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Convolutional neural networks have been applied to a wide variety of computer vision tasks. Recent advances in semantic segmentation have enabled their application to medical image segmentation. While most CNNs use two-dimensional kernels,…

Quantifying axon and myelin properties (e.g., axon diameter, myelin thickness, g-ratio) in histology images can provide useful information about microstructural changes caused by neurodegenerative diseases. Automatic tissue segmentation is…

Brain segmentation from neonatal MRI images is a very challenging task due to large changes in the shape of cerebral structures and variations in signal intensities reflecting the gestational process. In this context, there is a clear need…

The rise of Transformer architectures has advanced medical image segmentation, leading to hybrid models that combine Convolutional Neural Networks (CNNs) and Transformers. However, these models often suffer from excessive complexity and…

Surface reconstruction from point clouds is a fundamental challenge in computer graphics and medical imaging. In this paper, we explore the application of advanced neural network architectures for the accurate and efficient reconstruction…

Brain extraction, registration and segmentation are indispensable preprocessing steps in neuroimaging studies. The aim is to extract the brain from raw imaging scans (i.e., extraction step), align it with a target brain image (i.e.,…

MRI tumor segmentation remains a critical challenge in medical imaging, where volumetric analysis faces unique computational demands due to the complexity of 3D data. The spatially sequential arrangement of adjacent MRI slices provides…

The main objective of image segmentation is to divide an image into homogeneous regions for further analysis. This is a significant and crucial task in many applications such as medical imaging. Deep learning (DL) methods have been proposed…

The inability to acquire clean high-resolution (HR) electron microscopy (EM) images over a large brain tissue volume hampers many neuroscience studies. To address this challenge, we propose a deep-learning-based image super-resolution (SR)…

The performance of existing supervised neuron segmentation methods is highly dependent on the number of accurate annotations, especially when applied to large scale electron microscopy (EM) data. By extracting semantic information from…

Volumetric image segmentation with convolutional neural networks (CNNs) encounters several challenges, which are specific to medical images. Among these challenges are large volumes of interest, high class imbalances, and difficulties in…

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…

Electron microscopy (EM) imaging offers unparalleled resolution for analyzing neural tissues, crucial for uncovering the intricacies of synaptic connections and neural processes fundamental to understanding behavioral mechanisms. Recently,…

Accurate surface geometry representation is crucial in 3D visual computing. Explicit representations, such as polygonal meshes, and implicit representations, like signed distance functions, each have distinct advantages, making efficient…

Accurate image segmentation plays a crucial role in medical image analysis, yet it faces great challenges of various shapes, diverse sizes, and blurry boundaries. To address these difficulties, square kernel-based encoder-decoder…

Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document…

In medical imaging, there are clinically relevant segmentation tasks where the output mask is a projection to a subset of input image dimensions. In this work, we propose a novel convolutional neural network architecture that can…

Accurate segmentation of brain tumors from 3D multimodal MRI is vital for diagnosis and treatment planning across diverse brain tumors. This paper addresses the challenges posed by the BraTS 2023, presenting a unified transfer learning…

Semantic segmentation of electron microscopy (EM) is an essential step to efficiently obtain reliable morphological statistics. Despite the great success achieved using deep convolutional neural networks (CNNs), they still produce coarse…

X-ray computed tomography is a powerful tool for volumetric imaging, where three-dimensional (3D) images are generated from a large number of individual X-ray projection images. Collecting the required number of low noise projection images…