Related papers: An automated workflow for parallel processing of l…
The Large Synoptic Survey Telescope (LSST) is an ambitious astronomical survey with a similarly ambitious Data Management component. Data Management for LSST includes processing on both nightly and yearly cadences to generate transient…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
Over the last two decades, scientific workflow management systems (SWfMS) have emerged as a means to facilitate the design, execution, and monitoring of reusable scientific data processing pipelines. At the same time, the amounts of data…
Fluorescence microscopy is widely employed for the analysis of living biological samples; however, the utility of the resulting recordings is frequently constrained by noise, temporal variability, and inconsistent visualisation of signals…
In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution employs the point spread functions…
We propose, implement, and experimentally evaluate a runtime middleware to support high-throughput execution on hybrid cluster machines of large-scale analysis applications. A hybrid cluster machine consists of computation nodes which have…
Computational models have become one of the prevalent methods to model complex phenomena. To accurately model complex interactions, such as detailed biomolecular interactions, scientists often rely on multiscale models comprised of several…
Runtime scheduling and workflow systems are an increasingly popular algorithmic component in HPC because they allow full system utilization with relaxed synchronization requirements. There are so many special-purpose tools for task…
Fluorescence lifetime imaging microscopy (FLIM) provides detailed information about molecular interactions and biological processes. A major bottleneck for FLIM is image resolution at high acquisition speeds, due to the engineering and…
High-throughput imaging workflows, such as Parallel Rapid Imaging with Spectroscopic Mapping (PRISM), generate data at rates that exceed conventional real-time processing capabilities. We present a scalable FPGA-based preprocessing pipeline…
The rapid development of computation power and machine learning algorithms has paved the way for automating scientific discovery with a scanning probe microscope (SPM). The key elements towards operationalization of automated SPM are the…
Very High Resolution satellite and aerial imagery are used to monitor and conduct large scale surveys of ecological systems. Convolutional Neural Networks have successfully been employed to analyze such imagery to detect large animals and…
Scanning fluorescence correlation spectroscopy (SFCS) with a scan path perpendicular to the membrane plane was introduced to measure diffusion and interactions of fluorescent components in free standing biomembranes. Using a confocal laser…
We report a novel microscopy platform, termed Multi-Aperture Fourier ptychographic microscopy (MA-FPM), capable of realizing gigapixel complex field images with large data acquisition bandwidths - in gigapixels per second. MA-FPM is a…
Light sheet fluorescence microscopy (LSFM) has transformed the way we visualize biological tissues in three dimensions, offering high-resolution imaging while minimizing photo-induced damage to the samples. Recent breakthroughs in…
High-Level Synthesis allows hardware designers to create complex RTL designs using C/C++. The traditional HLS workflow involves iterations of C/C++ simulation for partial functional verification and HLS synthesis for coarse timing…
Occlusions between consecutive frames have long posed a significant challenge in optical flow estimation. The inherent ambiguity introduced by occlusions directly violates the brightness constancy constraint and considerably hinders…
By integrating a phase-only Spatial Light Modulator (SLM) into the illumination arm of a cylindrical-lens-based Selective Plane Illumination Microscope (SPIM), we have created a versatile system able to deliver high quality images by…
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
Modern parallel computing devices, such as the graphics processing unit (GPU), have gained significant traction in scientific and statistical computing. They are particularly well-suited to data-parallel algorithms such as the particle…