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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…
We present an end-to-end Convolutional Neural Network (CNN) approach for 3D reconstruction of knee bones directly from two bi-planar X-ray images. Clinically, capturing the 3D models of the bones is crucial for surgical planning, implant…
Reconstructing visual stimuli from non-invasive electroencephalography (EEG) remains challenging due to its low spatial resolution and high noise, particularly under realistic low-density electrode configurations. To address this, we…
Field-of-view and resolution trade-offs in X-Ray micro-computed tomography (micro-CT) imaging limit the characterization, analysis and model development of multi-scale porous systems. To this end, we developed an applied methodology…
Automation of brain tumors in 3D magnetic resonance images (MRIs) is key to assess the diagnostic and treatment of the disease. In recent years, convolutional neural networks (CNNs) have shown improved results in the task. However, high…
Retrospective analysis of brain MRI scans acquired in the clinic has the potential to enable neuroimaging studies with sample sizes much larger than those found in research datasets. However, analysing such clinical images "in the wild" is…
Magnetic resonance imaging (MRI) is an important non-invasive clinical tool that can produce high-resolution and reproducible images. However, a long scanning time is required for high-quality MR images, which leads to exhaustion and…
Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as…
Currently, connectomes (e.g., functional or structural brain graphs) can be estimated in humans at $\approx 1~mm^3$ scale using a combination of diffusion weighted magnetic resonance imaging, functional magnetic resonance imaging and…
Reconstructing visual stimulus images is a significant task in neural decoding, and up to now, most studies consider the functional magnetic resonance imaging (fMRI) as the signal source. However, the fMRI-based image reconstruction methods…
Neuron segmentation in electron microscopy (EM) aims to reconstruct the complete neuronal connectome; however, current deep learning-based methods are limited by their reliance on large-scale training data and extensive, time-consuming…
The reconstruction of cortical surfaces from brain magnetic resonance imaging (MRI) scans is essential for quantitative analyses of cortical thickness and sulcal morphology. Although traditional and deep learning-based algorithmic pipelines…
Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which…
Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts…
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…
Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional…
Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most…
Analysis and visualization of 3D microscopy images pose challenges due to anisotropic axial resolution, demanding volumetric super-resolution along the axial direction. While training a learning-based 3D super-resolution model seems to be a…
Fast and accurate MRI reconstruction is a key concern in modern clinical practice. Recently, numerous Deep-Learning methods have been proposed for MRI reconstruction, however, they usually fail to reconstruct sharp details from the…
Understanding how the brain encodes external stimuli and how these stimuli can be decoded from the measured brain activities are long-standing and challenging questions in neuroscience. In this paper, we focus on reconstructing the complex…