Segmentation of pelvic structures from preoperative images for surgical planning and guidance

Prostate cancer is one of the most frequently diagnosed malignancies globally and the second leading cause of cancer-related mortality in males in the developed world. In recent decades, many techniques have been proposed for prostate cancer diagnosis and treatment. With the development of imaging technologies such as CT and MRI, image-guided procedures have become increasingly important as a means to improve clinical outcomes. Analysis of the preoperative images and construction of 3D models prior to treatment would help doctors to better localize and visualize the structures of interest, plan the procedure, diagnose disease and guide the surgery or therapy. This requires efficient and robust medical image analysis and segmentation technologies to be developed. The thesis mainly focuses on the development of segmentation techniques in pelvic MRI for image-guided robotic-assisted laparoscopic radical prostatectomy and external-beam radiation therapy. A fully automated multi-atlas framework is proposed for bony pelvis segmentation in MRI, using the guidance of MRI AE-SDM. With the guidance of the AE-SDM, a multi-atlas segmentation algorithm is used to delineate the bony pelvis in a new \ac{MRI} where there is no CT available. The proposed technique outperforms state-of-the-art algorithms for MRI bony pelvis segmentation. With the SDM of pelvis and its segmented surface, an accurate 3D pelvimetry system is designed and implemented to measure a comprehensive set of pelvic geometric parameters for the examination of the relationship between these parameters and the difficulty of robotic-assisted laparoscopic radical prostatectomy. This system can be used in both manual and automated manner with a user-friendly interface. A fully automated and robust multi-atlas based segmentation has also been developed to delineate the prostate in diagnostic MR scans, which have large variation in both intensity and shape of prostate. Two image analysis techniques are proposed, including patch-based label fusion with local appearance-specific atlases and multi-atlas propagation via a manifold graph on a database of both labeled and unlabeled images when limited labeled atlases are available. The proposed techniques can achieve more robust and accurate segmentation results than other multi-atlas based methods. The seminal vesicles are also an interesting structure for therapy planning, particularly for external-beam radiation therapy. As existing methods fail for the very onerous task of segmenting the seminal vesicles, a multi-atlas learning framework via random decision forests with graph cuts refinement has further been proposed to solve this difficult problem. Motivated by the performance of this technique, I further extend the multi-atlas learning to segment the prostate fully automatically using multispectral (T1 and T2-weighted) MR images via hybrid \ac{RF} classifiers and a multi-image graph cuts technique. The proposed method compares favorably to the previously proposed multi-atlas based prostate segmentation. The work in this thesis covers different techniques for pelvic image segmentation in MRI. These techniques have been continually developed and refined, and their application to different specific problems shows ever more promising results.Open Acces

Holistic interpretation of visual data based on topology:semantic segmentation of architectural facades

The work presented in this dissertation is a step towards effectively incorporating contextual knowledge in the task of semantic segmentation. To date, the use of context has been confined to the genre of the scene with a few exceptions in the field. Research has been directed towards enhancing appearance descriptors. While this is unarguably important, recent studies show that computer vision has reached a near-human level of performance in relying on these descriptors when objects have stable distinctive surface properties and in proper imaging conditions. When these conditions are not met, humans exploit their knowledge about the intrinsic geometric layout of the scene to make local decisions. Computer vision lags behind when it comes to this asset. For this reason, we aim to bridge the gap by presenting algorithms for semantic segmentation of building facades making use of scene topological aspects. We provide a classification scheme to carry out segmentation and recognition simultaneously.The algorithm is able to solve a single optimization function and yield a semantic interpretation of facades, relying on the modeling power of probabilistic graphs and efficient discrete combinatorial optimization tools. We tackle the same problem of semantic facade segmentation with the neural network approach.We attain accuracy figures that are on-par with the state-of-the-art in a fully automated pipeline.Starting from pixelwise classifications obtained via Convolutional Neural Networks (CNN). These are then structurally validated through a cascade of Restricted Boltzmann Machines (RBM) and Multi-Layer Perceptron (MLP) that regenerates the most likely layout. In the domain of architectural modeling, there is geometric multi-model fitting. We introduce a novel guided sampling algorithm based on Minimum Spanning Trees (MST), which surpasses other propagation techniques in terms of robustness to noise. We make a number of additional contributions such as measure of model deviation which captures variations among fitted models

Generalizable deep learning based medical image segmentation

Deep learning is revolutionizing medical image analysis and interpretation. However, its real-world deployment is often hindered by the poor generalization to unseen domains (new imaging modalities and protocols). This lack of generalization ability is further exacerbated by the scarcity of labeled datasets for training: Data collection and annotation can be prohibitively expensive in terms of labor and costs because label quality heavily dependents on the expertise of radiologists. Additionally, unreliable predictions caused by poor model generalization pose safety risks to clinical downstream applications. To mitigate labeling requirements, we investigate and develop a series of techniques to strengthen the generalization ability and the data efficiency of deep medical image computing models. We further improve model accountability and identify unreliable predictions made on out-of-domain data, by designing probability calibration techniques. In the first and the second part of thesis, we discuss two types of problems for handling unexpected domains: unsupervised domain adaptation and single-source domain generalization. For domain adaptation we present a data-efficient technique that adapts a segmentation model trained on a labeled source domain (e.g., MRI) to an unlabeled target domain (e.g., CT), using a small number of unlabeled training images from the target domain. For domain generalization, we focus on both image reconstruction and segmentation. For image reconstruction, we design a simple and effective domain generalization technique for cross-domain MRI reconstruction, by reusing image representations learned from natural image datasets. For image segmentation, we perform causal analysis of the challenging cross-domain image segmentation problem. Guided by this causal analysis we propose an effective data-augmentation-based generalization technique for single-source domains. The proposed method outperforms existing approaches on a large variety of cross-domain image segmentation scenarios. In the third part of the thesis, we present a novel self-supervised method for learning generic image representations that can be used to analyze unexpected objects of interest. The proposed method is designed together with a novel few-shot image segmentation framework that can segment unseen objects of interest by taking only a few labeled examples as references. Superior flexibility over conventional fully-supervised models is demonstrated by our few-shot framework: it does not require any fine-tuning on novel objects of interest. We further build a publicly available comprehensive evaluation environment for few-shot medical image segmentation. In the fourth part of the thesis, we present a novel probability calibration model. To ensure safety in clinical settings, a deep model is expected to be able to alert human radiologists if it has low confidence, especially when confronted with out-of-domain data. To this end we present a plug-and-play model to calibrate prediction probabilities on out-of-domain data. It aligns the prediction probability in line with the actual accuracy on the test data. We evaluate our method on both artifact-corrupted images and images from an unforeseen MRI scanning protocol. Our method demonstrates improved calibration accuracy compared with the state-of-the-art method. Finally, we summarize the major contributions and limitations of our works. We also suggest future research directions that will benefit from the works in this thesis.Open Acces

Leveraging Supervoxels for Medical Image Volume Segmentation With Limited Supervision

The majority of existing methods for machine learning-based medical image segmentation are supervised models that require large amounts of fully annotated images. These types of datasets are typically not available in the medical domain and are difficult and expensive to generate. A wide-spread use of machine learning based models for medical image segmentation therefore requires the development of data-efficient algorithms that only require limited supervision. To address these challenges, this thesis presents new machine learning methodology for unsupervised lung tumor segmentation and few-shot learning based organ segmentation. When working in the limited supervision paradigm, exploiting the available information in the data is key. The methodology developed in this thesis leverages automatically generated supervoxels in various ways to exploit the structural information in the images. The work on unsupervised tumor segmentation explores the opportunity of performing clustering on a population-level in order to provide the algorithm with as much information as possible. To facilitate this population-level across-patient clustering, supervoxel representations are exploited to reduce the number of samples, and thereby the computational cost. In the work on few-shot learning-based organ segmentation, supervoxels are used to generate pseudo-labels for self-supervised training. Further, to obtain a model that is robust to the typically large and inhomogeneous background class, a novel anomaly detection-inspired classifier is proposed to ease the modelling of the background. To encourage the resulting segmentation maps to respect edges defined in the input space, a supervoxel-informed feature refinement module is proposed to refine the embedded feature vectors during inference. Finally, to improve trustworthiness, an architecture-agnostic mechanism to estimate model uncertainty in few-shot segmentation is developed. Results demonstrate that supervoxels are versatile tools for leveraging structural information in medical data when training segmentation models with limited supervision

Combining Features and Semantics for Low-level Computer Vision

Visual perception of depth and motion plays a significant role in understanding and navigating the environment. Reconstructing outdoor scenes in 3D and estimating the motion from video cameras are of utmost importance for applications like autonomous driving. The corresponding problems in computer vision have witnessed tremendous progress over the last decades, yet some aspects still remain challenging today. Striking examples are reflecting and textureless surfaces or large motions which cannot be easily recovered using traditional local methods. Further challenges include occlusions, large distortions and difficult lighting conditions. In this thesis, we propose to overcome these challenges by modeling non-local interactions leveraging semantics and contextual information. Firstly, for binocular stereo estimation, we propose to regularize over larger areas on the image using object-category specific disparity proposals which we sample using inverse graphics techniques based on a sparse disparity estimate and a semantic segmentation of the image. The disparity proposals encode the fact that objects of certain categories are not arbitrarily shaped but typically exhibit regular structures. We integrate them as non-local regularizer for the challenging object class 'car' into a superpixel-based graphical model and demonstrate its benefits especially in reflective regions. Secondly, for 3D reconstruction, we leverage the fact that the larger the reconstructed area, the more likely objects of similar type and shape will occur in the scene. This is particularly true for outdoor scenes where buildings and vehicles often suffer from missing texture or reflections, but share similarity in 3D shape. We take advantage of this shape similarity by localizing objects using detectors and jointly reconstructing them while learning a volumetric model of their shape. This allows to reduce noise while completing missing surfaces as objects of similar shape benefit from all observations for the respective category. Evaluations with respect to LIDAR ground-truth on a novel challenging suburban dataset show the advantages of modeling structural dependencies between objects. Finally, motivated by the success of deep learning techniques in matching problems, we present a method for learning context-aware features for solving optical flow using discrete optimization. Towards this goal, we present an efficient way of training a context network with a large receptive field size on top of a local network using dilated convolutions on patches. We perform feature matching by comparing each pixel in the reference image to every pixel in the target image, utilizing fast GPU matrix multiplication. The matching cost volume from the network's output forms the data term for discrete MAP inference in a pairwise Markov random field. Extensive evaluations reveal the importance of context for feature matching.Die visuelle Wahrnehmung von Tiefe und Bewegung spielt eine wichtige Rolle bei dem Verständnis und der Navigation in unserer Umwelt. Die 3D Rekonstruktion von Szenen im Freien und die Schätzung der Bewegung von Videokameras sind von größter Bedeutung für Anwendungen, wie das autonome Fahren. Die Erforschung der entsprechenden Probleme des maschinellen Sehens hat in den letzten Jahrzehnten enorme Fortschritte gemacht, jedoch bleiben einige Aspekte heute noch ungelöst. Beispiele hierfür sind reflektierende und texturlose Oberflächen oder große Bewegungen, bei denen herkömmliche lokale Methoden häufig scheitern. Weitere Herausforderungen sind niedrige Bildraten, Verdeckungen, große Verzerrungen und schwierige Lichtverhältnisse. In dieser Arbeit schlagen wir vor nicht-lokale Interaktionen zu modellieren, die semantische und kontextbezogene Informationen nutzen, um diese Herausforderungen zu meistern. Für die binokulare Stereo Schätzung schlagen wir zuallererst vor zusammenhängende Bereiche mit objektklassen-spezifischen Disparitäts Vorschlägen zu regularisieren, die wir mit inversen Grafik Techniken auf der Grundlage einer spärlichen Disparitätsschätzung und semantischen Segmentierung des Bildes erhalten. Die Disparitäts Vorschläge kodieren die Tatsache, dass die Gegenstände bestimmter Kategorien nicht willkürlich geformt sind, sondern typischerweise regelmäßige Strukturen aufweisen. Wir integrieren sie für die komplexe Objektklasse 'Auto' in Form eines nicht-lokalen Regularisierungsterm in ein Superpixel-basiertes grafisches Modell und zeigen die Vorteile vor allem in reflektierenden Bereichen. Zweitens nutzen wir für die 3D-Rekonstruktion die Tatsache, dass mit der Größe der rekonstruierten Fläche auch die Wahrscheinlichkeit steigt, Objekte von ähnlicher Art und Form in der Szene zu enthalten. Dies gilt besonders für Szenen im Freien, in denen Gebäude und Fahrzeuge oft vorkommen, die unter fehlender Textur oder Reflexionen leiden aber ähnlichkeit in der Form aufweisen. Wir nutzen diese ähnlichkeiten zur Lokalisierung von Objekten mit Detektoren und zur gemeinsamen Rekonstruktion indem ein volumetrisches Modell ihrer Form erlernt wird. Dies ermöglicht auftretendes Rauschen zu reduzieren, während fehlende Flächen vervollständigt werden, da Objekte ähnlicher Form von allen Beobachtungen der jeweiligen Kategorie profitieren. Die Evaluierung auf einem neuen, herausfordernden vorstädtischen Datensatz in Anbetracht von LIDAR-Entfernungsdaten zeigt die Vorteile der Modellierung von strukturellen Abhängigkeiten zwischen Objekten. Zuletzt, motiviert durch den Erfolg von Deep Learning Techniken bei der Mustererkennung, präsentieren wir eine Methode zum Erlernen von kontextbezogenen Merkmalen zur Lösung des optischen Flusses mittels diskreter Optimierung. Dazu stellen wir eine effiziente Methode vor um zusätzlich zu einem Lokalen Netzwerk ein Kontext-Netzwerk zu erlernen, das mit Hilfe von erweiterter Faltung auf Patches ein großes rezeptives Feld besitzt. Für das Feature Matching vergleichen wir mit schnellen GPU-Matrixmultiplikation jedes Pixel im Referenzbild mit jedem Pixel im Zielbild. Das aus dem Netzwerk resultierende Matching Kostenvolumen bildet den Datenterm für eine diskrete MAP Inferenz in einem paarweisen Markov Random Field. Eine umfangreiche Evaluierung zeigt die Relevanz des Kontextes für das Feature Matching

Multigranularity Representations for Human Inter-Actions: Pose, Motion and Intention

Tracking people and their body pose in videos is a central problem in computer vision. Standard tracking representations reason about temporal coherence of detected people and body parts. They have difficulty tracking targets under partial occlusions or rare body poses, where detectors often fail, since the number of training examples is often too small to deal with the exponential variability of such configurations. We propose tracking representations that track and segment people and their body pose in videos by exploiting information at multiple detection and segmentation granularities when available, whole body, parts or point trajectories. Detections and motion estimates provide contradictory information in case of false alarm detections or leaking motion affinities. We consolidate contradictory information via graph steering, an algorithm for simultaneous detection and co-clustering in a two-granularity graph of motion trajectories and detections, that corrects motion leakage between correctly detected objects, while being robust to false alarms or spatially inaccurate detections. We first present a motion segmentation framework that exploits long range motion of point trajectories and large spatial support of image regions. We show resulting video segments adapt to targets under partial occlusions and deformations. Second, we augment motion-based representations with object detection for dealing with motion leakage. We demonstrate how to combine dense optical flow trajectory affinities with repulsions from confident detections to reach a global consensus of detection and tracking in crowded scenes. Third, we study human motion and pose estimation. We segment hard to detect, fast moving body limbs from their surrounding clutter and match them against pose exemplars to detect body pose under fast motion. We employ on-the-fly human body kinematics to improve tracking of body joints under wide deformations. We use motion segmentability of body parts for re-ranking a set of body joint candidate trajectories and jointly infer multi-frame body pose and video segmentation. We show empirically that such multi-granularity tracking representation is worthwhile, obtaining significantly more accurate multi-object tracking and detailed body pose estimation in popular datasets

Segmentation multi-vues d'objet

There has been a growing interest for multi-camera systems and many interesting works have tried to tackle computer vision problems in this particular configuration. The general objective is to propose new multi-view oriented methods instead of applying limited monocular approaches independently for each viewpoint. The work in this thesis is an attempt to have a better understanding of the multi-view object segmentation problem and to propose an alternative approach making maximum use of the available information from different viewpoints. Multiple view segmentation consists in segmenting objects simultaneously in several views. Classic monocular segmentation approaches reason on a single image and do not benefit from the presence of several viewpoints. A key issue in that respect is to ensure propagation of segmentation information between views while minimizing complexity and computational cost. In this work, we first investigate the idea that examining measurements at the projections of a sparse set of 3D points is sufficient to achieve this goal. The proposed algorithm softly assigns each of these 3D samples to the scene background if it projects on the background region in at least one view, or to the foreground if it projects on foreground region in all views. A complete probabilistic framework is proposed to estimate foreground/background color models and the method is tested on various datasets from state of the art. Two different extensions of the sparse 3D sampling segmentation framework are proposed in two scenarios. In the first, we show the flexibility of the sparse sampling framework, by using variational inference to integrate Gaussian mixture models as appearance models. In the second scenario, we propose a study of how to incorporate depth measurements in multi-view segmentation. We present a quantitative evaluation, showing that typical color-based segmentation robustness issues due to color-space ambiguity between foreground and background, can be at least partially mitigated by using depth, and that multi-view color depth segmentation also improves over monocular color depth segmentation strategies. The various tests also showed the limitations of the proposed 3D sparse sampling approach which was the motivation to propose a new method based on a richer description of image regions using superpixels. This model, that expresses more subtle relationships of the problem trough a graph construction linking superpixels and 3D samples, is one of the contributions of this work. In this new framework, time related information is also integrated. With static views, results compete with state of the art methods but they are achieved with significantly fewer viewpoints. Results on videos demonstrate the benefit of segmentation propagation through geometric and temporal cues. Finally, the last part of the thesis explores the possibilities of tracking in uncalibrated multi-view scenarios. A summary of existing methods in this field is presented, in both mono-camera and multi-camera scenarios. We investigate the potential of using self-similarity matrices to describe and compare motion in the context of multi-view tracking.L'utilisation de systèmes multi-caméras est de plus en plus populaire et il y a un intérêt croissant à résoudre les problèmes de vision par ordinateur dans ce contexte particulier. L'objectif étant de ne pas se limiter à l'application des méthodes monoculaires mais de proposer de nouvelles approches intrinsèquement orientées vers les systèmes multi-caméras. Le travail de cette thèse a pour objectif une meilleure compréhension du problème de segmentation multi-vues, pour proposer une nouvelle approche qui tire meilleur parti de la redondance d'information inhérente à l'utilisation de plusieurs points de vue. La segmentation multi-vues est l'identification de l'objet observé simultanément dans plusieurs caméras et sa séparation de l'arrière-plan. Les approches monoculaires classiques raisonnent sur chaque image de manière indépendante et ne bénéficient pas de la présence de plusieurs points de vue. Une question clé de la segmentation multi-vues réside dans la propagation d'information sur la segmentation entres les images tout en minimisant la complexité et le coût en calcul. Dans ce travail, nous investiguons en premier lieu l'utilisation d'un ensemble épars d'échantillons de points 3D. L'algorithme proposé classe chaque point comme "vide" s'il se projette sur une région du fond et "occupé" s'il se projette sur une région avant-plan dans toutes les vues. Un modèle probabiliste est proposé pour estimer les modèles de couleur de l'avant-plan et de l'arrière-plan, que nous testons sur plusieurs jeux de données de l'état de l'art. Deux extensions du modèle sont proposées. Dans la première, nous montrons la flexibilité de la méthode proposée en intégrant les mélanges de Gaussiennes comme modèles d'apparence. Cette intégration est possible grâce à l'utilisation de l'inférence variationelle. Dans la seconde, nous montrons que le modèle bayésien basé sur les échantillons 3D peut aussi être utilisé si des mesures de profondeur sont présentes. Les résultats de l'évaluation montrent que les problèmes de robustesse, typiquement causés par les ambigüités couleurs entre fond et forme, peuvent être au moins partiellement résolus en utilisant cette information de profondeur. A noter aussi qu'une approche multi-vues reste meilleure qu'une méthode monoculaire utilisant l'information de profondeur. Les différents tests montrent aussi les limitations de la méthode basée sur un échantillonnage éparse. Cela a montré la nécessité de proposer un modèle reposant sur une description plus riche de l'apparence dans les images, en particulier en utilisant les superpixels. L'une des contributions de ce travail est une meilleure modélisation des contraintes grâce à un schéma par coupure de graphes liant les régions d'images aux échantillons 3D. Dans le cas statique, les résultats obtenus rivalisent avec ceux de l'état de l'art mais sont obtenus avec beaucoup moins de points de vue. Les résultats dans le cas dynamique montrent l'intérêt de la propagation de l'information de segmentation à travers la géométrie et le mouvement. Enfin, la dernière partie de cette thèse explore la possibilité d'améliorer le suivi dans les systèmes multi-caméras non calibrés. Un état de l'art sur le suivi monoculaire et multi-caméras est présenté et nous explorons l'utilisation des matrices d'autosimilarité comme moyen de décrire le mouvement et de le comparer entre plusieurs caméras