3D mapping and path planning from range data

This thesis reports research on mapping, terrain classification and path planning. These are classical problems in robotics, typically studied independently, and here we link such problems by framing them within a common proprioceptive modality, that of three-dimensional laser range scanning. The ultimate goal is to deliver navigation paths for challenging mobile robotics scenarios. For this reason we also deliver safe traversable regions from a previously computed globally consistent map. We first examine the problem of registering dense point clouds acquired at different instances in time. We contribute with a novel range registration mechanism for pairs of 3D range scans using point-to-point and point-to-line correspondences in a hierarchical correspondence search strategy. For the minimization we adopt a metric that takes into account not only the distance between corresponding points, but also the orientation of their relative reference frames. We also propose FaMSA, a fast technique for multi-scan point cloud alignment that takes advantage of the asserted point correspondences during sequential scan matching, using the point match history to speed up the computation of new scan matches. To properly propagate the model of the sensor noise and the scan matching, we employ first order error propagation, and to correct the error accumulation from local data alignment, we consider the probabilistic alignment of 3D point clouds using a delayed-state Extended Information Filter (EIF). In this thesis we adapt the Pose SLAM algorithm to the case of 3D range mapping, Pose SLAM is the variant of SLAM where only the robot trajectory is estimated and where sensor data is solely used to produce relative constraints between robot poses. These dense mapping techniques are tested in several scenarios acquired with our 3D sensors, producing impressively rich 3D environment models. The computed maps are then processed to identify traversable regions and to plan navigation sequences. In this thesis we present a pair of methods to attain high-level off-line classification of traversable areas, in which training data is acquired automatically from navigation sequences. Traversable features came from the robot footprint samples during manual robot motion, allowing us to capture terrain constrains not easy to model. Using only some of the traversed areas as positive training samples, our algorithms are tested in real scenarios to find the rest of the traversable terrain, and are compared with a naive parametric and some variants of the Support Vector Machine. Later, we contribute with a path planner that guarantees reachability at a desired robot pose with significantly lower computation time than competing alternatives. To search for the best path, our planner incrementally builds a tree using the A* algorithm, it includes a hybrid cost policy to efficiently expand the search tree, combining random sampling from the continuous space of kinematically feasible motion commands with a cost to goal metric that also takes into account the vehicle nonholonomic constraints. The planer also allows for node rewiring, and to speed up node search, our method includes heuristics that penalize node expansion near obstacles, and that limit the number of explored nodes. The method book-keeps visited cells in the configuration space, and disallows node expansion at those configurations in the first full iteration of the algorithm. We validate the proposed methods with experiments in extensive real scenarios from different very complex 3D outdoors environments, and compare it with other techniques such as the A*, RRT and RRT* algorithms.Esta tesis reporta investigación sobre el mapeo, clasificación de terreno y planificación de trayectorias. Estos son problemas clásicos en robótica los cuales generalmente se estudian de forma independiente, aquí se vinculan enmarcandolos con una modalidad propioceptiva común: un láser de rango 3D. El objetivo final es ofrecer trayectorias de navegación para escenarios complejos en el marco de la robótica móvil. Por esta razón también entregamos regiones transitables en un mapa global consistente calculado previamente. Primero examinamos el problema de registro de nubes de puntos adquiridas en diferentes instancias de tiempo. Contribuimos con un novedoso mecanismo de registro de pares de imagenes de rango 3D usando correspondencias punto a punto y punto a línea, en una estrategia de búsqueda de correspondencias jerárquica. Para la minimización optamos por una metrica que considera no sólo la distancia entre puntos, sino también la orientación de los marcos de referencia relativos. También proponemos FAMSA, una técnica para el registro rápido simultaneo de multiples nubes de puntos, la cual aprovecha las correspondencias de puntos obtenidas durante el registro secuencial, usando inicialmente la historia de correspondencias para acelerar el cálculo de las correspondecias en los nuevos registros de imagenes. Para propagar adecuadamente el modelo del ruido del sensor y del registro de imagenes, empleamos la propagación de error de primer orden, y para corregir el error acumulado del registro local, consideramos la alineación probabilística de nubes de puntos 3D utilizando un Filtro Extendido de Información de estados retrasados. En esta tesis adaptamos el algóritmo Pose SLAM para el caso de mapas con imagenes de rango 3D, Pose SLAM es la variante de SLAM donde solamente se estima la trayectoria del robot, usando los datos del sensor como restricciones relativas entre las poses robot. Estas técnicas de mapeo se prueban en varios escenarios adquiridos con nuestros sensores 3D produciendo modelos 3D impresionantes. Los mapas obtenidos se procesan para identificar regiones navegables y para planificar secuencias de navegación. Presentamos un par de métodos para lograr la clasificación de zonas transitables fuera de línea. Los datos de entrenamiento se adquieren de forma automática usando secuencias de navegación obtenidas manualmente. Las características transitables se captan de las huella de la trayectoria del robot, lo cual permite capturar restricciones del terreno difíciles de modelar. Con sólo algunas de las zonas transitables como muestras de entrenamiento positivo, nuestros algoritmos se prueban en escenarios reales para encontrar el resto del terreno transitable. Los algoritmos se comparan con algunas variantes de la máquina de soporte de vectores (SVM) y una parametrizacion ingenua. También, contribuimos con un planificador de trayectorias que garantiza llegar a una posicion deseada del robot en significante menor tiempo de cálculo a otras alternativas. Para buscar el mejor camino, nuestro planificador emplea un arbol de busqueda incremental basado en el algoritmo A*. Incluimos una póliza de coste híbrido para crecer de manera eficiente el árbol, combinando el muestro aleatorio del espacio continuo de comandos cinemáticos del robot con una métrica de coste al objetivo que también concidera las cinemática del robot. El planificador además permite reconectado de nodos, y, para acelerar la búsqueda de nodos, se incluye una heurística que penaliza la expansión de nodos cerca de los obstáculos, que limita el número de nodos explorados. El método conoce las céldas que ha visitado del espacio de configuraciones, evitando la expansión de nodos en configuraciones que han sido vistadas en la primera iteración completa del algoritmo. Los métodos propuestos se validán con amplios experimentos con escenarios reales en diferentes entornos exteriores, asi como su comparación con otras técnicas como los algoritmos A*, RRT y RRT*.Postprint (published version

Learning-based depth and pose prediction for 3D scene reconstruction in endoscopy

Colorectal cancer is the third most common cancer worldwide. Early detection and treatment of pre-cancerous tissue during colonoscopy is critical to improving prognosis. However, navigating within the colon and inspecting the endoluminal tissue comprehensively are challenging, and success in both varies based on the endoscopist's skill and experience. Computer-assisted interventions in colonoscopy show much promise in improving navigation and inspection. For instance, 3D reconstruction of the colon during colonoscopy could promote more thorough examinations and increase adenoma detection rates which are associated with improved survival rates. Given the stakes, this thesis seeks to advance the state of research from feature-based traditional methods closer to a data-driven 3D reconstruction pipeline for colonoscopy. More specifically, this thesis explores different methods that improve subtasks of learning-based 3D reconstruction. The main tasks are depth prediction and camera pose estimation. As training data is unavailable, the author, together with her co-authors, proposes and publishes several synthetic datasets and promotes domain adaptation models to improve applicability to real data. We show, through extensive experiments, that our depth prediction methods produce more robust results than previous work. Our pose estimation network trained on our new synthetic data outperforms self-supervised methods on real sequences. Our box embeddings allow us to interpret the geometric relationship and scale difference between two images of the same surface without the need for feature matches that are often unobtainable in surgical scenes. Together, the methods introduced in this thesis help work towards a complete, data-driven 3D reconstruction pipeline for endoscopy

Contribuciones a la estimación de la pose de la cámara en aplicaciones industriales de realidad aumentada

Augmented Reality (AR) aims to complement the visual perception of the user environment superimposing virtual elements. The main challenge of this technology is to combine the virtual and real world in a precise and natural way. To carry out this goal, estimating the user position and orientation in both worlds at all times is a crucial task. Currently, there are numerous techniques and algorithms developed for camera pose estimation. However, the use of synthetic square markers has become the fastest, most robust and simplest solution in these cases. In this scope, a big number of marker detection systems have been developed. Nevertheless, most of them presents some limitations, (1) their unattractive and non-customizable visual appearance prevent their use in industrial products and (2) the detection rate is drastically reduced in presence of noise, blurring and occlusions. In this doctoral dissertation the above-mentioned limitations are addressed. In first place, a comparison has been made between the different marker detection systems currently available in the literature, emphasizing the limitations of each. Secondly, a novel approach to design, detect and track customized markers capable of easily adapting to the visual limitations of commercial products has been developed. In third place, a method that combines the detection of black and white square markers with keypoints and contours has been implemented to estimate the camera position in AR applications. The main motivation of this work is to offer a versatile alternative (based on contours and keypoints) in cases where, due to noise, blurring or occlusions, it is not possible to identify markers in the images. Finally, a method for reconstruction and semantic segmentation of 3D objects using square markers in photogrammetry processes has been presented.La Realidad Aumentada (AR) tiene como objetivo complementar la percepción visual del entorno circunstante al usuario mediante la superposición de elementos virtuales. El principal reto de dicha tecnología se basa en fusionar, de forma precisa y natural, el mundo virtual con el mundo real. Para llevar a cabo dicha tarea, es de vital importancia conocer en todo momento tanto la posición, así como la orientación del usuario en ambos mundos. Actualmente, existen un gran número de técnicas de estimación de pose. No obstante, el uso de marcadores sintéticos cuadrados se ha convertido en la solución más rápida, robusta y sencilla utilizada en estos casos. En este ámbito de estudio, existen un gran número de sistemas de detección de marcadores ampliamente extendidos. Sin embargo, su uso presenta ciertas limitaciones, (1) su aspecto visual, poco atractivo y nada customizable impiden su uso en ciertos productos industriales en donde la personalización comercial es un aspecto crucial y (2) la tasa de detección se ve duramente decrementada ante la presencia de ruido, desenfoques y oclusiones Esta tesis doctoral se ocupa de las limitaciones anteriormente mencionadas. En primer lugar, se ha realizado una comparativa entre los diferentes sistemas de detección de marcadores actualmente en uso, enfatizando las limitaciones de cada uno. En segundo lugar, se ha desarrollado un novedoso enfoque para diseñar, detectar y trackear marcadores personalizados capaces de adaptarse fácilmente a las limitaciones visuales de productos comerciales. En tercer lugar, se ha implementado un método que combina la detección de marcadores cuadrados blancos y negros con keypoints y contornos, para estimar de la posición de la cámara en aplicaciones AR. La principal motivación de este trabajo se basa en ofrecer una alternativa versátil (basada en contornos y keypoints) en aquellos casos donde, por motivos de ruido, desenfoques u oclusiones no sea posible identificar marcadores en las imágenes. Por último, se ha desarrollado un método de reconstrucción y segmentación semántica de objetos 3D utilizando marcadores cuadrados en procesos de fotogrametría

Influence of complex environments on LiDAR-Based robot navigation

La navigation sécuritaire et efficace des robots mobiles repose grandement sur l’utilisation des capteurs embarqués. L’un des capteurs qui est de plus en plus utilisé pour cette tâche est le Light Detection And Ranging (LiDAR). Bien que les recherches récentes montrent une amélioration des performances de navigation basée sur les LiDARs, faire face à des environnements non structurés complexes ou des conditions météorologiques difficiles reste problématique. Dans ce mémoire, nous présentons une analyse de l’influence de telles conditions sur la navigation basée sur les LiDARs. Notre première contribution est d’évaluer comment les LiDARs sont affectés par les flocons de neige durant les tempêtes de neige. Pour ce faire, nous créons un nouvel ensemble de données en faisant l’acquisition de données durant six précipitations de neige. Une analyse statistique de ces ensembles de données, nous caractérisons la sensibilité de chaque capteur et montrons que les mesures de capteurs peuvent être modélisées de manière probabilistique. Nous montrons aussi que les précipitations de neige ont peu d’influence au-delà de 10 m. Notre seconde contribution est d’évaluer l’impact de structures tridimensionnelles complexes présentes en forêt sur les performances d’un algorithme de reconnaissance d’endroits. Nous avons acquis des données dans un environnement extérieur structuré et en forêt, ce qui permet d’évaluer l’influence de ces derniers sur les performances de reconnaissance d’endroits. Notre hypothèse est que, plus deux balayages laser sont proches l’un de l’autre, plus la croyance que ceux-ci proviennent du même endroit sera élevée, mais modulé par le niveau de complexité de l’environnement. Nos expériences confirment que la forêt, avec ses réseaux de branches compliqués et son feuillage, produit plus de données aberrantes et induit une chute plus rapide des performances de reconnaissance en fonction de la distance. Notre conclusion finale est que, les environnements complexes étudiés influencent négativement les performances de navigation basée sur les LiDARs, ce qui devrait être considéré pour développer des algorithmes de navigation robustes.To ensure safe and efficient navigation, mobile robots heavily rely on their ability to use on-board sensors. One such sensor, increasingly used for robot navigation, is the Light Detection And Ranging (LiDAR). Although recent research showed improvement in LiDAR-based navigation, dealing with complex unstructured environments or difficult weather conditions remains problematic. In this thesis, we present an analysis of the influence of such challenging conditions on LiDAR-based navigation. Our first contribution is to evaluate how LiDARs are affected by snowflakes during snowstorms. To this end, we create a novel dataset by acquiring data during six snowfalls using four sensors simultaneously. Based on statistical analysis of this dataset, we characterized the sensitivity of each device and showed that sensor measurements can be modelled in a probabilistic manner. We also showed that falling snow has little impact beyond a range of 10 m. Our second contribution is to evaluate the impact of complex of three-dimensional structures, present in forests, on the performance of a LiDAR-based place recognition algorithm. We acquired data in structured outdoor environment and in forest, which allowed evaluating the impact of the environment on the place recognition performance. Our hypothesis was that the closer two scans are acquired from each other, the higher the belief that the scans originate from the same place will be, but modulated by the level of complexity of the environments. Our experiments confirmed that forests, with their intricate network of branches and foliage, produce more outliers and induce recognition performance to decrease more quickly with distance when compared with structured outdoor environment. Our conclusion is that falling snow conditions and forest environments negatively impact LiDAR-based navigation performance, which should be considered to develop robust navigation algorithms

AN AUTOMATED, DEEP LEARNING APPROACH TO SYSTEMATICALLY & SEQUENTIALLY DERIVE THREE-DIMENSIONAL KNEE KINEMATICS DIRECTLY FROM TWO-DIMENSIONAL FLUOROSCOPIC VIDEO

Total knee arthroplasty (TKA), also known as total knee replacement, is a surgical procedure to replace damaged parts of the knee joint with artificial components. It aims to relieve pain and improve knee function. TKA can improve knee kinematics and reduce pain, but it may also cause altered joint mechanics and complications. Proper patient selection, implant design, and surgical technique are important for successful outcomes. Kinematics analysis plays a vital role in TKA by evaluating knee joint movement and mechanics. It helps assess surgery success, guides implant and technique selection, informs implant design improvements, detects problems early, and improves patient outcomes. However, evaluating the kinematics of patients using conventional approaches presents significant challenges. The reliance on 3D CAD models limits applicability, as not all patients have access to such models. Moreover, the manual and time-consuming nature of the process makes it impractical for timely evaluations. Furthermore, the evaluation is confined to laboratory settings, limiting its feasibility in various locations. This study aims to address these limitations by introducing a new methodology for analyzing in vivo 3D kinematics using an automated deep learning approach. The proposed methodology involves several steps, starting with image segmentation of the femur and tibia using a robust deep learning approach. Subsequently, 3D reconstruction of the implants is performed, followed by automated registration. Finally, efficient knee kinematics modeling is conducted. The final kinematics results showed potential for reducing workload and increasing efficiency. The algorithms demonstrated high speed and accuracy, which could enable real-time TKA kinematics analysis in the operating room or clinical settings. Unlike previous studies that relied on sponsorships and limited patient samples, this algorithm allows the analysis of any patient, anywhere, and at any time, accommodating larger subject populations and complete fluoroscopic sequences. Although further improvements can be made, the study showcases the potential of machine learning to expand access to TKA analysis tools and advance biomedical engineering applications

Precision Monitoring for Disease Progression in Patients with Multiple Sclerosis: A Deep Learning Approach

Artificial intelligence has tremendous potential in a range of clinical applications. Leveraging recent advances in deep learning, the works in this thesis has generated a range of technologies for patients with Multiple Sclerosis (MS) that facilitate precision monitoring using routine MRI and clinical assessments; and contribute to realising the goal of personalised disease management. MS is a chronic inflammatory demyelinating disease of the central nervous system (CNS), characterised by focal demyelinating plaques in the brain and spinal cord; and progressive neurodegeneration. Despite success in cohort studies and clinical trials, the measurement of disease activity using conventional imaging biomarkers in real-world clinical practice is limited to qualitative assessment of lesion activity, which is time consuming and prone to human error. Quantitative measures, such as T2 lesion load, volumetric assessment of lesion activity and brain atrophy, are constrained by challenges associated with handling real-world data variances. In this thesis, DeepBVC was developed for robust brain atrophy assessment through imaging synthesis, while a lesion segmentation model was developed using a novel federated learning framework, Fed-CoT, to leverage large data collaborations. With existing quantitative brain structural analyses, this work has developed an effective deep learning analysis pipeline, which delivers a fully automated suite of MS-specific clinical imaging biomarkers to facilitate the precision monitoring of patients with MS and response to disease modifying therapy. The framework for individualised MRI-guided management in this thesis was complemented by a disease prognosis model, based on a Large Language Model, providing insights into the risks of clinical worsening over the subsequent 3 years. The value and performance of the MS biomarkers in this thesis are underpinned by extensive validation in real-world, multi-centre data from more than 1030 patients

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise