.5 from 16.01% to 30.97%. The framework also achieved a recall of 94.51%. These results demonstrate the potential of weakly supervised spatiotemporal learning to substantially reduce spatial annotation requirements for polyp localization in colonoscopy videos.