Landmark Localization, Feature Matching and Biomarker Discovery from Magnetic Resonance Images

The work presented in this thesis proposes several methods that can be roughly divided into three different categories: I) landmark localization in medical images, II) feature matching for image registration, and III) biomarker discovery in neuroimaging. The first part deals with the identification of anatomical landmarks. The motivation stems from the fact that the manual identification and labeling of these landmarks is very time consuming and prone to observer errors, especially when large datasets must be analyzed. In this thesis we present three methods to tackle this challenge: A landmark descriptor based on local self-similarities (SS), a subspace building framework based on manifold learning and a sparse coding landmark descriptor based on data-specific learned dictionary basis. The second part of this thesis deals with finding matching features between a pair of images. These matches can be used to perform a registration between them. Registration is a powerful tool that allows mapping images in a common space in order to aid in their analysis. Accurate registration can be challenging to achieve using intensity based registration algorithms. Here, a framework is proposed for learning correspondences in pairs of images by matching SS features and random sample and consensus (RANSAC) is employed as a robust model estimator to learn a deformation model based on feature matches. Finally, the third part of the thesis deals with biomarker discovery using machine learning. In this section a framework for feature extraction from learned low-dimensional subspaces that represent inter-subject variability is proposed. The manifold subspace is built using data-driven regions of interest (ROI). These regions are learned via sparse regression, with stability selection. Also, probabilistic distribution models for different stages in the disease trajectory are estimated for different class populations in the low-dimensional manifold and used to construct a probabilistic scoring function.Open Acces

Automatic quantification of radiographic knee osteoarthritis severity and associated diagnostic features using deep convolutional neural networks

“Automatic Quantification of Radiographic Knee Osteoarthritis Severity and Associated Diagnostic Features using Deep Convolutional Neural Networks” A. Joseph Antony Due to the increasing prevalence of knee Osteoarthritis (OA), a debilitating kneejoint degradation, and total joint arthoplasty as a serious consequence, there is a need for effective clinical and scientific tools to assess knee OA in its early stages. This thesis investigates the use of machine learning algorithms and deep learning architectures, in particular convolutional neural networks (CNN), to quantify the severity and clinical radiographic features of knee OA. The goal is to offer novel and effective solutions to automatically assess the severity of knee OA achieving on par with human accuracy. Instead of conventional hand-crafted features, it is proposed in this thesis that automatically learning features in a supervised manner can be more effective for fine-grained knee OA image classification. The main contributions of this thesis are as follows. First, the use of off-the-shelf CNNs are investigated for classifying knee OA images through transfer learning by fine-tuning the CNNs. Second, CNNs are trained from scratch to quantify the knee OA severity optimising a weighted ratio of two loss functions: categorical cross entropy and mean-squared error. Third, CNNs are jointly trained to quantify the clinical features of knee OA: joint space narrowing (JSN) and osteophytes along with the KL grades. This improves the overall quantification of knee OA severity producing simultaneous predictions of KL grades, JSN and osteophytes. Two public datasets are used to evaluate the approaches, the OAI and the MOST, with extremely promising results that outperform existing approaches. In summary, this thesis primarily contributes to the field of automated methods for localisation and quantification of radiographic knee OA

Magnetic Resonance Imaging for the Functional Analysis of Tissues and Biomaterials

Articular cartilage provides mechanical load dissipation and lubrication between joints, and additionally provides protects from abrasion. At present, there are no treatments to cure or attenuate the degradation of cartilage. Early detection and the ability to monitor the progression of osteoarthritis is important for developing effective therapies. However, few reliable imaging biomarkers exist to detect cartilage disease before advanced degeneration in the tissue. One specialized MRI technique, termed displacements under applied loading by MRI (dualMRI), was developed to measure displacements and strain in musculoskeletal tissues, hydrogels and engineered constructs. However, deformation information does not directly describe spatial distributions of tissue properties (e.g. stiffness), which is critical to the understanding of disease progression. To achieve the stiffness measurement, we developed and validated an inverse modeling workflow that combined dualMRI, to directly measure intratissue deformation, with topology optimization in the application of heterogeneous (layered) materials representative of the complex gradient architecture of articular cartilage. We successfully reconstructed bi-layer stiffness from ideal displacements calculated from forward simulation as well as from experimental data measured from dualMRI. To monitor the progression of osteoarthritis, we measured and analyzed biomechanical changes of sheep stifle cartilage after meniscectomy. We found that 2nd principal strain and max shear strain in the femur contact region are sensitive to cartilage degeneration at different stages and compared to more conventional methods like quantitative MRI. To investigate the biomechanical changes in articular cartilage with defect and repair, we implanted decellularized cartilage implant into sheep cartilage defect and evaluate the repair results using quantitative MRI and dualMRI. We found that implants placed in joints demonstrated lower strains compared to joints with untreated defects

Studies on neutron diffraction and X-ray radiography for material inspection

Among the different probes to study the structures of the bio and structural materials, X-ray and neutron are widely used because of their distinctive usefulness in investigating different structures. X-ray radiography and neutron diffraction are two widely known non-destructive techniques for material inspection. Here we demonstrate the design of neutron diffractometer with low power source and analyze the digital image produced by the X-ray radiography instead of neutron diffraction because of the availability of the data. Neutron diffraction is a powerful tool for understanding the behavior of crystal structures and phase behaviors of materials. While neutron diffraction capabilities continue to explore new frontiers of materials science, such capabilities currently exist in limited places, which require high neutron flux. The study seeks to design a low-resolution neutron diffraction system that can be installed on low power reactors (e.g. 250 kW thermal power). The performance of the diffractometer is estimated using Monte-Carlo ray-tracing simulations with McStas with an application in material science. Both monochromatic and polychromatic configurations are considered in order to maximize the net diffracted neutron flux at the detectors with reasonable resolution. On the other hand, considering X-ray radiography as a structure inspecting technique, analysis of dental X-ray panorama is performed for the detection of oral lesions. A novel automatic computer-aided method to identify dental lesions from dental X-ray is presented. Morphological operations, intensity profile analysis, automated seed point selection, region growing, feature extraction and neural network application are carried out to perform the job. Results show that the performance of the proposed method surpasses existing automated methods utilizing dental X-rays --Abstract, page iii

Book of Abstracts 15th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 3rd Conference on Imaging and Visualization

In this edition, the two events will run together as a single conference, highlighting the strong connection with the Taylor & Francis journals: Computer Methods in Biomechanics and Biomedical Engineering (John Middleton and Christopher Jacobs, Eds.) and Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization (JoãoManuel R.S. Tavares, Ed.). The conference has become a major international meeting on computational biomechanics, imaging andvisualization. In this edition, the main program includes 212 presentations. In addition, sixteen renowned researchers will give plenary keynotes, addressing current challenges in computational biomechanics and biomedical imaging. In Lisbon, for the first time, a session dedicated to award the winner of the Best Paper in CMBBE Journal will take place. We believe that CMBBE2018 will have a strong impact on the development of computational biomechanics and biomedical imaging and visualization, identifying emerging areas of research and promoting the collaboration and networking between participants. This impact is evidenced through the well-known research groups, commercial companies and scientific organizations, who continue to support and sponsor the CMBBE meeting series. In fact, the conference is enriched with five workshops on specific scientific topics and commercial software.info:eu-repo/semantics/draf

Going Deep in Medical Image Analysis: Concepts, Methods, Challenges and Future Directions

Medical Image Analysis is currently experiencing a paradigm shift due to Deep Learning. This technology has recently attracted so much interest of the Medical Imaging community that it led to a specialized conference in `Medical Imaging with Deep Learning' in the year 2018. This article surveys the recent developments in this direction, and provides a critical review of the related major aspects. We organize the reviewed literature according to the underlying Pattern Recognition tasks, and further sub-categorize it following a taxonomy based on human anatomy. This article does not assume prior knowledge of Deep Learning and makes a significant contribution in explaining the core Deep Learning concepts to the non-experts in the Medical community. Unique to this study is the Computer Vision/Machine Learning perspective taken on the advances of Deep Learning in Medical Imaging. This enables us to single out `lack of appropriately annotated large-scale datasets' as the core challenge (among other challenges) in this research direction. We draw on the insights from the sister research fields of Computer Vision, Pattern Recognition and Machine Learning etc.; where the techniques of dealing with such challenges have already matured, to provide promising directions for the Medical Imaging community to fully harness Deep Learning in the future