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Segmentation of magnetic resonance images (MRI) facilitates analysis of human brain development by delineating anatomical structures. However, in infants and young children, accurate segmentation is challenging due to development and…

Accurate measurement of fetal head circumference is crucial for estimating fetal growth during routine prenatal screening. Prior to measurement, it is necessary to accurately identify and segment the region of interest, specifically the…

Abnormal iron accumulation in the brain subcortical nuclei has been reported to be correlated to various neurodegenerative diseases, which can be measured through the magnetic susceptibility from the quantitative susceptibility mapping…

Segmentation is one of the most important tasks in MRI medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, head segmentation is commonly used for measuring and…

In this paper, we propose an end-to-end deep neural network for solving the problem of imbalanced large and small organ segmentation in head and neck (HaN) CT images. To conduct radiotherapy planning for nasopharyngeal cancer, more than 10…

3D medical image processing with deep learning greatly suffers from a lack of data. Thus, studies carried out in this field are limited compared to works related to 2D natural image analysis, where very large datasets exist. As a result,…

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,…

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…

Segmentation of brain structures from magnetic resonance (MR) scans plays an important role in the quantification of brain morphology. Since 3D deep learning models suffer from high computational cost, 2D deep learning methods are favored…

Removing skull artifacts from functional magnetic images (fMRI) is a well understood and frequently encountered problem. Because the fMRI field has grown mostly due to human studies, many new tools were developed to handle human data.…

Detection of brain tumor using a segmentation based approach is critical in cases, where survival of a subject depends on an accurate and timely clinical diagnosis. Gliomas are the most commonly found tumors having irregular shape and…

Brain extraction is a fundamental step for most brain imaging studies. In this paper, we investigate the problem of skull stripping and propose complementary segmentation networks (CompNets) to accurately extract the brain from T1-weighted…

One of the most common tasks in medical imaging is semantic segmentation. Achieving this segmentation automatically has been an active area of research, but the task has been proven very challenging due to the large variation of anatomy…

Purpose: The goal of this work was to develop a deep network for whole-head segmentation including clinical MRIs with abnormal anatomy, and compile the first public benchmark dataset for this purpose. We collected 98 MRIs with volumetric…

We introduce DeepNAT, a 3D Deep convolutional neural network for the automatic segmentation of NeuroAnaTomy in T1-weighted magnetic resonance images. DeepNAT is an end-to-end learning-based approach to brain segmentation that jointly learns…

This paper addresses the task of nuclei segmentation in high-resolution histopathological images. We propose an auto- matic end-to-end deep neural network algorithm for segmenta- tion of individual nuclei. A nucleus-boundary model is…

Brain tumor segmentation is a critical task in medical image analysis, aiding in the diagnosis and treatment planning of brain tumor patients. The importance of automated and accurate brain tumor segmentation cannot be overstated. It…

3D human segmentation has seen noticeable progress in re-cent years. It, however, still remains a challenge to date. In this paper, weintroduce a deep patch-based method for 3D human segmentation. Wefirst extract a local surface patch for…

Accurate brain tissue segmentation in Magnetic Resonance Imaging (MRI) has attracted the attention of medical doctors and researchers since variations in tissue volume help in diagnosing and monitoring neurological diseases. Several…

Brain morphometry from magnetic resonance imaging (MRI) is a consolidated biomarker for many neurodegenerative diseases. Recent advances in this domain indicate that deep convolutional neural networks can infer morphometric measurements…