A Quantitative Evaluation of Dense 3D Reconstruction of Sinus Anatomy from Monocular Endoscopic Video

Generating accurate 3D reconstructions from endoscopic video is a promising avenue for longitudinal radiation-free analysis of sinus anatomy and surgical outcomes. Several methods for monocular reconstruction have been proposed, yielding visually pleasant 3D anatomical structures by retrieving relative camera poses with structure-from-motion-type algorithms and fusion of monocular depth estimates. However, due to the complex properties of the underlying algorithms and endoscopic scenes, the reconstruction pipeline may perform poorly or fail unexpectedly. Further, acquiring medical data conveys additional challenges, presenting difficulties in quantitatively benchmarking these models, understanding failure cases, and identifying critical components that contribute to their precision. In this work, we perform a quantitative analysis of a self-supervised approach for sinus reconstruction using endoscopic sequences paired with optical tracking and high-resolution computed tomography acquired from nine ex-vivo specimens. Our results show that the generated reconstructions are in high agreement with the anatomy, yielding an average point-to-mesh error of 0.91 mm between reconstructions and CT segmentations. However, in a point-to-point matching scenario, relevant for endoscope tracking and navigation, we found average target registration errors of 6.58 mm. We identified that pose and depth estimation inaccuracies contribute equally to this error and that locally consistent sequences with shorter trajectories generate more accurate reconstructions. These results suggest that achieving global consistency between relative camera poses and estimated depths with the anatomy is essential. In doing so, we can ensure proper synergy between all components of the pipeline for improved reconstructions that will facilitate clinical application of this innovative technology

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Tracking and Mapping in Medical Computer Vision: A Review

As computer vision algorithms are becoming more capable, their applications in clinical systems will become more pervasive. These applications include diagnostics such as colonoscopy and bronchoscopy, guiding biopsies and minimally invasive interventions and surgery, automating instrument motion and providing image guidance using pre-operative scans. Many of these applications depend on the specific visual nature of medical scenes and require designing and applying algorithms to perform in this environment. In this review, we provide an update to the field of camera-based tracking and scene mapping in surgery and diagnostics in medical computer vision. We begin with describing our review process, which results in a final list of 515 papers that we cover. We then give a high-level summary of the state of the art and provide relevant background for those who need tracking and mapping for their clinical applications. We then review datasets provided in the field and the clinical needs therein. Then, we delve in depth into the algorithmic side, and summarize recent developments, which should be especially useful for algorithm designers and to those looking to understand the capability of off-the-shelf methods. We focus on algorithms for deformable environments while also reviewing the essential building blocks in rigid tracking and mapping since there is a large amount of crossover in methods. Finally, we discuss the current state of the tracking and mapping methods along with needs for future algorithms, needs for quantification, and the viability of clinical applications in the field. We conclude that new methods need to be designed or combined to support clinical applications in deformable environments, and more focus needs to be put into collecting datasets for training and evaluation.Comment: 31 pages, 17 figure

SERV-CT: A disparity dataset from cone-beam CT for validation of endoscopic 3D reconstruction

In computer vision, reference datasets from simulation and real outdoor scenes have been highly successful in promoting algorithmic development in stereo reconstruction. Endoscopic stereo reconstruction for surgical scenes gives rise to specific problems, including the lack of clear corner features, highly specular surface properties and the presence of blood and smoke. These issues present difficulties for both stereo reconstruction itself and also for standardised dataset production. Previous datasets have been produced using computed tomography (CT) or structured light reconstruction on phantom or ex vivo models. We present a stereo-endoscopic reconstruction validation dataset based on cone-beam CT (SERV-CT). Two ex vivo small porcine full torso cadavers were placed within the view of the endoscope with both the endoscope and target anatomy visible in the CT scan. Subsequent orientation of the endoscope was manually aligned to match the stereoscopic view and benchmark disparities, depths and occlusions are calculated. The requirement of a CT scan limited the number of stereo pairs to 8 from each ex vivo sample. For the second sample an RGB surface was acquired to aid alignment of smooth, featureless surfaces. Repeated manual alignments showed an RMS disparity accuracy of around 2 pixels and a depth accuracy of about 2 mm. A simplified reference dataset is provided consisting of endoscope image pairs with corresponding calibration, disparities, depths and occlusions covering the majority of the endoscopic image and a range of tissue types, including smooth specular surfaces, as well as significant variation of depth. We assessed the performance of various stereo algorithms from online available repositories. There is a significant variation between algorithms, highlighting some of the challenges of surgical endoscopic images. The SERV-CT dataset provides an easy to use stereoscopic validation for surgical applications with smooth reference disparities and depths covering the majority of the endoscopic image. This complements existing resources well and we hope will aid the development of surgical endoscopic anatomical reconstruction algorithms

Intelligent frame selection for anatomic reconstruction from endoscopic video

Using endoscopic video, it is possible to perform 3D re-construction of the anatomy using the well known epipolar constraint between matched feature points. Through this constraint, it is possible to recover the translation and rota-tion between camera positions and thus reconstruct the 3D anatomy by triangulation. However, these motion estimates are not stable for small camera motions. In this work, we propose a covariance estimation scheme to select pairs of frames which give rise to stable motion estimates, i.e. min-imal variance with respect to pixel match error. We param-eterize the essential matrix using a minimal 5 parameter representation and estimate motion covariance based upon the estimated feature match variance. The proposed algo-rithm is applied to endoscopic video sequences recorded in porcine sinus passages in order to extract stable motion es-timates. 1

Towards Quantitative Endoscopy with Vision Intelligence

In this thesis, we work on topics related to quantitative endoscopy with vision-based intelligence. Specifically, our works revolve around the topic of video reconstruction in endoscopy, where many challenges exist, such as texture scarceness, illumination variation, multimodality, etc., and these prevent prior works from working effectively and robustly. To this end, we propose to combine the strength of expressivity of deep learning approaches and the rigorousness and accuracy of non-linear optimization algorithms to develop a series of methods to confront such challenges towards quantitative endoscopy. We first propose a retrospective sparse reconstruction method that can estimate a high-accuracy and density point cloud and high-completeness camera trajectory from a monocular endoscopic video with state-of-the-art performance. To enable this, replacing the role of a hand-crafted local descriptor, a deep image feature descriptor is developed to boost the feature matching performance in a typical sparse reconstruction algorithm. A retrospective surface reconstruction pipeline is then proposed to estimate a textured surface model from a monocular endoscopic video, where self-supervised depth and descriptor learning and surface fusion technique is involved. We show that the proposed method performs superior to a popular dense reconstruction method and the estimate reconstructions are in good agreement with the surface models obtained from CT scans. To align video-reconstructed surface models with pre-operative imaging such as CT, we introduce a global point cloud registration algorithm that is robust to resolution mismatch that often happens in such multi-modal scenarios. Specifically, a geometric feature descriptor is developed where a novel network normalization technique is used to help a 3D network produce more consistent and distinctive geometric features for samples with different resolutions. The proposed geometric descriptor achieves state-of-the-art performance, based on our evaluation. Last but not least, a real-time SLAM system that estimates a surface geometry and camera trajectory from a monocular endoscopic video is developed, where deep representations for geometry and appearance and non-linear factor graph optimization are used. We show that the proposed SLAM system performs favorably compared with a state-of-the-art feature-based SLAM system

Endoscopic Motion Estimation using Video and CT

Functional Endoscopic Sinus Surgery (FESS) is a surgical procedure that otolaryngologists have adopted to treat sinus diseases. Aiming for accurate treatments and less complications, surgeons are usually guided with an endoscopic navigation system when performing the surgery. The state-of-the-art navigation systems report a submillimeter positioning error. This significantly reduces intraopertive time and improves surgical outcomes. Navigating endoscope is similar to Visual Odometry (VO) or Simultaneous Localization and Mapping (SLAM), all of which require an estimation of camera poses and motions in an unknown environment. Feature-based methods and direct methods are two common approaches for VO and Visual SLAM for motion estimation, but both methods have drawbacks. Feature computation and feature extraction consume are usually not computationally effective, while direct methods suffer from local optima. One recent alternative is called Semi-Direct Method, or hybrid method, which overcomes the drawbacks by applying optimization that is used in direct method to the selected features. In this work, we introduce a novel endoscopic navigation system for FESS which uses both prescanned CT model and 2D endoscope video. The system is able to texture map the CT model in real time for visualization and refine the pose estimation of the endoscope from different prior estimates

Medical SLAM in an autonomous robotic system

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-operative morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilities by observing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted instruments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This thesis addresses the ambitious goal of achieving surgical autonomy, through the study of the anatomical environment by Initially studying the technology present and what is needed to analyze the scene: vision sensors. A novel endoscope for autonomous surgical task execution is presented in the first part of this thesis. Which combines a standard stereo camera with a depth sensor. This solution introduces several key advantages, such as the possibility of reconstructing the 3D at a greater distance than traditional endoscopes. Then the problem of hand-eye calibration is tackled, which unites the vision system and the robot in a single reference system. Increasing the accuracy in the surgical work plan. In the second part of the thesis the problem of the 3D reconstruction and the algorithms currently in use were addressed. In MIS, simultaneous localization and mapping (SLAM) can be used to localize the pose of the endoscopic camera and build ta 3D model of the tissue surface. Another key element for MIS is to have real-time knowledge of the pose of surgical tools with respect to the surgical camera and underlying anatomy. Starting from the ORB-SLAM algorithm we have modified the architecture to make it usable in an anatomical environment by adding the registration of the pre-operative information of the intervention to the map obtained from the SLAM. Once it has been proven that the slam algorithm is usable in an anatomical environment, it has been improved by adding semantic segmentation to be able to distinguish dynamic features from static ones. All the results in this thesis are validated on training setups, which mimics some of the challenges of real surgery and on setups that simulate the human body within Autonomous Robotic Surgery (ARS) and Smart Autonomous Robotic Assistant Surgeon (SARAS) projects

Medical SLAM in an autonomous robotic system

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-operative morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilities by observing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted instruments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This thesis addresses the ambitious goal of achieving surgical autonomy, through the study of the anatomical environment by Initially studying the technology present and what is needed to analyze the scene: vision sensors. A novel endoscope for autonomous surgical task execution is presented in the first part of this thesis. Which combines a standard stereo camera with a depth sensor. This solution introduces several key advantages, such as the possibility of reconstructing the 3D at a greater distance than traditional endoscopes. Then the problem of hand-eye calibration is tackled, which unites the vision system and the robot in a single reference system. Increasing the accuracy in the surgical work plan. In the second part of the thesis the problem of the 3D reconstruction and the algorithms currently in use were addressed. In MIS, simultaneous localization and mapping (SLAM) can be used to localize the pose of the endoscopic camera and build ta 3D model of the tissue surface. Another key element for MIS is to have real-time knowledge of the pose of surgical tools with respect to the surgical camera and underlying anatomy. Starting from the ORB-SLAM algorithm we have modified the architecture to make it usable in an anatomical environment by adding the registration of the pre-operative information of the intervention to the map obtained from the SLAM. Once it has been proven that the slam algorithm is usable in an anatomical environment, it has been improved by adding semantic segmentation to be able to distinguish dynamic features from static ones. All the results in this thesis are validated on training setups, which mimics some of the challenges of real surgery and on setups that simulate the human body within Autonomous Robotic Surgery (ARS) and Smart Autonomous Robotic Assistant Surgeon (SARAS) projects