Compression of MRI brain images based on automatic extraction of tumor region

In the compression of medical images, region of interest (ROI) based techniques seem to be promising, as they can result in high compression ratios while maintaining the quality of region of diagnostic importance, the ROI, when image is reconstructed. In this article, we propose a set-up for compression of brain magnetic resonance imaging (MRI) images based on automatic extraction of tumor. Our approach is to first separate the tumor, the ROI in our case, from brain image, using support vector machine (SVM) classification and region extraction step. Then, tumor region (ROI) is compressed using Arithmetic coding, a lossless compression technique. The non-tumorous region, non-region of interest (NROI), is compressed using a lossy compression technique formed by a combination of discrete wavelet transform (DWT), set partitioning in hierarchical trees (SPIHT) and arithmetic coding (AC). The classification performance parameters, like, dice coefficient, sensitivity, positive predictive value and accuracy are tabulated. In the case of compression, we report, performance parameters like mean square error and peak signal to noise ratio for a given set of bits per pixel (bpp) values. We found that the compression scheme considered in our setup gives promising results as compared to other schemes

Multi-modal and multi-dimensional biomedical image data analysis using deep learning

There is a growing need for the development of computational methods and tools for automated, objective, and quantitative analysis of biomedical signal and image data to facilitate disease and treatment monitoring, early diagnosis, and scientific discovery. Recent advances in artificial intelligence and machine learning, particularly in deep learning, have revolutionized computer vision and image analysis for many application areas. While processing of non-biomedical signal, image, and video data using deep learning methods has been very successful, high-stakes biomedical applications present unique challenges such as different image modalities, limited training data, need for explainability and interpretability etc. that need to be addressed. In this dissertation, we developed novel, explainable, and attention-based deep learning frameworks for objective, automated, and quantitative analysis of biomedical signal, image, and video data. The proposed solutions involve multi-scale signal analysis for oraldiadochokinesis studies; ensemble of deep learning cascades using global soft attention mechanisms for segmentation of meningeal vascular networks in confocal microscopy; spatial attention and spatio-temporal data fusion for detection of rare and short-term video events in laryngeal endoscopy videos; and a novel discrete Fourier transform driven class activation map for explainable-AI and weakly-supervised object localization and segmentation for detailed vocal fold motion analysis using laryngeal endoscopy videos. Experiments conducted on the proposed methods showed robust and promising results towards automated, objective, and quantitative analysis of biomedical data, that is of great value for potential early diagnosis and effective disease progress or treatment monitoring.Includes bibliographical references

Learning to segment in images and videos with different forms of supervision

Much progress has been made in image and video segmentation over the last years. To a large extent, the success can be attributed to the strong appearance models completely learned from data, in particular using deep learning methods. However, to perform best these methods require large representative datasets for training with expensive pixel-level annotations, which in case of videos are prohibitive to obtain. Therefore, there is a need to relax this constraint and to consider alternative forms of supervision, which are easier and cheaper to collect. In this thesis, we aim to develop algorithms for learning to segment in images and videos with different levels of supervision. First, we develop approaches for training convolutional networks with weaker forms of supervision, such as bounding boxes or image labels, for object boundary estimation and semantic/instance labelling tasks. We propose to generate pixel-level approximate groundtruth from these weaker forms of annotations to train a network, which allows to achieve high-quality results comparable to the full supervision quality without any modifications of the network architecture or the training procedure. Second, we address the problem of the excessive computational and memory costs inherent to solving video segmentation via graphs. We propose approaches to improve the runtime and memory efficiency as well as the output segmentation quality by learning from the available training data the best representation of the graph. In particular, we contribute with learning must-link constraints, the topology and edge weights of the graph as well as enhancing the graph nodes - superpixels - themselves. Third, we tackle the task of pixel-level object tracking and address the problem of the limited amount of densely annotated video data for training convolutional networks. We introduce an architecture which allows training with static images only and propose an elaborate data synthesis scheme which creates a large number of training examples close to the target domain from the given first frame mask. With the proposed techniques we show that densely annotated consequent video data is not necessary to achieve high-quality temporally coherent video segmentation results. In summary, this thesis advances the state of the art in weakly supervised image segmentation, graph-based video segmentation and pixel-level object tracking and contributes with the new ways of training convolutional networks with a limited amount of pixel-level annotated training data.In der Bild- und Video-Segmentierung wurden im Laufe der letzten Jahre große Fortschritte erzielt. Dieser Erfolg beruht weitgehend auf starken Appearance Models, die vollständig aus Daten gelernt werden, insbesondere mit Deep Learning Methoden. Für beste Performanz benötigen diese Methoden jedoch große repräsentative Datensätze für das Training mit teuren Annotationen auf Pixelebene, die bei Videos unerschwinglich sind. Deshalb ist es notwendig, diese Einschränkung zu überwinden und alternative Formen des überwachten Lernens in Erwägung zu ziehen, die einfacher und kostengünstiger zu sammeln sind. In dieser Arbeit wollen wir Algorithmen zur Segmentierung von Bildern und Videos mit verschiedenen Ebenen des überwachten Lernens entwickeln. Zunächst entwickeln wir Ansätze zum Training eines faltenden Netzwerkes (convolutional network) mit schwächeren Formen des überwachten Lernens, wie z.B. Begrenzungsrahmen oder Bildlabel, für Objektbegrenzungen und Semantik/Instanz- Klassifikationsaufgaben. Wir schlagen vor, aus diesen schwächeren Formen von Annotationen eine annähernde Ground Truth auf Pixelebene zu generieren, um ein Netzwerk zu trainieren, das hochwertige Ergebnisse ermöglicht, die qualitativ mit denen bei voll überwachtem Lernen vergleichbar sind, und dies ohne Änderung der Netzwerkarchitektur oder des Trainingsprozesses. Zweitens behandeln wir das Problem des beträchtlichen Rechenaufwands und Speicherbedarfs, das der Segmentierung von Videos mittels Graphen eigen ist. Wir schlagen Ansätze vor, um sowohl die Laufzeit und Speichereffizienz als auch die Qualität der Segmentierung zu verbessern, indem aus den verfügbaren Trainingsdaten die beste Darstellung des Graphen gelernt wird. Insbesondere leisten wir einen Beitrag zum Lernen mit must-link Bedingungen, zur Topologie und zu Kantengewichten des Graphen sowie zu verbesserten Superpixeln. Drittens gehen wir die Aufgabe des Objekt-Tracking auf Pixelebene an und befassen uns mit dem Problem der begrenzten Menge von dicht annotierten Videodaten zum Training eines faltenden Netzwerkes. Wir stellen eine Architektur vor, die das Training nur mit statischen Bildern ermöglicht, und schlagen ein aufwendiges Schema zur Datensynthese vor, das aus der gegebenen ersten Rahmenmaske eine große Anzahl von Trainingsbeispielen ähnlich der Zieldomäne schafft. Mit den vorgeschlagenen Techniken zeigen wir, dass dicht annotierte zusammenhängende Videodaten nicht erforderlich sind, um qualitativ hochwertige zeitlich kohärente Resultate der Segmentierung von Videos zu erhalten. Zusammenfassend lässt sich sagen, dass diese Arbeit den Stand der Technik in schwach überwachter Segmentierung von Bildern, graphenbasierter Segmentierung von Videos und Objekt-Tracking auf Pixelebene weiter entwickelt, und mit neuen Formen des Trainings faltender Netzwerke bei einer begrenzten Menge von annotierten Trainingsdaten auf Pixelebene einen Beitrag leistet

Ultrasound Imaging Innovations for Visualization and Quantification of Vascular Biomarkers

The existence of plaque in the carotid arteries, which provide circulation to the brain, is a known risk for stroke and dementia. Alas, this risk factor is present in 25% of the adult population. Proper assessment of carotid plaque may play a significant role in preventing and managing stroke and dementia. However, current plaque assessment routines have known limitations in assessing individual risk for future cardiovascular events. There is a practical need to derive new vascular biomarkers that are indicative of cardiovascular risk based on hemodynamic information. Nonetheless, the derivation of these biomarkers is not a trivial technical task because none of the existing clinical imaging modalities have adequate time resolution to track the spatiotemporal dynamics of arterial blood flow that is pulsatile in nature. The goal of this dissertation is to devise a new ultrasound imaging framework to measure vascular biomarkers related to turbulent flow, intra-plaque microvasculature, and blood flow rate. Central to the proposed framework is the use of high frame rate ultrasound (HiFRUS) imaging principles to track hemodynamic events at fine temporal resolution (through using frame rates of greater than 1000 frames per second). The existence of turbulent flow and intra-plaque microvessels, as well as anomalous blood flow rate, are all closely related to the formation and progression of carotid plaque. Therefore, quantifying these biomarkers can improve the identification of individuals with carotid plaque who are at risk for future cardiovascular events. To facilitate the testing and the implementation of the proposed imaging algorithms, this dissertation has included the development of new experimental models (in the form of flow phantoms) and a new HiFRUS imaging platform with live scanning and on-demand playback functionalities. Pilot studies were also carried out on rats and human volunteers. Results generally demonstrated the real-time performance and the practical efficacy of the proposed algorithms. The proposed ultrasound imaging framework is expected to improve carotid plaque risk classification and, in turn, facilitate timely identification of at-risk individuals. It may also be used to derive new insights on carotid plaque formation and progression to aid disease management and the development of personalized treatment strategies