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Deep Convolutional Neural Networks (CNNs) i.e. Residual Networks (ResNets) have been used successfully for many computer vision tasks, but are difficult to scale to 3D volumetric medical data. Memory is increasingly often the bottleneck…

Convolutional neural networks (CNNs) have been successfully used for brain tumor segmentation, specifically, fully convolutional networks (FCNs). FCNs can segment a set of voxels at once, having a direct spatial correspondence between units…

Resting-state functional MRI (rs-fMRI) scans hold the potential to serve as a diagnostic or prognostic tool for a wide variety of conditions, such as autism, Alzheimer's disease, and stroke. While a growing number of studies have…

Early detection and segmentation of skin lesions is crucial for timely diagnosis and treatment, necessary to improve the survival rate of patients. However, manual delineation is time consuming and subject to intra- and inter-observer…

Convolutional neural networks (CNNs) for biomedical image analysis are often of very large size, resulting in high memory requirement and high latency of operations. Searching for an acceptable compressed representation of the base CNN for…

In this paper, we propose a novel Convolutional Neural Network (CNN) architecture for learning multi-scale feature representations with good tradeoffs between speed and accuracy. This is achieved by using a multi-branch network, which has…

Neuroscientists classify neurons into different types that perform similar computations at different locations in the visual field. Traditional methods for neural system identification do not capitalize on this separation of 'what' and…

Electron microscopic connectomics is an ambitious research direction with the goal of studying comprehensive brain connectivity maps by using high-throughput, nano-scale microscopy. One of the main challenges in connectomics research is…

Recently, accurate mandible segmentation in CT scans based on deep learning methods has attracted much attention. However, there still exist two major challenges, namely, metal artifacts among mandibles and large variations in shape or size…

Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of…

Multiple Sclerosis (MS) is an autoimmune disease that leads to lesions in the central nervous system. Magnetic resonance (MR) images provide sufficient imaging contrast to visualize and detect lesions, particularly those in the white…

This paper analyzes the use of 3D Convolutional Neural Networks for brain tumor segmentation in MR images. We address the problem using three different architectures that combine fine and coarse features to obtain the final segmentation. We…

Machine Learning has considerably improved medical image analysis in the past years. Although data-driven approaches are intrinsically adaptive and thus, generic, they often do not perform the same way on data from different imaging…

Semantic image segmentation, which becomes one of the key applications in image processing and computer vision domain, has been used in multiple domains such as medical area and intelligent transportation. Lots of benchmark datasets are…

Deep Convolutional Neural Networks (DCNNs) are used extensively in medical image segmentation and hence 3D navigation for robot-assisted Minimally Invasive Surgeries (MISs). However, current DCNNs usually use down sampling layers for…

In today's digital age, Convolutional Neural Networks (CNNs), a subset of Deep Learning (DL), are widely used for various computer vision tasks such as image classification, object detection, and image segmentation. There are numerous types…

Whole brain segmentation from structural magnetic resonance imaging (MRI) is a prerequisite for most morphological analyses, but is computationally intense and can therefore delay the availability of image markers after scan acquisition. We…

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,…

Objective: Multiple Sclerosis (MS) is an autoimmune, and demyelinating disease that leads to lesions in the central nervous system. This disease can be tracked and diagnosed using Magnetic Resonance Imaging (MRI). Up to now a multitude of…

Computer-aided medical image analysis plays a significant role in assisting medical practitioners for expert clinical diagnosis and deciding the optimal treatment plan. At present, convolutional neural networks (CNN) are the preferred…