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Imaging through scattering is a pervasive and difficult problem in many biological applications. The high background and the exponentially attenuated target signals due to scattering fundamentally limits the imaging depth of fluorescence…

Three-dimensional (3D) fluorescence microscopy in general requires axial scanning to capture images of a sample at different planes. Here we demonstrate that a deep convolutional neural network can be trained to virtually refocus a 2D…

We present 3DeepCT, a deep neural network for computed tomography, which performs 3D reconstruction of scattering volumes from multi-view images. Our architecture is dictated by the stationary nature of atmospheric cloud fields. The task of…

High-fidelity electron microscopy simulations required for quantitative crystal structure refinements face a fundamental challenge: while physical interactions are well-described theoretically, real-world experimental effects are…

Relying on either deep models or physical models are two mainstream approaches for solving inverse sample reconstruction problems in programmable illumination computational microscopy. Solutions based on physical models possess strong…

Phase retrieval, the problem of recovering lost phase information from measured intensity alone, is an inverse problem that is widely faced in various imaging modalities ranging from astronomy to nanoscale imaging. The current process of…

Deep neural networks have emerged as effective tools for computational imaging including quantitative phase microscopy of transparent samples. To reconstruct phase from intensity, current approaches rely on supervised learning with training…

Autonomous synthesis and characterization of inorganic materials requires the automatic and accurate analysis of X-ray diffraction spectra. For this task, we designed a probabilistic deep learning algorithm to identify complex multi-phase…

Advances in fluorescence microscopy enable acquisition of 3D image volumes with better image quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images and…

In medical imaging analysis, deep learning has shown promising results. We frequently rely on volumetric data to segment medical images, necessitating the use of 3D architectures, which are commended for their capacity to capture interslice…

A modulated icosahedral shell with an inclusion is a concise description of many viruses, including recently-discovered large double-stranded DNA ones. Many X-ray scattering patterns of such viruses show major polygonal fringes, which can…

Neural implicit representations have become a popular choice for modeling surfaces due to their adaptability in resolution and support for complex topology. While previous works have achieved impressive reconstruction quality by training on…

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own…

Traditional iterative reconstruction methods are accurate but computationally expensive, limiting their use in high-throughput and real-time ptychography. Recent deep learning approaches improve speed, but often predict phase as a Euclidean…

The inverse scattering problem is of critical importance in a number of fields, including medical imaging, sonar, sensing, non-destructive evaluation, and several others. The problem of interest can vary from detecting the shape to the…

Statistical shape modeling (SSM) directly from 3D medical images is an underutilized tool for detecting pathology, diagnosing disease, and conducting population-level morphology analysis. Deep learning frameworks have increased the…

Many deep learning based automated medical image segmentation systems, in reality, face difficulties in deployment due to the cost of massive data annotation and high latency in model iteration. We propose a dynamic interactive learning…

The deep neural network is a research hotspot for histopathological image analysis, which can improve the efficiency and accuracy of diagnosis for pathologists or be used for disease screening. The whole slide pathological image can reach…

3D shape reconstruction typically requires identifying object features or textures in multiple images of a subject. This approach is not viable when the subject is semi-transparent and moving in and out of focus. Here we overcome these…

Automated cell segmentation in microscopy images is essential for biomedical research, yet conventional methods are labor-intensive and prone to error. While deep learning-based approaches have proven effective, they often require large…