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In this study we explore the possibility to use deep learning for the reconstruction of phase images from 4D scanning transmission electron microscopy (4D-STEM) data. The process can be divided into two main steps. First, the complex…

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…

Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure…

Cryo-electron microscopy (cryo-EM) allows for the high-resolution reconstruction of 3D structures of proteins and other biomolecules. Successful reconstruction of both shape and movement greatly helps understand the fundamental processes of…

Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological…

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces…

Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…

Accurate determination of three-dimensional (3D) atomic structures is crucial for understanding and controlling the properties of nanomaterials. Atomic electron tomography (AET) offers non-destructive atomic imaging with picometer-level…

Segmentation has been a major task in neuroimaging. A large number of automated methods have been developed for segmenting healthy and diseased brain tissues. In recent years, deep learning techniques have attracted a lot of attention as a…

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…

The prospect of neural reconstruction from Electron Microscopy (EM) images has been elucidated by the automatic segmentation algorithms. Although segmentation algorithms eliminate the necessity of tracing the neurons by hand, significant…

Deep learning has been shown to produce state of the art results in many tasks in biomedical imaging, especially in segmentation. Moreover, segmentation of the cerebrovascular structure from magnetic resonance angiography is a challenging…

Motivation: Cellular Electron CryoTomography (CECT) is an emerging 3D imaging technique that visualizes subcellular organization of single cells at submolecular resolution and in near-native state. CECT captures large numbers of…

Dual energy computed tomography (DECT) has become of particular interest in clinic recent years. The DECT scan comprises two images, corresponding to two photon attenuation coefficients maps of the objects. Meanwhile, the DECT images are…

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS)…

Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information,…

Medical image segmentation is a fundamental task in the community of medical image analysis. In this paper, a novel network architecture, referred to as Convolution, Transformer, and Operator (CTO), is proposed. CTO employs a combination of…

Curvilinear structures frequently appear in microscopy imaging as the object of interest. Crystallographic defects, i.e., dislocations, are one of the curvilinear structures that have been repeatedly investigated under transmission electron…

Cryo-electron tomography (cryoET) is a crucial technique for unveiling the structure of protein complexes. Automatically analyzing tomograms captured by cryoET is an essential step toward understanding cellular structures. In this paper, we…

Although deep encoder-decoder networks have achieved astonishing performance for mitochondria segmentation from electron microscopy (EM) images, they still produce coarse segmentations with lots of discontinuities and false positives.…