LightNeuS: Neural Surface Reconstruction in Endoscopy using Illumination Decline

We propose a new approach to 3D reconstruction from sequences of images acquired by monocular endoscopes. It is based on two key insights. First, endoluminal cavities are watertight, a property naturally enforced by modeling them in terms of a signed distance function. Second, the scene illumination is variable. It comes from the endoscope's light sources and decays with the inverse of the squared distance to the surface. To exploit these insights, we build on NeuS, a neural implicit surface reconstruction technique with an outstanding capability to learn appearance and a SDF surface model from multiple views, but currently limited to scenes with static illumination. To remove this limitation and exploit the relation between pixel brightness and depth, we modify the NeuS architecture to explicitly account for it and introduce a calibrated photometric model of the endoscope's camera and light source. Our method is the first one to produce watertight reconstructions of whole colon sections. We demonstrate excellent accuracy on phantom imagery. Remarkably, the watertight prior combined with illumination decline, allows to complete the reconstruction of unseen portions of the surface with acceptable accuracy, paving the way to automatic quality assessment of cancer screening explorations, measuring the global percentage of observed mucosa.

SimCol3D -- 3D Reconstruction during Colonoscopy Challenge

Colorectal cancer is one of the most common cancers in the world. While colonoscopy is an effective screening technique, navigating an endoscope through the colon to detect polyps is challenging. A 3D map of the observed surfaces could enhance the identification of unscreened colon tissue and serve as a training platform. However, reconstructing the colon from video footage remains unsolved due to numerous factors such as self-occlusion, reflective surfaces, lack of texture, and tissue deformation that limit feature-based methods. Learning-based approaches hold promise as robust alternatives, but necessitate extensive datasets. By establishing a benchmark, the 2022 EndoVis sub-challenge SimCol3D aimed to facilitate data-driven depth and pose prediction during colonoscopy. The challenge was hosted as part of MICCAI 2022 in Singapore. Six teams from around the world and representatives from academia and industry participated in the three sub-challenges: synthetic depth prediction, synthetic pose prediction, and real pose prediction. This paper describes the challenge, the submitted methods, and their results. We show that depth prediction in virtual colonoscopy is robustly solvable, while pose estimation remains an open research question.

EndoMapper dataset of complete calibrated endoscopy procedures

Computer-assisted systems are becoming broadly used in medicine. In endoscopy, most research focuses on automatic detection of polyps or other pathologies, but localization and navigation of the endoscope is completely performed manually by physicians. To broaden this research and bring spatial Artificial Intelligence to endoscopies, data from complete procedures are needed. This data will be used to build a 3D mapping and localization systems that can perform special task like, for example, detect blind zones during exploration, provide automatic polyp measurements, guide doctors to a polyp found in a previous exploration and retrieve previous images of the same area aligning them for easy comparison. These systems will provide an improvement in the quality and precision of the procedures while lowering the burden on the physicians. This paper introduces the Endomapper dataset, the first collection of complete endoscopy sequences acquired during regular medical practice, including slow and careful screening explorations, making secondary use of medical data. Its original purpose is to facilitate the development and evaluation of VSLAM (Visual Simultaneous Localization and Mapping) methods in real endoscopy data. The first release of the dataset is composed of 59 sequences with more than 15 hours of video. It is also the first endoscopic dataset that includes both the computed geometric and photometric endoscope calibration with the original calibration videos. Meta-data and annotations associated to the dataset varies from anatomical landmark and description of the procedure labeling, tools segmentation masks, COLMAP 3D reconstructions, simulated sequences with groundtruth and meta-data related to special cases, such as sequences from the same patient. This information will improve the research in endoscopic VSLAM, as well as other research lines, and create new research lines.

SD-DefSLAM: Semi-Direct Monocular SLAM for Deformable and Intracorporeal Scenes

Conventional SLAM techniques strongly rely on scene rigidity to solve data association, ignoring dynamic parts of the scene. In this work we present Semi-Direct DefSLAM (SD-DefSLAM), a novel monocular deformable SLAM method able to map highly deforming environments, built on top of DefSLAM. To robustly solve data association in challenging deforming scenes, SD-DefSLAM combines direct and indirect methods: an enhanced illumination-invariant Lucas-Kanade tracker for data association, geometric Bundle Adjustment for pose and deformable map estimation, and bag-of-words based on feature descriptors for camera relocation. Dynamic objects are detected and segmented-out using a CNN trained for the specific application domain. We thoroughly evaluate our system in two public datasets. The mandala dataset is a SLAM benchmark with increasingly aggressive deformations. The Hamlyn dataset contains intracorporeal sequences that pose serious real-life challenges beyond deformation like weak texture, specular reflections, surgical tools and occlusions. Our results show that SD-DefSLAM outperforms DefSLAM in point tracking, reconstruction accuracy and scale drift thanks to the improvement in all the data association steps, being the first system able to robustly perform SLAM inside the human body.

ORB-SLAM3: An Accurate Open-Source Library for Visual, Visual-Inertial and Multi-Map SLAM

This paper presents ORB-SLAM3, the first system able to perform visual, visual-inertial and multi-map SLAM with monocular, stereo and RGB-D cameras, using pin-hole and fisheye lens models. The first main novelty is a feature-based tightly-integrated visual-inertial SLAM system that fully relies on Maximum-a-Posteriori (MAP) estimation, even during the IMU initialization phase. The result is a system that operates robustly in real-time, in small and large, indoor and outdoor environments, and is 2 to 5 times more accurate than previous approaches. The second main novelty is a multiple map system that relies on a new place recognition method with improved recall. Thanks to it, ORB-SLAM3 is able to survive to long periods of poor visual information: when it gets lost, it starts a new map that will be seamlessly merged with previous maps when revisiting mapped areas. Compared with visual odometry systems that only use information from the last few seconds, ORB-SLAM3 is the first system able to reuse in all the algorithm stages all previous information. This allows to include in bundle adjustment co-visible keyframes, that provide high parallax observations boosting accuracy, even if they are widely separated in time or if they come from a previous mapping session. Our experiments show that, in all sensor configurations, ORB-SLAM3 is as robust as the best systems available in the literature, and significantly more accurate. Notably, our stereo-inertial SLAM achieves an average accuracy of 3.6 cm on the EuRoC drone and 9 mm under quick hand-held motions in the room of TUM-VI dataset, a setting representative of AR/VR scenarios. For the benefit of the community we make public the source code.

Inertial-Only Optimization for Visual-Inertial Initialization

We formulate for the first time visual-inertial initialization as an optimal estimation problem, in the sense of maximum-a-posteriori (MAP) estimation. This allows us to properly take into account IMU measurement uncertainty, which was neglected in previous methods that either solved sets of algebraic equations, or minimized ad-hoc cost functions using least squares. Our exhaustive initialization tests on EuRoC dataset show that our proposal largely outperforms the best methods in the literature, being able to initialize in less than 4 seconds in almost any point of the trajectory, with a scale error of 5.3% on average. This initialization has been integrated into ORB-SLAM Visual-Inertial boosting its robustness and efficiency while maintaining its excellent accuracy.