Joint segmentation and classification of retinal arteries/veins from fundus images

Objective Automatic artery/vein (A/V) segmentation from fundus images is required to track blood vessel changes occurring with many pathologies including retinopathy and cardiovascular pathologies. One of the clinical measures that quantifies vessel changes is the arterio-venous ratio (AVR) which represents the ratio between artery and vein diameters. This measure significantly depends on the accuracy of vessel segmentation and classification into arteries and veins. This paper proposes a fast, novel method for semantic A/V segmentation combining deep learning and graph propagation. Methods A convolutional neural network (CNN) is proposed to jointly segment and classify vessels into arteries and veins. The initial CNN labeling is propagated through a graph representation of the retinal vasculature, whose nodes are defined as the vessel branches and edges are weighted by the cost of linking pairs of branches. To efficiently propagate the labels, the graph is simplified into its minimum spanning tree. Results The method achieves an accuracy of 94.8% for vessels segmentation. The A/V classification achieves a specificity of 92.9% with a sensitivity of 93.7% on the CT-DRIVE database compared to the state-of-the-art-specificity and sensitivity, both of 91.7%. Conclusion The results show that our method outperforms the leading previous works on a public dataset for A/V classification and is by far the fastest. Significance The proposed global AVR calculated on the whole fundus image using our automatic A/V segmentation method can better track vessel changes associated to diabetic retinopathy than the standard local AVR calculated only around the optic disc.Comment: Preprint accepted in Artificial Intelligence in Medicin

Combining Shape and Learning for Medical Image Analysis

Automatic methods with the ability to make accurate, fast and robust assessments of medical images are highly requested in medical research and clinical care. Excellent automatic algorithms are characterized by speed, allowing for scalability, and an accuracy comparable to an expert radiologist. They should produce morphologically and physiologically plausible results while generalizing well to unseen and rare anatomies. Still, there are few, if any, applications where today\u27s automatic methods succeed to meet these requirements.\ua0The focus of this thesis is two tasks essential for enabling automatic medical image assessment, medical image segmentation and medical image registration. Medical image registration, i.e. aligning two separate medical images, is used as an important sub-routine in many image analysis tools as well as in image fusion, disease progress tracking and population statistics. Medical image segmentation, i.e. delineating anatomically or physiologically meaningful boundaries, is used for both diagnostic and visualization purposes in a wide range of applications, e.g. in computer-aided diagnosis and surgery.The thesis comprises five papers addressing medical image registration and/or segmentation for a diverse set of applications and modalities, i.e. pericardium segmentation in cardiac CTA, brain region parcellation in MRI, multi-organ segmentation in CT, heart ventricle segmentation in cardiac ultrasound and tau PET registration. The five papers propose competitive registration and segmentation methods enabled by machine learning techniques, e.g. random decision forests and convolutional neural networks, as well as by shape modelling, e.g. multi-atlas segmentation and conditional random fields

Deep learning for cardiac image segmentation: A review

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Human Treelike Tubular Structure Segmentation: A Comprehensive Review and Future Perspectives

Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure provides insights into disease diagnosis, treatment planning, and prognosis. Manually labelling extensive data by radiologists is often time-consuming and error-prone. As a result, automated or semi-automated computational models have become a popular research field of medical imaging in the past two decades, and many have been developed to date. In this survey, we aim to provide a comprehensive review of currently publicly available datasets, segmentation algorithms, and evaluation metrics. In addition, current challenges and future research directions are discussed.Comment: 30 pages, 19 figures, submitted to CBM journa

Towards New Classes of Intelligent Cognitive Information Systems for Semantic Pattern Classification

This paper introduces two new classes of specialised vision systems called UBIAS and E-UBIAS. Such systems belong to the group of cognitive reasoning systems and are designed for the semantic analysis of visual patterns in the form of medical images. Proposed systems are predecessors of a new generation of intelligent systems dedicated for understanding medical diagnostic visualization and using this data as biometric characteristics

Human treelike tubular structure segmentation: A comprehensive review and future perspectives

Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure provides insights into disease diagnosis, treatment planning, and prognosis. Manually labelling extensive data by radiologists is often time-consuming and error-prone. As a result, automated or semi-automated computational models have become a popular research field of medical imaging in the past two decades, and many have been developed to date. In this survey, we aim to provide a comprehensive review of currently publicly available datasets, segmentation algorithms, and evaluation metrics. In addition, current challenges and future research directions are discussed