Visual SLAM for Measurement and Augmented Reality in Laparoscopic Surgery

In spite of the great advances in laparoscopic surgery, this type of surgery still shows some difficulties during its realization, mainly caused by its complex maneuvers and, above all, by the loss of the depth perception. Unlike classical open surgery --laparotomy-- where surgeons have direct contact with organs and a complete 3D perception, laparoscopy is carried out by means of specialized instruments, and a monocular camera (laparoscope) in which the 3D scene is projected into a 2D plane --image. The main goal of this thesis is to face with this loss of depth perception by making use of Simultaneous Localization and Mapping (SLAM) algorithms developed in the fields of robotics and computer vision during the last years. These algorithms allow to localize, in real time (25 $\thicksim$ 30 frames per second), a camera that moves freely inside an unknown rigid environment while, at the same time, they build a map of this environment by exploiting images gathered by that camera. These algorithms have been extensively validated both in man-made environments (buildings, rooms, ...) and in outdoor environments, showing robustness to occlusions, sudden camera motions, or clutter. This thesis tries to extend the use of these algorithms to laparoscopic surgery. Due to the intrinsic nature of internal body images (they suffer from deformations, specularities, variable illumination conditions, limited movements, ...), applying this type of algorithms to laparoscopy supposes a real challenge. Knowing the camera (laparoscope) location with respect to the scene (abdominal cavity) and the 3D map of that scene opens new interesting possibilities inside the surgical field. This knowledge enables to do augmented reality annotations directly on the laparoscopic images (e.g. alignment of preoperative 3D CT models); intracavity 3D distance measurements; or photorealistic 3D reconstructions of the abdominal cavity recovering synthetically the lost depth. These new facilities provide security and rapidity to surgical procedures without disturbing the classical procedure workflow. Hence, these tools are available inside the surgeon's armory, being the surgeon who decides to use them or not. Additionally, knowledge of the camera location with respect to the patient's abdominal cavity is fundamental for future development of robots that can operate automatically since, knowing this location, the robot will be able to localize other tools controlled by itself with respect to the patient. In detail, the contributions of this thesis are: - To demonstrate the feasibility of applying SLAM algorithms to laparoscopy showing experimentally that using robust data association is a must. - To robustify one of these algorithms, in particular the monocular EKF-SLAM algorithm, by adapting a relocalization system and improving data association with a robust matching algorithm. - To develop of a robust matching method (1-Point RANSAC algorithm). - To develop a new surgical procedure to ease the use of visual SLAM in laparoscopy. - To make an extensive validation of the robust EKF-SLAM (EKF + relocalization + 1-Point RANSAC) obtaining millimetric errors and working in real time both on simulation and real human surgeries. The selected surgery has been the ventral hernia repair. - To demonstrate the potential of these algorithms in laparoscopy: they recover synthetically the depth of the operative field which is lost by using monocular laparoscopes, enable the insertion of augmented reality annotations, and allow to perform distance measurements using only a laparoscopic tool (to define the real scale) and laparoscopic images. - To make a clinical validation showing that these algorithms allow to shorten surgical times of operations and provide more security to the surgical procedures

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

Monocular slam for deformable scenarios.

El problema de localizar la posición de un sensor en un mapa incierto que se estima simultáneamente se conoce como Localización y Mapeo Simultáneo --SLAM--. Es un problema desafiante comparable al paradigma del huevo y la gallina. Para ubicar el sensor necesitamos conocer el mapa, pero para construir el mapa, necesitamos la posición del sensor. Cuando se utiliza un sensor visual, por ejemplo, una cámara, se denomina Visual SLAM o VSLAM. Los sensores visuales para SLAM se dividen entre los que proporcionan información de profundidad (por ejemplo, cámaras RGB-D o equipos estéreo) y los que no (por ejemplo, cámaras monoculares o cámaras de eventos). En esta tesis hemos centrado nuestra investigación en SLAM con cámaras monoculares.Debido a la falta de percepción de profundidad, el SLAM monocular es intrínsecamente más duro en comparación con el SLAM con sensores de profundidad. Los trabajos estado del arte en VSLAM monocular han asumido normalmente que la escena permanece rígida durante toda la secuencia, lo que es una suposición factible para entornos industriales y urbanos. El supuesto de rigidez aporta las restricciones suficientes al problema y permite reconstruir un mapa fiable tras procesar varias imágenes. En los últimos años, el interés por el SLAM ha llegado a las áreas médicas donde los algoritmos SLAM podrían ayudar a orientar al cirujano o localizar la posición de un robot. Sin embargo, a diferencia de los escenarios industriales o urbanos, en secuencias dentro del cuerpo, todo puede deformarse eventualmente y la suposición de rigidez acaba siendo inválida en la práctica, y por extensión, también los algoritmos de SLAM monoculares. Por lo tanto, nuestro objetivo es ampliar los límites de los algoritmos de SLAM y concebir el primer sistema SLAM monocular capaz de hacer frente a la deformación de la escena.Los sistemas de SLAM actuales calculan la posición de la cámara y la estructura del mapa en dos subprocesos concurrentes: la localización y el mapeo. La localización se encarga de procesar cada imagen para ubicar el sensor de forma continua, en cambio el mapeo se encarga de construir el mapa de la escena. Nosotros hemos adoptado esta estructura y concebimos tanto la localización deformable como el mapeo deformable ahora capaces de recuperar la escena incluso con deformación.Nuestra primera contribución es la localización deformable. La localización deformable utiliza la estructura del mapa para recuperar la pose de la cámara con una única imagen. Simultáneamente, a medida que el mapa se deforma durante la secuencia, también recupera la deformación del mapa para cada fotograma. Hemos propuesto dos familias de localización deformable. En el primer algoritmo de localización deformable, asumimos que todos los puntos están embebidos en una superficie denominada plantilla. Podemos recuperar la deformación de la superficie gracias a un modelo de deformación global que permite estimar la deformación más probable del objeto. Con nuestro segundo algoritmo de localización deformable, demostramos que es posible recuperar la deformación del mapa sin un modelo de deformación global, representando el mapa como surfels individuales. Nuestros resultados experimentales mostraron que, recuperando la deformación del mapa, ambos métodos superan tanto en robustez como en precisión a los métodos rígidos.Nuestra segunda contribución es la concepción del mapeo deformable. Es el back-end del algoritmo SLAM y procesa un lote de imágenes para recuperar la estructura del mapa para todas las imágenes y hacer crecer el mapa ensamblando las observaciones parciales del mismo. Tanto la localización deformable como el mapeo que se ejecutan en paralelo y juntos ensamblan el primer SLAM monocular deformable: \emph{DefSLAM}. Una evaluación ampliada de nuestro método demostró, tanto en secuencias controladas por laboratorio como en secuencias médicas, que nuestro método procesa con éxito secuencias en las que falla el sistema monocular SLAM actual.Nuestra tercera contribución son dos métodos para explotar la información fotométrica en SLAM monocular deformable. Por un lado, SD-DefSLAM que aprovecha el emparejamiento semi-directo para obtener un emparejamiento mucho más fiable de los puntos del mapa en las nuevas imágenes, como consecuencia, se demostró que es más robusto y estable en secuencias médicas. Por otro lado, proponemos un método de Localización Deformable Directa y Dispersa en el que usamos un error fotométrico directo para rastrear la deformación de un mapa modelado como un conjunto de surfels 3D desconectados. Podemos recuperar la deformación de múltiples superficies desconectadas, deformaciones no isométricas o superficies con una topología cambiante.<br /

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

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