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NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM. The network is trained on 5,000 T1-weighted brain MRI scans from the UK Biobank Imaging…
Primary neuronal cultures have been widely used to study neuronal morphology, neurophysiology, neurodegenerative processes, and molecular mechanism of synaptic plasticity underlying learning and memory. Yet, the unique behavioral properties…
Accurate and reliable nuclei identification is an essential part of quantification in microscopy. A range of mathematical and machine learning approaches are used but all methods have limitations. Such limitations include sensitivity to…
Semantic segmentation of neuronal structures in 3D high-resolution fluorescence microscopy imaging of the human brain cortex can take advantage of bidimensional CNNs, which yield good results in neuron localization but lead to inaccurate…
Fluorescence microscopy is a widely used method among cell biologists for studying the localization and co-localization of fluorescent protein. For microbial cell biologists, these studies often include tedious and time-consuming manual…
MR images of fetuses allow clinicians to detect brain abnormalities in an early stage of development. The cornerstone of volumetric and morphologic analysis in fetal MRI is segmentation of the fetal brain into different tissue classes.…
A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for…
Segmentations are often necessary for the analysis of image data. They are used to identify different objects, for example cell nuclei, mitochondria, or complete cells in microscopic images. There might be features in the data, that cannot…
Fluorescence Microcopy Calcium Imaging is a fundamental tool to in-vivo record and analyze large scale neuronal activities simultaneously at a single cell resolution. Automatic and precise detection of behaviorally relevant neuron activity…
Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors,…
State-of-the-art methods for semantic segmentation of images involve computationally intensive neural network architectures. Most of these methods are not adaptable to high-resolution image segmentation due to memory and other computational…
Automatic segmentation in MR brain images is important for quantitative analysis in large-scale studies with images acquired at all ages. This paper presents a method for the automatic segmentation of MR brain images into a number of tissue…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity…
Automatic lymph node segmentation is the cornerstone for advances in computer vision tasks for early detection and staging of cancer. Traditional segmentation methods are constrained by manual delineation and variability in operator…
Analysis of retinal fundus images is essential for eye-care physicians in the diagnosis, care and treatment of patients. Accurate fundus and/or retinal vessel maps give rise to longitudinal studies able to utilize multimedia image…
Purpose: Accurate wound segmentation is essential for automated DESIGN-R scoring. However, existing models such as FUSegNet, which are trained primarily on foot ulcer datasets, often fail to generalize to wounds on other body sites.…
Advances in optical neuroimaging techniques now allow neural activity to be recorded with cellular resolution in awake and behaving animals. Brain motion in these recordings pose a unique challenge. The location of individual neurons must…
Identifying the extent of brain tumors is a significant challenge in brain cancer treatment. The main difficulty is in the approximate detection of tumor size. Magnetic resonance imaging (MRI) has become a critical diagnostic tool. However,…
Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…