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With a video data source, such as multispectral video acquired during administration of fluorescent tracers, extraction of time-resolved data typically requires the compensation of motion. While this can be done manually, which is arduous,…
This article presents MuMFiM, an open source application for multiscale modeling of fibrous materials on massively parallel computers. MuMFiM uses two scales to represent fibrous materials such as biological network materials (extracellular…
Over the past decade, deep learning (DL) research in computer vision has been growing rapidly, with many advances in DL-based image analysis methods for biomedical problems. In this work, we introduce MMV_Im2Im, a new open-source python…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
Full-field optical coherence tomography (FF-OCT) offers label-free, high-resolution imaging of biological samples but remains limited by slow acquisition due to piezoelectric mirror modulation. We present a continuous-scanning FF-OCT method…
We demonstrate in vivo endoscopic optical coherence tomography (OCT) imaging in the forward direction using a flexible fiber bundle. In comparison to current conventional forward looking probe schemes, our approach simplifies the endoscope…
We present a comprehensive methodology for the simulation of astronomical images from optical survey telescopes. We use a photon Monte Carlo approach to construct images by sampling photons from models of astronomical source populations,…
With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse…
We present an MPI-parallel algorithm for the in-situ visualization of computational data that is built around a distributed linear forest-of-octrees data structure. Such octrees are frequently used in element-based numerical simulations;…
Visualizing and navigating through large astronomy images from a remote location with current astronomy display tools can be a frustrating experience in terms of speed and ergonomics, especially on mobile devices. In this paper, we present…
Libpsht (or "library for Performant Spherical Harmonic Transforms") is a collection of algorithms for efficient conversion between spatial-domain and spectral-domain representations of data defined on the sphere. The package supports…
Summary: VTX is a molecular visualization software capable to handle most molecular structures and dynamics trajectories file formats. It features a real-time high-performance molecular graphics engine, based on modern OpenGL, optimized for…
Despite having achieved real-time performance in mesh construction, most of the current LiDAR odometry and meshing methods may struggle to deal with complex scenes due to relying on explicit meshing schemes. They are usually sensitive to…
The increasingly popular light sheet microscopy techniques generate very large 3D time-lapse recordings of living biological specimen. The necessity to make large volumetric datasets available for interactive visualization and analysis has…
Optical Coherence Tomography (OCT) has become an indispensable tool for investigating mesoscopic features in soft matter and fluid mechanics. Its ability to provide high-resolution, non-invasive measurements in both spatial and temporal…
With the development of high-speed electron detectors, four-dimensional scanning transmission electron microscopy (4D-STEM) has emerged as a powerful tool for characterizing microstructures in material science and life science. However, the…
Twisted light carrying orbital angular momentum (OAM) provides an additional degree of freedom for modern optics and an emerging resource for both classical and quantum information technologies. Its inherently infinite dimensions can…
Cardiovascular MRI (CMR) is a non-invasive imaging modality that provides excellent soft-tissue contrast without the use of ionizing radiation. Physiological motions and limited speed of MRI data acquisition necessitate development of…
The physical size of optical imaging systems is one of the greatest constraints on their use, limiting the performance and deployment of a range of systems from telescopes to mobile phone cameras. Spaceplates are nonlocal optical devices…
Statistical Parametric Mapping (SPM) is an integrated set of methods for testing hypotheses about the brain's structure and function, using data from imaging devices. These methods are implemented in an open source software package, SPM,…