Computational Modeling for Abnormal Brain Tissue Segmentation, Brain Tumor Tracking, and Grading

This dissertation proposes novel texture feature-based computational models for quantitative analysis of abnormal tissues in two neurological disorders: brain tumor and stroke. Brain tumors are the cells with uncontrolled growth in the brain tissues and one of the major causes of death due to cancer. On the other hand, brain strokes occur due to the sudden interruption of the blood supply which damages the normal brain tissues and frequently causes death or persistent disability. Clinical management of these brain tumors and stroke lesions critically depends on robust quantitative analysis using different imaging modalities including Magnetic Resonance (MR) and Digital Pathology (DP) images. Due to uncontrolled growth and infiltration into the surrounding tissues, the tumor regions appear with a significant texture variation in the static MRI volume and also in the longitudinal imaging study. Consequently, this study developed computational models using novel texture features to segment abnormal brain tissues (tumor, and stroke lesions), tracking the change of tumor volume in longitudinal images, and tumor grading in MR images. Manual delineation and analysis of these abnormal tissues in large scale is tedious, error-prone, and often suffers from inter-observer variability. Therefore, efficient computational models for robust segmentation of different abnormal tissues is required to support the diagnosis and analysis processes. In this study, brain tissues are characterized with novel computational modeling of multi-fractal texture features for multi-class brain tumor tissue segmentation (BTS) and extend the method for ischemic stroke lesions in MRI. The robustness of the proposed segmentation methods is evaluated using a huge amount of private and public domain clinical data that offers competitive performance when compared with that of the state-of-the-art methods. Further, I analyze the dynamic texture behavior of tumor volume in longitudinal imaging and develop post-processing frame-work using three-dimensional (3D) texture features. These post-processing methods are shown to reduce the false positives in the BTS results and improve the overall segmentation result in longitudinal imaging. Furthermore, using this improved segmentation results the change of tumor volume has been quantified in three types such as stable, progress, and shrinkage as observed by the volumetric changes of different tumor tissues in longitudinal images. This study also investigates a novel non-invasive glioma grading, for the first time in literature, that uses structural MRI only. Such non-invasive glioma grading may be useful before an invasive biopsy is recommended. This study further developed an automatic glioma grading scheme using the invasive cell nuclei morphology in DP images for cross-validation with the same patients. In summary, the texture-based computational models proposed in this study are expected to facilitate the clinical management of patients with the brain tumors and strokes by automating large scale imaging data analysis, reducing human error, inter-observer variability, and producing repeatable brain tumor quantitation and grading

Prediction of Thrombectomy Functional Outcomes using Multimodal Data

Recent randomised clinical trials have shown that patients with ischaemic stroke {due to occlusion of a large intracranial blood vessel} benefit from endovascular thrombectomy. However, predicting outcome of treatment in an individual patient remains a challenge. We propose a novel deep learning approach to directly exploit multimodal data (clinical metadata information, imaging data, and imaging biomarkers extracted from images) to estimate the success of endovascular treatment. We incorporate an attention mechanism in our architecture to model global feature inter-dependencies, both channel-wise and spatially. We perform comparative experiments using unimodal and multimodal data, to predict functional outcome (modified Rankin Scale score, mRS) and achieve 0.75 AUC for dichotomised mRS scores and 0.35 classification accuracy for individual mRS scores.Comment: Accepted at Medical Image Understanding and Analysis (MIUA) 202

Machine Learning in Medical Image Analysis

Machine learning is playing a pivotal role in medical image analysis. Many algorithms based on machine learning have been applied in medical imaging to solve classification, detection, and segmentation problems. Particularly, with the wide application of deep learning approaches, the performance of medical image analysis has been significantly improved. In this thesis, we investigate machine learning methods for two key challenges in medical image analysis: The first one is segmentation of medical images. The second one is learning with weak supervision in the context of medical imaging. The first main contribution of the thesis is a series of novel approaches for image segmentation. First, we propose a framework based on multi-scale image patches and random forests to segment small vessel disease (SVD) lesions on computed tomography (CT) images. This framework is validated in terms of spatial similarity, estimated lesion volumes, visual score ratings and was compared with human experts. The results showed that the proposed framework performs as well as human experts. Second, we propose a generic convolutional neural network (CNN) architecture called the DRINet for medical image segmentation. The DRINet approach is robust in three different types of segmentation tasks, which are multi-class cerebrospinal fluid (CSF) segmentation on brain CT images, multi-organ segmentation on abdomen CT images, and multi-class tumour segmentation on brain magnetic resonance (MR) images. Finally, we propose a CNN-based framework to segment acute ischemic lesions on diffusion weighted (DW)-MR images, where the lesions are highly variable in terms of position, shape, and size. Promising results were achieved on a large clinical dataset. The second main contribution of the thesis is two novel strategies for learning with weak supervision. First, we propose a novel strategy called context restoration to make use of the images without annotations. The context restoration strategy is a proxy learning process based on the CNN, which extracts semantic features from images without using annotations. It was validated on classification, localization, and segmentation problems and was superior to existing strategies. Second, we propose a patch-based framework using multi-instance learning to distinguish normal and abnormal SVD on CT images, where there are only coarse-grained labels available. Our framework was observed to work better than classic methods and clinical practice.Open Acces

CNN and Rf based Early Detection of Brain Stroke Using Bio-Electrical Signals

The brain is a vital component of the body that is in control of involuntary and voluntary movements such as walking,   memory, and vision. Nowadays, some of the most prevalent brain disorders include Alzheimer's disease, brain tumors, and epilepsy (paralysis or stroke).  As a result, stroke has become a significant global health concern, with high rates of mortality and disability. Importantly, approximately two-thirds of all strokes occur in developing countries, highlighting the significant burden of this condition in these regions. Therefore, emphasizing the timely detection and appropriate treatment of brain tumors is crucial. Given the high potential for mortality or severe disability associated with stroke disease, prioritizing active primary prevention and early identification of prognostic symptoms is of paramount importance. Ischemic stroke and hemorrhagic stroke are the two primary classifications for stroke diseases. Each type calls for specific emergency treatments, such as the administration of thrombolytics or coagulants, tailored to their respective underlying mechanisms. However, to effectively manage stroke, it is crucial to promptly identify the precursor symptoms in real-time, as they can vary among individuals. Timely professional treatment within the appropriate treatment window is essential and should be provided by a medical institution. In contrast, prior research has primarily centered around the formulation of acute treatment strategies or clinical guidelines subsequent to the occurrence of a stroke, rather than giving sufficient attention to the early identification of prognostic symptoms. Specifically, recent research has extensively utilized image analysis techniques, such as computed tomography (CT) or magnetic resonance imaging (MRI), as a primary approach for detecting and predicting prognostic symptoms in stroke patients. Traditional methodologies not only encounter difficulties in achieving early real-time diagnosis but also exhibit limitations in terms of prolonged testing duration and high testing costs. In this study, we introduce a novel system that employs machine learning techniques to predict and semantically interpret prognostic symptoms of stroke. Our approach utilizes real-time measurement of multi-modal bio-signals, namely electrocardiogram (ECG) and photoplethysmography (PPG), with a specific focus on the elderly population. To facilitate real-time prediction of stroke disease during walking, we have developed a stroke disease prediction system that incorporates a hybrid ensemble architecture. This architecture synergistically combines Convolutional Neural Network (CNN) and Random Forest (RF) models, enabling accurate and timely prognostication of stroke disease. The suggested method prioritises the convenience of use of bio-signal sensors for the elderly by collecting bio-signals from three electrodes placed on the index finger. These signals include ECG and PPG, and they are obtained while the participants walk. The CNN-RF model delivers satisfactory prediction accuracy when using raw ECG and PPG data. F1-Score, Sensitivity, Specificity, and Accuracy were the performance parameters used to evaluated the model's performance