Related papers: USID and Pycroscopy -- Open frameworks for storing…
We propose a new file format named "H5MD" for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD…
This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome…
The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…
Scientific data across physics, materials science, and materials engineering often lacks adherence to FAIR principles (Barker et al., 2022; Jacobsen et al., 2020; M. D. Wilkinson et al., 2016; S. R. Wilkinson et al., 2025) due to…
Hyperspectral imaging (HSI) is an advanced sensing modality that simultaneously captures spatial and spectral information, enabling non-invasive, label-free analysis of material, chemical, and biological properties. This Primer presents a…
Despite image reconstruction becoming more widespread when interpreting OIFITS Data, model fitting in u,v space often remains the best way to interpret data, either because of the sparsity of the data, or because a quantitative measurement…
SHallow REcurrent Decoders (SHRED) provide a deep learning strategy for modeling high-dimensional dynamical systems and/or spatiotemporal data from dynamical system snapshot observations. PySHRED is a Python package that implements SHRED…
New and upgraded radio interferometers produce data at massive rates and will require significant improvements in analysis techniques to reach their promised levels of performance in a routine manner. Until these techniques are fully…
Dataframes are a popular abstraction to represent, prepare, and analyze data. Despite the remarkable success of dataframe libraries in Rand Python, dataframes face performance issues even on moderately large datasets. Moreover, there is…
The digitization of biological specimens has revolutionized the field of morphology, creating large collections of 3D data, and microCT in particular. This revolution was initially supported by the development of open-source software tools,…
Spectropolarimetry, the observation of polarization and intensity as a function of wavelength, is a powerful tool in stellar astrophysics. It is particularly useful for characterizing stars and circumstellar material, and for tracing the…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
The quest for deeper understanding of biological systems has driven the acquisition of increasingly larger multidimensional image datasets. Inspecting and manipulating data of this complexity is very challenging in traditional visualization…
We present a new version of the FIT3D and Pipe3D codes, two packages to derive properties of the stellar populations and the ionized emission lines from optical spectroscopy and integral field spectroscopy data respectively. The new codes…
With advanced imaging, sequencing, and profiling technologies, multiple omics data become increasingly available and hold promises for many healthcare applications such as cancer diagnosis and treatment. Multimodal learning for integrative…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Digital computational outputs are now ubiquitous in the research workflow and the way in which these data are stored and cataloged is becoming more standardized across fields of research. However, even with accessible data and code, the…
Research in ultrasound imaging is limited in reproducibility by two factors: First, many existing ultrasound pipelines are protected by intellectual property, rendering exchange of code difficult. Second, most pipelines are implemented in…
The rapid expansion of the Internet of Things (IoT) and smart home ecosystems has led to a fragmented landscape of user data management across consumer electronics (CE) such as Smart TVs, gaming consoles, and set-top boxes. Current…