Related papers: Toward an Automated HPC Pipeline for Processing La…

Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…

Reconstructing a map of neuronal connectivity is a critical challenge in contemporary neuroscience. Recent advances in high-throughput serial section electron microscopy (EM) have produced massive 3D image volumes of nanoscale brain tissue…

The construction of large-scale, high-quality datasets is a fundamental prerequisite for developing robust and generalizable foundation models in motor imagery (MI)-based brain-computer interfaces (BCIs). However, EEG signals collected from…

The study of neurocognitive tasks requiring accurate localisation of activity often rely on functional Magnetic Resonance Imaging, a widely adopted technique that makes use of a pipeline of data processing modules, each involving a variety…

If we are ever to unravel the mysteries of brain function at its most fundamental level, we will need a precise understanding of how its component neurons connect to each other. Electron Microscopes (EM) can now provide the nanometer…

In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…

Reconstructing a synaptic wiring diagram, or connectome, from electron microscopy (EM) images of brain tissue currently requires many hours of manual annotation or proofreading (Kasthuri and Lichtman, 2010; Lichtman and Sanes, 2008; Seung,…

This paper describes a scalable active learning pipeline prototype for large-scale brain mapping that leverages high performance computing power. It enables high-throughput evaluation of algorithm results, which, after human review, are…

Identifying complex neural circuitry from electron microscopic (EM) images may help unlock the mysteries of the brain. However, identifying this circuitry requires time-consuming, manual tracing (proofreading) due to the size and intricacy…

High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…

Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely…

A central problem in neuroscience is reconstructing neuronal circuits on the synapse level. Due to a wide range of scales in brain architecture such reconstruction requires imaging that is both high-resolution and high-throughput. Existing…

Human brain activity generates scalp potentials (electroencephalography EEG), intracranial potentials (iEEG), and external magnetic fields (magnetoencephalography MEG), all capable of being recorded, often simultaneously, for use in…

Massive upgrades to science infrastructure are driving data velocities upwards while stimulating adoption of increasingly data-intensive analytics. While next-generation exascale supercomputers promise strong support for I/O-intensive…

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…

The advent of modern, high-speed electron detectors has made the collection of multidimensional hyperspectral transmission electron microscopy datasets, such as 4D-STEM, a routine. However, many microscopists find such experiments daunting…

Electroencephalography (EEG) and local field potentials (LFP) are two widely used techniques to record electrical activity from the brain. These signals are used in both the clinical and research domains for multiple applications. However,…

The Open Knowledgebase of Interatomic Models (OpenKIM) is an NSF Science Gateway that archives fully functional computer implementations of interatomic models (potentials and force fields) and simulation codes that use them to compute…

Multiview light sheet fluorescence microscopy (LSFM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing…

We present HSIM: a dedicated pipeline for simulating observations with the HARMONI integral field spectrograph on the European Extremely Large Telescope. HSIM takes high spectral and spatial resolution input data-cubes, encoding physical…