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High-quality labeled data is essential to successfully train supervised machine learning models. Although a large amount of unlabeled data is present in the medical domain, labeling poses a major challenge: medical professionals who can…

Magnetic Resonance Imaging (MRI) is widely used in routine clinical diagnosis and treatment. However, variations in MRI acquisition protocols result in different appearances of normal and diseased tissue in the images. Convolutional neural…

Convolutional neural networks demonstrated outstanding empirical results in computer vision and speech recognition tasks where labeled training data is abundant. In medical imaging, there is a huge variety of possible imaging modalities and…

Radiation therapy (RT) is widely employed in the clinic for the treatment of head and neck (HaN) cancers. An essential step of RT planning is the accurate segmentation of various organs-at-risks (OARs) in HaN CT images. Nevertheless,…

Deep convolutional neural networks (CNNs), especially fully convolutional networks, have been widely applied to automatic medical image segmentation problems, e.g., multi-organ segmentation. Existing CNN-based segmentation methods mainly…

While deep convolutional neural networks (CNNs) have shown a great success in single-label image classification, it is important to note that real world images generally contain multiple labels, which could correspond to different objects,…

This thesis studies how the segmentation results, produced by convolutional neural networks (CNN), is different from each other when applied to small biomedical datasets. We use different architectures, parameters and hyper-parameters,…

Segmentation of focal (localized) brain pathologies such as brain tumors and brain lesions caused by multiple sclerosis and ischemic strokes are necessary for medical diagnosis, surgical planning and disease development as well as other…

Large annotated datasets are vital for training segmentation models, but pixel-level labeling is time-consuming, error-prone, and often requires scarce expert annotators, especially in medical imaging. In contrast, coarse annotations are…

Image segmentation is a fundamental and challenging problem in computer vision with applications spanning multiple areas, such as medical imaging, remote sensing, and autonomous vehicles. Recently, convolutional neural networks (CNNs) have…

Many successful methods developed for medical image analysis that are based on machine learning use supervised learning approaches, which often require large datasets annotated by experts to achieve high accuracy. However, medical data…

In recent years, deep convolutional neural networks (CNNs) have shown record-shattering performance in a variety of computer vision problems, such as visual object recognition, detection and segmentation. These methods have also been…

The delineation of tumor target and organs-at-risk is critical in the radiotherapy treatment planning. Automatic segmentation can be used to reduce the physician workload and improve the consistency. However, the quality assurance of the…

Organ at risk (OAR) segmentation is a crucial step for treatment planning and outcome determination in radiotherapy treatments of cancer patients. Several deep learning based segmentation algorithms have been developed in recent years,…

In this paper we present a methodology that uses convolutional neural networks (CNNs) for segmentation by iteratively growing predicted mask regions in each coordinate direction. The CNN is used to predict class probability scores in a…

Segmentation and classification of cell nuclei in histopathology images using deep neural networks (DNNs) can save pathologists' time for diagnosing various diseases, including cancers, by automating cell counting and morphometric…

Training a Convolutional Neural Network (CNN) for semantic segmentation typically requires to collect a large amount of accurate pixel-level annotations, a hard and expensive task. In contrast, simple image tags are easier to gather. With…

Semantic image segmentation is one of the most important tasks in medical image analysis. Most state-of-the-art deep learning methods require a large number of accurately annotated examples for model training. However, accurate annotation…

Deep learning for medical image classification faces three major challenges: 1) the number of annotated medical images for training are usually small; 2) regions of interest (ROIs) are relatively small with unclear boundaries in the whole…

We propose a dual pathway, 11-layers deep, three-dimensional Convolutional Neural Network for the challenging task of brain lesion segmentation. The devised architecture is the result of an in-depth analysis of the limitations of current…