Reproducible White Matter Tract Segmentation Using 3D U-Net on a Large-scale DTI Dataset

Tract-specific diffusion measures, as derived from brain diffusion MRI, have been linked to white matter tract structural integrity and neurodegeneration. As a consequence, there is a large interest in the automatic segmentation of white matter tract in diffusion tensor MRI data. Methods based on the tractography are popular for white matter tract segmentation. However, because of the limited consistency and long processing time, such methods may not be suitable for clinical practice. We therefore developed a novel convolutional neural network based method to directly segment white matter tract trained on a low-resolution dataset of 9149 DTI images. The method is optimized on input, loss function and network architecture selections. We evaluated both segmentation accuracy and reproducibility, and reproducibility of determining tract-specific diffusion measures. The reproducibility of the method is higher than that of the reference standard and the determined diffusion measures are consistent. Therefore, we expect our method to be applicable in clinical practice and in longitudinal analysis of white matter microstructure.Comment: Machine Learning in Medical Imaging (MLMI), 201

Tractographie de la matière blanche par réseaux de neurones récurrents

La matière blanche du cerveau fait encore l'objet de nombreuses études. Grâce à l'IRM de diffusion, on peut étudier de façon non invasive la connectivité du cerveau avec une précision sans précédent. La reconstruction de la matière blanche --- la tractographie --- n'est pas parfaite cependant. En effet, la tractographie tend à reconstruire tous les chemins possibles au sein de la matière blanche; l'expertise des neuroanatomistes est donc requise pour distinguer les chemins qui sont possibles anatomiquement de ceux qui résultent d'une mauvaise reconstruction. Cette connaissance est difficile à exprimer et à codifier sous forme de règles logiques. L'intelligence artificielle a refait surface dans les années 1990 --- suite à une amélioration remarquable de la vitesse des processeurs --- en tant que solution viable à plusieurs problèmes qui étaient considérés comme fondamentalement > et quasi impossibles à résoudre pour une machine. Celle-ci représente un outil unique pour intégrer l'expertise des neuroanatomistes dans le processus de reconstruction de la matière blanche, sans avoir à fournir de règles explicitement. Un modèle peut ainsi apprendre la définition d'un chemin valide à partir d'exemples valides, pour ensuite reproduire ce qu'il a appris, sans répéter les erreurs classiques. Plus particulièrement, les réseaux de neurones récurrents sont une famille de modèles créés spécifiquement pour le traitement de séquences de données. Comme une fibre de matière blanche est représentée par une séquence de points, le lien se fait naturellement. Malgré leur potentiel énorme, l'application des réseaux récurrents à la tractographie fait face à plusieurs problèmes techniques. Cette thèse se veut très exploratoire, et détaille donc les débuts de l'utilisation des réseaux de neurones récurrents pour la tractographie par apprentissage, des problèmes qui sont apparus suite à la création d'une multitude d'algorithmes basés sur l'intelligence artificielle, ainsi que des solutions développées pour répondre à ces problèmes. Les résultats de cette thèse ont démontré le potentiel des réseaux de neurones récurrents pour la reconstruction de la matière blanche, en plus de contribuer à l’avancement du domaine grâce à la création d’une base de données publique pour la tractographie par apprentissage

Deep Learning for Depth, Ego-Motion, Optical Flow Estimation, and Semantic Segmentation

Visual Simultaneous Localization and Mapping (SLAM) is crucial for robot perception. Visual odometry (VO) is one of the essential components for SLAM, which can estimate the depth map of scenes and the ego-motion of a camera in unknown environments. Most previous work in this area uses geometry-based approaches. Recently, deep learning methods have opened a new door for this area. At present, most research under deep learning frameworks focuses on improving the accuracy of estimation results and reducing the dependence of enormous labelled training data. This thesis presents the work for exploring the deep learning technologies to estimate different tasks, such as depth, ego-motion, optical flow, and semantic segmentation, under the VO framework. Firstly, a stacked generative adversarial network is proposed to estimate the depth and ego-motion. It consists of a stack of GAN layers, of which the lowest layer estimates the depth and ego-motion while the higher layers estimate the spatial features. It can also capture the temporal dynamics due to the use of a recurrent representation across the layers. Secondly, digging into the internal network structure design, a novel recurrent spatial-temporal network(RSTNet)is proposed to estimate depth and ego-motion and optical flow and dynamic objects. This network can extract and retain more spatial and temporal features. Thedynamicobjectsaredetectedbyusingopticalflowdifferencebetweenfullflow and rigid flow. Finally, a semantic segmentation network is proposed, producing semantic segmentation results together with depth and ego-motion estimation results. All of the proposed contributions are tested and evaluated on open public datasets. The comparisons with other methods are provided. The results show that our proposed networks outperform the state-of-the-art methods of depth, ego-motion, and dynamic objects estimations

The Functional, Ecological, and Evolutionary Morphology of Sea Lampreys (Petromyzon marinus)

Lampreys (Petromyzontiformes) are jawless vertebrates with an evolutionary history lasting at least 360 million years and are often used in comparisons with jawed vertebrates because some of their morphological aspects, such as the segmented trunk musculature with curved myosepta and a non-mineralized skeleton fibrous skeleton, are thought to resemble the condition of early vertebrates before the evolution of jaws. Although earlier authors studied the morphology of the skeleto-muscular system of the trunk of lampreys, their studies are not detailed and complete enough to allow a functional and biomechanical analysis that is needed as a basis for modeling the mechanics of lamprey locomotion and for understanding the causal roles played by the anatomical structures within the trunk. Questions remain, such as what is the architecture of the trunk fibroskeleton, and how does it function with the musculature to bend the trunk? This dissertation studied the functional, ecological and evolutionary morphology of the trunk of Sea Lampreys (Petromyzon marinus) as well as its relevance in understanding the environmental history of landlocked lamprey populations. Functional morphology revealed that the fibroskeleton of the trunk is a self-supporting concatenated system of fibers, which creates a scaffold for the musculature and transmits forces to bend the trunk during swimming. Ecological morphology demonstrated the adaptive advantage of the fibroskeleton’s architecture, which enables the movements that are performed during migration and spawning and gives lampreys the capacity to colonize upstream realms. These results help explain the evolutionary morphology of lampreys, which likely originated in freshwater as algal feeders and evolved into parasites after going through an intermediary scavenging stage. When these insights are applied to the evolution of landlocked Sea Lampreys, it becomes evident that their entry into freshwater lakes occurred as soon as they were able to reach them and that populations likely became established in Lake Ontario, Lake Champlain, and the Finger Lakes thousands of years ago. This insight undermines the current status of landlocked Sea Lampreys as invasive species in these lakes and the case for their eradication. Hence, this dissertation provides a comprehensive and integrative analysis of lamprey biology from their anatomy to environmental policy

SIVO: Semantically Informed Visual Odometry and Mapping

Accurate localization is a requirement for any autonomous mobile robot. In recent years, cameras have proven to be a reliable, cheap, and effective sensor to achieve this goal. Visual simultaneous localization and mapping (SLAM) algorithms determine camera motion by tracking the motion of reference points from the scene. However, these references must be static, as well as viewpoint, scale, and rotation invariant in order to ensure accurate localization. This is especially paramount for long-term robot operation, where we require our references to be stable over long durations and also require careful point selection to maintain the runtime and storage complexity of the algorithm while the robot navigates through its environment. In this thesis, we present SIVO (Semantically Informed Visual Odometry and Mapping), a novel feature selection method for visual SLAM which incorporates machine learning and neural network uncertainty into an information-theoretic approach to feature selection. The emergence of deep learning techniques has resulted in remarkable advances in scene understanding, and our method supplements traditional visual SLAM with this contextual knowledge. Our algorithm selects points which provide significant information to reduce the uncertainty of the state estimate while ensuring that the feature is detected to be a static object repeatedly, with a high confidence. This is done by evaluating the reduction in Shannon entropy between the current state entropy, and the joint entropy of the state given the addition of the new feature with the classification entropy of the feature from a Bayesian neural network. Our method is evaluated against ORB SLAM2 and the ground truth of the KITTI odometry dataset. Overall, SIVO performs comparably to ORB SLAM2 (average of 0.17% translation error difference, 6.2 × 10 −5 deg/m rotation error difference) while removing 69% of the map points on average. As the reference points selected are from static objects (building, traffic signs, etc.), the map generated using our algorithm is suitable for long-term localization