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Automatic blood vessel extraction from 3D medical images is crucial for vascular disease diagnoses. Existing methods based on convolutional neural networks (CNNs) may suffer from discontinuities of extracted vessels when segmenting such…

Building discriminative representations for 3D data has been an important task in computer graphics and computer vision research. Convolutional Neural Networks (CNNs) have shown to operate on 2D images with great success for a variety of…

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…

A wide range of techniques can be considered for segmentation of images of nanostructured surfaces. Manually segmenting these images is time-consuming and results in a user-dependent segmentation bias, while there is currently no consensus…

Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have…

Automatic segmentation of fine-grained brain structures remains a challenging task. Current segmentation methods mainly utilize 2D and 3D deep neural networks. The 2D networks take image slices as input to produce coarse segmentation in…

Computer Aided Diagnosis has emerged as an indispensible technique for validating the opinion of radiologists in CT interpretation. This paper presents a deep 3D Convolutional Neural Network (CNN) architecture for automated CT scan-based…

Quantitative analysis of cell nuclei in microscopic images is an essential yet challenging source of biological and pathological information. The major challenge is accurate detection and segmentation of densely packed nuclei in images…

CNN-based volumetric methods that label individual voxels now dominate the field of biomedical segmentation. However, 3D surface representations are often required for proper analysis. They can be obtained by post-processing the labeled…

Three-dimensional (3D) fluorescence microscopy in general requires axial scanning to capture images of a sample at different planes. Here we demonstrate that a deep convolutional neural network can be trained to virtually refocus a 2D…

Convolutional neural networks (CNN) for multi-class segmentation of medical images are widely used today. Especially models with multiple outputs that can separately predict segmentation classes (regions) without relying on a probabilistic…

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…

Accurate automatic liver and tumor segmentation plays a vital role in treatment planning and disease monitoring. Recently, deep convolutional neural network (DCNNs) has obtained tremendous success in 2D and 3D medical image segmentation.…

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…

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…

Microvascular anatomy is known to be involved in various neurological disorders. However, understanding these disorders is hindered by the lack of imaging modalities capable of capturing the comprehensive three-dimensional vascular network…

The automated analysis of microscopy images is a challenge in the context of single-cell tracking and quantification. This work has as goals the study of the performance of deep learning for segmenting microscopy images and the improvement…

Nuclei segmentation is a fundamental task in histopathology image analysis. Typically, such segmentation tasks require significant effort to manually generate accurate pixel-wise annotations for fully supervised training. To alleviate such…

Accurate and automatic organ segmentation from 3D radiological scans is an important yet challenging problem for medical image analysis. Specifically, the pancreas demonstrates very high inter-patient anatomical variability in both its…

Cell segmentation and tracking in microscopy images are of great significance to new discoveries in biology and medicine. In this study, we propose a novel approach to combine cell segmentation and cell tracking into a unified end-to-end…