Inferring Geodesic Cerebrovascular Graphs: Image Processing, Topological Alignment and Biomarkers Extraction

A vectorial representation of the vascular network that embodies quantitative features - location, direction, scale, and bifurcations - has many potential neuro-vascular applications. Patient-specific models support computer-assisted surgical procedures in neurovascular interventions, while analyses on multiple subjects are essential for group-level studies on which clinical prediction and therapeutic inference ultimately depend. This first motivated the development of a variety of methods to segment the cerebrovascular system. Nonetheless, a number of limitations, ranging from data-driven inhomogeneities, the anatomical intra- and inter-subject variability, the lack of exhaustive ground-truth, the need for operator-dependent processing pipelines, and the highly non-linear vascular domain, still make the automatic inference of the cerebrovascular topology an open problem. In this thesis, brain vessels’ topology is inferred by focusing on their connectedness. With a novel framework, the brain vasculature is recovered from 3D angiographies by solving a connectivity-optimised anisotropic level-set over a voxel-wise tensor field representing the orientation of the underlying vasculature. Assuming vessels joining by minimal paths, a connectivity paradigm is formulated to automatically determine the vascular topology as an over-connected geodesic graph. Ultimately, deep-brain vascular structures are extracted with geodesic minimum spanning trees. The inferred topologies are then aligned with similar ones for labelling and propagating information over a non-linear vectorial domain, where the branching pattern of a set of vessels transcends a subject-specific quantized grid. Using a multi-source embedding of a vascular graph, the pairwise registration of topologies is performed with the state-of-the-art graph matching techniques employed in computer vision. Functional biomarkers are determined over the neurovascular graphs with two complementary approaches. Efficient approximations of blood flow and pressure drop account for autoregulation and compensation mechanisms in the whole network in presence of perturbations, using lumped-parameters analog-equivalents from clinical angiographies. Also, a localised NURBS-based parametrisation of bifurcations is introduced to model fluid-solid interactions by means of hemodynamic simulations using an isogeometric analysis framework, where both geometry and solution profile at the interface share the same homogeneous domain. Experimental results on synthetic and clinical angiographies validated the proposed formulations. Perspectives and future works are discussed for the group-wise alignment of cerebrovascular topologies over a population, towards defining cerebrovascular atlases, and for further topological optimisation strategies and risk prediction models for therapeutic inference. Most of the algorithms presented in this work are available as part of the open-source package VTrails

Discrete and Continuous Optimization for Motion Estimation

The study of motion estimation reaches back decades and has become one of the central topics of research in computer vision. Even so, there are situations where current approaches fail, such as when there are extreme lighting variations, significant occlusions, or very large motions. In this thesis, we propose several approaches to address these issues. First, we propose a novel continuous optimization framework for estimating optical flow based on a decomposition of the image domain into triangular facets. We show how this allows for occlusions to be easily and naturally handled within our optimization framework without any post-processing. We also show that a triangular decomposition enables us to use a direct Cholesky decomposition to solve the resulting linear systems by reducing its memory requirements. Second, we introduce a simple method for incorporating additional temporal information into optical flow using inertial estimates of the flow, which leads to a significant reduction in error. We evaluate our methods on several datasets and achieve state-of-the-art results on MPI-Sintel. Finally, we introduce a discrete optimization framework for optical flow computation. Discrete approaches have generally been avoided in optical flow because of the relatively large label space that makes them computationally expensive. In our approach, we use recent advances in image segmentation to build a tree-structured graphical model that conforms to the image content. We show how the optimal solution to these discrete optical flow problems can be computed efficiently by making use of optimization methods from the object recognition literature, even for large images with hundreds of thousands of labels

Automatic Autism Spectrum Disorder Detection Using Artificial Intelligence Methods with MRI Neuroimaging: A Review

Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and structural (sMRI) neuroimaging methods. However, the process of diagnosing ASD with fMRI and sMRI for specialists is often laborious and time-consuming; therefore, several computer-aided design systems (CADS) based on artificial intelligence (AI) have been developed to assist the specialist physicians. Conventional machine learning (ML) and deep learning (DL) are the most popular schemes of AI used for diagnosing ASD. This study aims to review the automated detection of ASD using AI. We review several CADS that have been developed using ML techniques for the automated diagnosis of ASD using MRI modalities. There has been very limited work on the use of DL techniques to develop automated diagnostic models for ASD. A summary of the studies developed using DL is provided in the appendix. Then, the challenges encountered during the automated diagnosis of ASD using MRI and AI techniques are described in detail. Additionally, a graphical comparison of studies using ML and DL to diagnose ASD automatically is discussed. We conclude by suggesting future approaches to detecting ASDs using AI techniques and MRI neuroimaging

Large-Scale Textured 3D Scene Reconstruction

Die Erstellung dreidimensionaler Umgebungsmodelle ist eine fundamentale Aufgabe im Bereich des maschinellen Sehens. Rekonstruktionen sind für eine Reihe von Anwendungen von Nutzen, wie bei der Vermessung, dem Erhalt von Kulturgütern oder der Erstellung virtueller Welten in der Unterhaltungsindustrie. Im Bereich des automatischen Fahrens helfen sie bei der Bewältigung einer Vielzahl an Herausforderungen. Dazu gehören Lokalisierung, das Annotieren großer Datensätze oder die vollautomatische Erstellung von Simulationsszenarien. Die Herausforderung bei der 3D Rekonstruktion ist die gemeinsame Schätzung von Sensorposen und einem Umgebunsmodell. Redundante und potenziell fehlerbehaftete Messungen verschiedener Sensoren müssen in eine gemeinsame Repräsentation der Welt integriert werden, um ein metrisch und photometrisch korrektes Modell zu erhalten. Gleichzeitig muss die Methode effizient Ressourcen nutzen, um Laufzeiten zu erreichen, welche die praktische Nutzung ermöglichen. In dieser Arbeit stellen wir ein Verfahren zur Rekonstruktion vor, das fähig ist, photorealistische 3D Rekonstruktionen großer Areale zu erstellen, die sich über mehrere Kilometer erstrecken. Entfernungsmessungen aus Laserscannern und Stereokamerasystemen werden zusammen mit Hilfe eines volumetrischen Rekonstruktionsverfahrens fusioniert. Ringschlüsse werden erkannt und als zusätzliche Bedingungen eingebracht, um eine global konsistente Karte zu erhalten. Das resultierende Gitternetz wird aus Kamerabildern texturiert, wobei die einzelnen Beobachtungen mit ihrer Güte gewichtet werden. Für eine nahtlose Erscheinung werden die unbekannten Belichtungszeiten und Parameter des optischen Systems mitgeschätzt und die Bilder entsprechend korrigiert. Wir evaluieren unsere Methode auf synthetischen Daten, realen Sensordaten unseres Versuchsfahrzeugs und öffentlich verfügbaren Datensätzen. Wir zeigen qualitative Ergebnisse großer innerstädtischer Bereiche, sowie quantitative Auswertungen der Fahrzeugtrajektorie und der Rekonstruktionsqualität. Zuletzt präsentieren wir mehrere Anwendungen und zeigen somit den Nutzen unserer Methode für Anwendungen im Bereich des automatischen Fahrens

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

Methods for Real-time Visualization and Interaction with Landforms

This thesis presents methods to enrich data modeling and analysis in the geoscience domain with a particular focus on geomorphological applications. First, a short overview of the relevant characteristics of the used remote sensing data and basics of its processing and visualization are provided. Then, two new methods for the visualization of vector-based maps on digital elevation models (DEMs) are presented. The first method uses a texture-based approach that generates a texture from the input maps at runtime taking into account the current viewpoint. In contrast to that, the second method utilizes the stencil buffer to create a mask in image space that is then used to render the map on top of the DEM. A particular challenge in this context is posed by the view-dependent level-of-detail representation of the terrain geometry. After suitable visualization methods for vector-based maps have been investigated, two landform mapping tools for the interactive generation of such maps are presented. The user can carry out the mapping directly on the textured digital elevation model and thus benefit from the 3D visualization of the relief. Additionally, semi-automatic image segmentation techniques are applied in order to reduce the amount of user interaction required and thus make the mapping process more efficient and convenient. The challenge in the adaption of the methods lies in the transfer of the algorithms to the quadtree representation of the data and in the application of out-of-core and hierarchical methods to ensure interactive performance. Although high-resolution remote sensing data are often available today, their effective resolution at steep slopes is rather low due to the oblique acquisition angle. For this reason, remote sensing data are suitable to only a limited extent for visualization as well as landform mapping purposes. To provide an easy way to supply additional imagery, an algorithm for registering uncalibrated photos to a textured digital elevation model is presented. A particular challenge in registering the images is posed by large variations in the photos concerning resolution, lighting conditions, seasonal changes, etc. The registered photos can be used to increase the visual quality of the textured DEM, in particular at steep slopes. To this end, a method is presented that combines several georegistered photos to textures for the DEM. The difficulty in this compositing process is to create a consistent appearance and avoid visible seams between the photos. In addition to that, the photos also provide valuable means to improve landform mapping. To this end, an extension of the landform mapping methods is presented that allows the utilization of the registered photos during mapping. This way, a detailed and exact mapping becomes feasible even at steep slopes

Using contour information and segmentation for object registration, modeling and retrieval

This thesis considers different aspects of the utilization of contour information and syntactic and semantic image segmentation for object registration, modeling and retrieval in the context of content-based indexing and retrieval in large collections of images. Target applications include retrieval in collections of closed silhouettes, holistic w ord recognition in handwritten historical manuscripts and shape registration. Also, the thesis explores the feasibility of contour-based syntactic features for improving the correspondence of the output of bottom-up segmentation to semantic objects present in the scene and discusses the feasibility of different strategies for image analysis utilizing contour information, e.g. segmentation driven by visual features versus segmentation driven by shape models or semi-automatic in selected application scenarios. There are three contributions in this thesis. The first contribution considers structure analysis based on the shape and spatial configuration of image regions (socalled syntactic visual features) and their utilization for automatic image segmentation. The second contribution is the study of novel shape features, matching algorithms and similarity measures. Various applications of the proposed solutions are presented throughout the thesis providing the basis for the third contribution which is a discussion of the feasibility of different recognition strategies utilizing contour information. In each case, the performance and generality of the proposed approach has been analyzed based on extensive rigorous experimentation using as large as possible test collections

Automatic autism spectrum disorder detection using artificial intelligence methods with MRI neuroimaging: A review

Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and structural (sMRI) neuroimaging methods. However, diagnosing ASD with fMRI and sMRI for specialists is often laborious and time-consuming; therefore, several computer-aided design systems (CADS) based on artificial intelligence (AI) have been developed to assist specialist physicians. Conventional machine learning (ML) and deep learning (DL) are the most popular schemes of AI used for diagnosing ASD. This study aims to review the automated detection of ASD using AI. We review several CADS that have been developed using ML techniques for the automated diagnosis of ASD using MRI modalities. There has been very limited work on the use of DL techniques to develop automated diagnostic models for ASD. A summary of the studies developed using DL is provided in the Supplementary Appendix. Then, the challenges encountered during the automated diagnosis of ASD using MRI and AI techniques are described in detail. Additionally, a graphical comparison of studies using ML and DL to diagnose ASD automatically is discussed. We suggest future approaches to detecting ASDs using AI techniques and MRI neuroimaging.Qatar National Librar

The robot's vista space : a computational 3D scene analysis

Swadzba A. The robot's vista space : a computational 3D scene analysis. Bielefeld (Germany): Bielefeld University; 2011.The space that can be explored quickly from a fixed view point without locomotion is known as the vista space. In indoor environments single rooms and room parts follow this definition. The vista space plays an important role in situations with agent-agent interaction as it is the directly surrounding environment in which the interaction takes place. A collaborative interaction of the partners in and with the environment requires that both partners know where they are, what spatial structures they are talking about, and what scene elements they are going to manipulate. This thesis focuses on the analysis of a robot's vista space. Mechanisms for extracting relevant spatial information are developed which enable the robot to recognize in which place it is, to detect the scene elements the human partner is talking about, and to segment scene structures the human is changing. These abilities are addressed by the proposed holistic, aligned, and articulated modeling approach. For a smooth human-robot interaction, the computed models should be aligned to the partner's representations. Therefore, the design of the computational models is based on the combination of psychological results from studies on human scene perception with basic physical properties of the perceived scene and the perception itself. The holistic modeling realizes a categorization of room percepts based on the observed 3D spatial layout. Room layouts have room type specific features and fMRI studies have shown that some of the human brain areas being active in scene recognition are sensitive to the 3D geometry of a room. With the aligned modeling, the robot is able to extract the hierarchical scene representation underlying a scene description given by a human tutor. Furthermore, it is able to ground the inferred scene elements in its own visual perception of the scene. This modeling follows the assumption that cognition and language schematize the world in the same way. This is visible in the fact that a scene depiction mainly consists of relations between an object and its supporting structure or between objects located on the same supporting structure. Last, the articulated modeling equips the robot with a methodology for articulated scene part extraction and fast background learning under short and disturbed observation conditions typical for human-robot interaction scenarios. Articulated scene parts are detected model-less by observing scene changes caused by their manipulation. Change detection and background learning are closely coupled because change is defined phenomenologically as variation of structure. This means that change detection involves a comparison of currently visible structures with a representation in memory. In range sensing this comparison can be nicely implement as subtraction of these two representations. The three modeling approaches enable the robot to enrich its visual perceptions of the surrounding environment, the vista space, with semantic information about meaningful spatial structures useful for further interaction with the environment and the human partner

Variational methods and its applications to computer vision

Many computer vision applications such as image segmentation can be formulated in a ''variational'' way as energy minimization problems. Unfortunately, the computational task of minimizing these energies is usually difficult as it generally involves non convex functions in a space with thousands of dimensions and often the associated combinatorial problems are NP-hard to solve. Furthermore, they are ill-posed inverse problems and therefore are extremely sensitive to perturbations (e.g. noise). For this reason in order to compute a physically reliable approximation from given noisy data, it is necessary to incorporate into the mathematical model appropriate regularizations that require complex computations. The main aim of this work is to describe variational segmentation methods that are particularly effective for curvilinear structures. Due to their complex geometry, classical regularization techniques cannot be adopted because they lead to the loss of most of low contrasted details. In contrast, the proposed method not only better preserves curvilinear structures, but also reconnects some parts that may have been disconnected by noise. Moreover, it can be easily extensible to graphs and successfully applied to different types of data such as medical imagery (i.e. vessels, hearth coronaries etc), material samples (i.e. concrete) and satellite signals (i.e. streets, rivers etc.). In particular, we will show results and performances about an implementation targeting new generation of High Performance Computing (HPC) architectures where different types of coprocessors cooperate. The involved dataset consists of approximately 200 images of cracks, captured in three different tunnels by a robotic machine designed for the European ROBO-SPECT project.Open Acces