10 research outputs found

    3D shape instantiation for intra-operative navigation from a single 2D projection

    Get PDF
    Unlike traditional open surgery where surgeons can see the operation area clearly, in robot-assisted Minimally Invasive Surgery (MIS), a surgeon’s view of the region of interest is usually limited. Currently, 2D images from fluoroscopy, Magnetic Resonance Imaging (MRI), endoscopy or ultrasound are used for intra-operative guidance as real-time 3D volumetric acquisition is not always possible due to the acquisition speed or exposure constraints. 3D reconstruction, however, is key to navigation in complex in vivo geometries and can help resolve this issue. Novel 3D shape instantiation schemes are developed in this thesis, which can reconstruct the high-resolution 3D shape of a target from limited 2D views, especially a single 2D projection or slice. To achieve a complete and automatic 3D shape instantiation pipeline, segmentation schemes based on deep learning are also investigated. These include normalization schemes for training U-Nets and network architecture design of Atrous Convolutional Neural Networks (ACNNs). For U-Net normalization, four popular normalization methods are reviewed, then Instance-Layer Normalization (ILN) is proposed. It uses a sigmoid function to linearly weight the feature map after instance normalization and layer normalization, and cascades group normalization after the weighted feature map. Detailed validation results potentially demonstrate the practical advantages of the proposed ILN for effective and robust segmentation of different anatomies. For network architecture design in training Deep Convolutional Neural Networks (DCNNs), the newly proposed ACNN is compared to traditional U-Net where max-pooling and deconvolutional layers are essential. Only convolutional layers are used in the proposed ACNN with different atrous rates and it has been shown that the method is able to provide a fully-covered receptive field with a minimum number of atrous convolutional layers. ACNN enhances the robustness and generalizability of the analysis scheme by cascading multiple atrous blocks. Validation results have shown the proposed method achieves comparable results to the U-Net in terms of medical image segmentation, whilst reducing the trainable parameters, thus improving the convergence and real-time instantiation speed. For 3D shape instantiation of soft and deforming organs during MIS, Sparse Principle Component Analysis (SPCA) has been used to analyse a 3D Statistical Shape Model (SSM) and to determine the most informative scan plane. Synchronized 2D images are then scanned at the most informative scan plane and are expressed in a 2D SSM. Kernel Partial Least Square Regression (KPLSR) has been applied to learn the relationship between the 2D and 3D SSM. It has been shown that the KPLSR-learned model developed in this thesis is able to predict the intra-operative 3D target shape from a single 2D projection or slice, thus permitting real-time 3D navigation. Validation results have shown the intrinsic accuracy achieved and the potential clinical value of the technique. The proposed 3D shape instantiation scheme is further applied to intra-operative stent graft deployment for the robot-assisted treatment of aortic aneurysms. Mathematical modelling is first used to simulate the stent graft characteristics. This is then followed by the Robust Perspective-n-Point (RPnP) method to instantiate the 3D pose of fiducial markers of the graft. Here, Equally-weighted Focal U-Net is proposed with a cross-entropy and an additional focal loss function. Detailed validation has been performed on patient-specific stent grafts with an accuracy between 1-3mm. Finally, the relative merits and potential pitfalls of all the methods developed in this thesis are discussed, followed by potential future research directions and additional challenges that need to be tackled.Open Acces

    Deep Learning in Cardiology

    Full text link
    The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

    Machine learning approaches for lung cancer diagnosis.

    Get PDF
    The enormity of changes and development in the field of medical imaging technology is hard to fathom, as it does not just represent the technique and process of constructing visual representations of the body from inside for medical analysis and to reveal the internal structure of different organs under the skin, but also it provides a noninvasive way for diagnosis of various disease and suggest an efficient ways to treat them. While data surrounding all of our lives are stored and collected to be ready for analysis by data scientists, medical images are considered a rich source that could provide us with a huge amount of data, that could not be read easily by physicians and radiologists, with valuable information that could be used in smart ways to discover new knowledge from these vast quantities of data. Therefore, the design of computer-aided diagnostic (CAD) system, that can be approved for use in clinical practice that aid radiologists in diagnosis and detecting potential abnormalities, is of a great importance. This dissertation deals with the development of a CAD system for lung cancer diagnosis, which is the second most common cancer in men after prostate cancer and in women after breast cancer. Moreover, lung cancer is considered the leading cause of cancer death among both genders in USA. Recently, the number of lung cancer patients has increased dramatically worldwide and its early detection doubles a patient’s chance of survival. Histological examination through biopsies is considered the gold standard for final diagnosis of pulmonary nodules. Even though resection of pulmonary nodules is the ideal and most reliable way for diagnosis, there is still a lot of different methods often used just to eliminate the risks associated with the surgical procedure. Lung nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. A pulmonary nodule is the first indication to start diagnosing lung cancer. Lung nodules can be benign (normal subjects) or malignant (cancerous subjects). Large (generally defined as greater than 2 cm in diameter) malignant nodules can be easily detected with traditional CT scanning techniques. However, the diagnostic options for small indeterminate nodules are limited due to problems associated with accessing small tumors. Therefore, additional diagnostic and imaging techniques which depends on the nodules’ shape and appearance are needed. The ultimate goal of this dissertation is to develop a fast noninvasive diagnostic system that can enhance the accuracy measures of early lung cancer diagnosis based on the well-known hypotheses that malignant nodules have different shape and appearance than benign nodules, because of the high growth rate of the malignant nodules. The proposed methodologies introduces new shape and appearance features which can distinguish between benign and malignant nodules. To achieve this goal a CAD system is implemented and validated using different datasets. This CAD system uses two different types of features integrated together to be able to give a full description to the pulmonary nodule. These two types are appearance features and shape features. For the appearance features different texture appearance descriptors are developed, namely the 3D histogram of oriented gradient, 3D spherical sector isosurface histogram of oriented gradient, 3D adjusted local binary pattern, 3D resolved ambiguity local binary pattern, multi-view analytical local binary pattern, and Markov Gibbs random field. Each one of these descriptors gives a good description for the nodule texture and the level of its signal homogeneity which is a distinguishable feature between benign and malignant nodules. For the shape features multi-view peripheral sum curvature scale space, spherical harmonics expansions, and different group of fundamental geometric features are utilized to describe the nodule shape complexity. Finally, the fusion of different combinations of these features, which is based on two stages is introduced. The first stage generates a primary estimation for every descriptor. Followed by the second stage that consists of an autoencoder with a single layer augmented with a softmax classifier to provide us with the ultimate classification of the nodule. These different combinations of descriptors are combined into different frameworks that are evaluated using different datasets. The first dataset is the Lung Image Database Consortium which is a benchmark publicly available dataset for lung nodule detection and diagnosis. The second dataset is our local acquired computed tomography imaging data that has been collected from the University of Louisville hospital and the research protocol was approved by the Institutional Review Board at the University of Louisville (IRB number 10.0642). These frameworks accuracy was about 94%, which make the proposed frameworks demonstrate promise to be valuable tool for the detection of lung cancer

    The radiological investigation of musculoskeletal tumours : chairperson's introduction

    No full text

    Infective/inflammatory disorders

    Get PDF

    Data-centric Design and Training of Deep Neural Networks with Multiple Data Modalities for Vision-based Perception Systems

    Get PDF
    224 p.Los avances en visión artificial y aprendizaje automático han revolucionado la capacidad de construir sistemas que procesen e interpreten datos digitales, permitiéndoles imitar la percepción humana y abriendo el camino a un amplio rango de aplicaciones. En los últimos años, ambas disciplinas han logrado avances significativos,impulsadas por los progresos en las técnicas de aprendizaje profundo(deep learning). El aprendizaje profundo es una disciplina que utiliza redes neuronales profundas (DNNs, por sus siglas en inglés) para enseñar a las máquinas a reconocer patrones y hacer predicciones basadas en datos. Los sistemas de percepción basados en el aprendizaje profundo son cada vez más frecuentes en diversos campos, donde humanos y máquinas colaboran para combinar sus fortalezas.Estos campos incluyen la automoción, la industria o la medicina, donde mejorar la seguridad, apoyar el diagnóstico y automatizar tareas repetitivas son algunos de los objetivos perseguidos.Sin embargo, los datos son uno de los factores clave detrás del éxito de los algoritmos de aprendizaje profundo. La dependencia de datos limita fuertemente la creación y el éxito de nuevas DNN. La disponibilidad de datos de calidad para resolver un problema específico es esencial pero difícil de obtener, incluso impracticable,en la mayoría de los desarrollos. La inteligencia artificial centrada en datos enfatiza la importancia de usar datos de alta calidad que transmitan de manera efectiva lo que un modelo debe aprender. Motivada por los desafíos y la necesidad de los datos, esta tesis formula y valida cinco hipótesis sobre la adquisición y el impacto de los datos en el diseño y entrenamiento de las DNNs.Específicamente, investigamos y proponemos diferentes metodologías para obtener datos adecuados para entrenar DNNs en problemas con acceso limitado a fuentes de datos de gran escala. Exploramos dos posibles soluciones para la obtención de datos de entrenamiento, basadas en la generación de datos sintéticos. En primer lugar, investigamos la generación de datos sintéticos utilizando gráficos 3D y el impacto de diferentes opciones de diseño en la precisión de los DNN obtenidos. Además, proponemos una metodología para automatizar el proceso de generación de datos y producir datos anotados variados, mediante la replicación de un entorno 3D personalizado a partir de un archivo de configuración de entrada. En segundo lugar, proponemos una red neuronal generativa(GAN) que genera imágenes anotadas utilizando conjuntos de datos anotados limitados y datos sin anotaciones capturados en entornos no controlados

    Sparsely Activated Networks: A new method for decomposing and compressing data

    Full text link
    Recent literature on unsupervised learning focused on designing structural priors with the aim of learning meaningful features, but without considering the description length of the representations. In this thesis, first we introduce the{\phi}metric that evaluates unsupervised models based on their reconstruction accuracy and the degree of compression of their internal representations. We then present and define two activation functions (Identity, ReLU) as base of reference and three sparse activation functions (top-k absolutes, Extrema-Pool indices, Extrema) as candidate structures that minimize the previously defined metric φ\varphi. We lastly present Sparsely Activated Networks (SANs) that consist of kernels with shared weights that, during encoding, are convolved with the input and then passed through a sparse activation function. During decoding, the same weights are convolved with the sparse activation map and subsequently the partial reconstructions from each weight are summed to reconstruct the input. We compare SANs using the five previously defined activation functions on a variety of datasets (Physionet, UCI-epilepsy, MNIST, FMNIST) and show that models that are selected using φ\varphi have small description representation length and consist of interpretable kernels.Comment: PhD Thesis in Greek, 158 pages for the main text, 23 supplementary pages for presentation, arXiv:1907.06592, arXiv:1904.13216, arXiv:1902.1112
    corecore