ColonAdapter: Geometry Estimation Through Foundation Model Adaptation for 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.

Accurate monocular depth estimation is critical in colonoscopy for lesion localization and navigation. Foundation models trained on natural images fail to generalize directly to colonoscopy. We identify the core issue not as a semantic gap, but as a statistical shift in the frequency domain: colonoscopy images lack the strong high-frequency edge and texture gradients that these models rely on for geometric reasoning. To address this, we propose SpecDepth, a parameter-efficient adaptation framework that preserves the robust geometric representations of the pre-trained models while adapting to the colonoscopy domain. Its key innovation is an adaptive spectral rectification module, which uses a learnable wavelet decomposition to explicitly model and amplify the attenuated high-frequency components in feature maps. Different from conventional fine-tuning that risks distorting high-level semantic features, this targeted, low-level adjustment realigns the input signal with the original inductive bias of the foundational model. On the public C3VD and SimCol3D datasets, SpecDepth achieved state-of-the-art performance with an absolute relative error of 0.022 and 0.027, respectively. Our work demonstrates that directly addressing spectral mismatches is a highly effective strategy for adapting vision foundation models to specialized medical imaging tasks. The code will be released publicly after the manuscript is accepted for publication.

Geometric estimation including depth estimation and scene reconstruction is a crucial technique for colonoscopy which can provide surgeons with 3D spatial perception and navigation. However, geometric ground truth in colonoscopy is difficult to obtain due to narrow and enclosed space of the colon, while there is a large feature gap between simulated data and realistic data caused by artifacts and illumination. In this paper, we present CoGE, a novel framework for online monocular geometric estimation during colonoscopy. Firstly, we propose an illumination-aware supervision module based on the Retinex theory to address illumination diversity in different colonoscopy scenes. Moreover, a structure-aware perception module is proposed based on wavelet decomposition to extract common structural and local features of the colon. Both quantitative and qualitative results demonstrate that the proposed model solely trained on simulated data achieves state-of-the-art performance in geometric estimation for both simulated and realistic scenes.