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DOE OSTI2023

The importance of recruitment and retention in Heliophysics: it’s not just a pipeline problem

A major obstacle in cultivating a robust Heliophysics (and broader scientific) community is the lack of diversity throughout science, technology, engineering, and mathematics (STEM) fields. For many years, this has been understood as a “leaky pipeline” analogy, in which predominately minority students initially interested in STEM gradually fall (or are pushed) out of the field on their way to a scientific research position. However, this ignores critical structural and policy issues which drive even later career Ph.D.s out of a career in Heliophysics. We identify here several systemic problems that inhibit many from participating fully in the Heliophysics community, including soft money pressure, lack of accessibility and equity, power imbalances, lack of accountability, friction in collaboration, and difficulties in forming mentorship bonds. We present several recommendations to empower research-supporting organizations to help create a culture of inclusion, openness, and innovative science.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRSDate not supplied

Transcriptomics Processing Pipelines for Space Biology: An Open Source and Consensus-Driven Approach

Transcriptomics holds significant value in elucidating the relationship between gene expression, experimental factors, biological factors, and various types of omics data. Enhancing our understanding of these connections is paramount for foundational biology, which plays a pivotal role in devising solutions for challenges pertinent to both space travel and terrestrial life. The NASA GeneLab project, part of the Open Science Data Repository (OSDR.nasa.gov), seeks to accelerate space biology research through cataloging and democratizing ‘omics data, including transcriptomics. Since raw omics data are largely inaccessible to non-bioinformaticians, GeneLab works with the scientific community via the Open Science Analysis Working Groups (AWGs) to develop standard processing pipelines to generate and publish processed data. Unlike raw data, processed data have greater immediate value to diverse users with varying technical backgrounds and computational capabilities. Standardizing processing workflows is essential to match the pace of raw data generation, ensure reproducibility, and enable standardized processed data for comparison across datasets. As of June 2023, transcriptomics studies comprise over half of GeneLab datasets hosted on the OSDR, including data from bulk RNA-seq and Affymetrix or Agilent 1-Channel DNA microarray assays. In collaboration with the AWGs, GeneLab developed consensus processing pipelines for these transcriptomics data types that includes quality control, background correction (microarray only), data normalization and quantification, culminating in the detection and annotation of differentially expressed genes. The work presented here describes Nextflow implementations of GeneLab’s consensus transcriptomics pipelines that automates and accelerates processing of these datasets. In addition to the core data processing, these workflows also include raw data staging and a robust verification and validation program to identify errors in real-time, stop additional downstream computation, and preserve computational resources. These workflows are used to generate GeneLab processed data hosted on the OSDR, and are publicly available as open source software for others to use at: https://github.com/nasa/GeneLab_Data_Processing.

Jonathan Oribello↗

DOE OSTI2026

Wyoming Trails Carbon Hub (WyoTCH)

The Wyoming Trails Carbon Hub (WyoTCH) project completed a front-end engineering and design (FEED) study for a commercial-scale, open-access carbon dioxide (CO 2 ) transport pipeline in Wyoming under U.S. Department of Energy (DOE) Award DEFE0032347, funded through the Bipartisan Infrastructure Law Carbon Capture Technology Program and administered by the National Energy Technology Laboratory. The project’s approach of designing a multi-source, multi-destination pipeline, rather than a dedicated line serving a single project, would lower the barrier to entry for individual CO 2 projects. The projects would leverage Wyoming's concentrated industrial and power generation CO 2 sources, its existing CO 2 pipeline infrastructure, and its extensive CO 2 storage and utilization capacity. This is the project's final technical report.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2025

Leveraging unlabeled SEM datasets with self-supervised learning for enhanced particle segmentation

Scanning Electron Microscopes (SEMs) are widely used in experimental science laboratories, often requiring cumbersome and repetitive user analysis. Automating SEM image analysis processes is highly desirable to address this challenge. In particle sample analysis, Machine Learning (ML) has emerged as the most effective approach for particle segmentation. However, the time-intensive process of manually annotating thousands of SEM images limits the applicability of supervised learning approaches. Self-Supervised Learning (SSL) offers a promising alternative by enabling knowledge extraction from raw, unlabeled data. This study presents a framework for evaluating SSL techniques in SEM image analysis, focusing on novel methods leveraging the ConvNeXtV2 architecture for particle detection. A dataset comprising 25,000 SEM images is curated to benchmark these proposed SSL methods. The results demonstrate that ConvNeXtV2 models, with varying parameter counts, consistently outperform other techniques in particle detection across different length scales, achieving up to a 34% reduction in relative error compared to established SSL methods. Furthermore, an ablation study explores the relationship between dataset size and SSL performance, providing actionable insights for practitioners regarding model selection and resource efficiency. This research advances the integration of SSL into autonomous analysis pipelines and supports its application in accelerating materials science discovery.

Rettenberger, Luca↗

DOE OSTI2020

Improving the Success of Underrepresented Populations in Computer and Computational Science Research with the CRA-W Women and URMD Grad Cohort Workshops

The Computing Research Association’s Committee on Widening Participation (CRA-WP) aims to increase the number of individual researchers from underrepresented groups in computing (UGC) (including women, underrepresented minorities, and persons with disabilities) who participate and succeed in computer science research at every stage of the research pipeline. Achieving these objectives requires that an increasing number of individuals from UGC start and progress to the next stage. The CRA-WP Grad Cohort Workshops are focused at the graduate level to maximize the likelihood participants will successfully complete their graduate degrees. Factors such as role models, skills, competence, confidence, mentoring, social support, and development of identity as a researcher help students to persist in graduate school, while factors such as sexism, racism, and dissatisfaction with their graduate program may cause them to leave. We, therefore, help first, second, and third year students build their skills, research strategies, and confidence; meet potential mentors from outside their institutions; develop connections with each other and with their research communities; and inform them about strategies for successful publishing, speaking, and advisor management strategies. By targeting early graduate students, we seek to help them stay in graduate school and in research.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NASA NTRS2013

The Hopkins Ultraviolet Telescope: The Final Archive

The Hopkins Ultraviolet Telescope (HUT) was a 0.9 m telescope and moderate-resolution (Delta)lambda equals 3 A) far-ultraviolet (820-1850 Å) spectrograph that flew twice on the space shuttle, in 1990 December (Astro-1, STS-35) and 1995 March (Astro-2, STS-67). The resulting spectra were originally archived in a nonstandard format that lacked important descriptive metadata. To increase their utility, we have modified the original datareduction software to produce a new and more user-friendly data product, a time-tagged photon list similar in format to the Intermediate Data Files (IDFs) produced by the Far Ultraviolet Spectroscopic Explorer calibration pipeline. We have transferred all relevant pointing and instrument-status information from locally-archived science and engineering databases into new FITS header keywords for each data set. Using this new pipeline, we have reprocessed the entire HUT archive from both missions, producing a new set of calibrated spectral products in a modern FITS format that is fully compliant with Virtual Observatory requirements. For each exposure, we have generated quicklook plots of the fully-calibrated spectrum and associated pointing history information. Finally, we have retrieved from our archives HUT TV guider images, which provide information on aperture positioning relative to guide stars, and converted them into FITS-format image files. All of these new data products are available in the new HUT section of the Mikulski Archive for Space Telescopes (MAST), along with historical and reference documents from both missions. In this article, we document the improved data-processing steps applied to the data and show examples of the new data products.

Hopkins↗

NASA NTRS2018

Astro-H/Hitomi Data Analysis, Processing, and Archive

Astro-H is the x-ray/gamma-ray mission led by Japan with international participation, launched on February 17, 2016. Soon after launch, Astro-H was renamed Hitomi. The payload consists of four different instruments (SXS, SXI, HXI, and SGD) that operate simultaneously to cover the energy range from 0.3 keV up to 600 keV. On March 27, 2016, JAXA lost contact with the satellite and, on April 28, they announced the cessation of the efforts to restore mission operations. Hitomi collected about one months worth of data with its instruments. This paper presents the analysis software and the data processing pipeline created to calibrate and analyze the Hitomi science data, along with the plan for the archive. These activities have been a collaborative effort shared between scientists and software engineers working in several institutes in Japan and United States.

Angelini, Lorella↗

NASA NTRSDate not supplied

GeoNEX: A geostationary earth observatory at NASA Earth eXchange: Earth monitoring from operational geostationary satellite systems

The latest generation of geostationary satellites (Himawari 8/9, GOES-16/17, FY-4, GK-2A) carries sensors that closely mimic the spatial and spectral characteristics of widely used polar-orbiting, global monitoring sensors such as MODIS and VIIRS. When combined, data from various currently operating/planned geostationary platforms provide a geo-ring of hyper-temporal (5-10 minutes), multispectral observations at spatial resolutions as high as 500 m. These high frequency observations offer exciting new possibilities for monitoring our planet, including better retrievals of geophysical variables by overcoming cloud cover, enabling studies of diurnally varying phenomena in the atmosphere, land, and the oceans, and support operational decision-making in agriculture, hydrology and disaster management. The NASA Earth Exchange (NEX) team, in collaboration with scientists from JAXA, KARI, NOAA and other international institutions, created the GeoNEX (www.nasa.gov/geonex) pipeline to integrate data from all available geostationary platforms and produce and distribute spatially, temporally, and radiometrically consistent data for the earth science community. We envision various institutions adapting the Geo component (e.g., GeoNOAA, GeoKARI, GeoChiba, GeoJAXA, GeoCMA) and customizing the pipeline and downstream products to serve the local/regional research and applied science communities.

Ramakrishna R Nemani↗

NASA NTRSDate not supplied

GeoNEX: A Geostationary Earth Observatory

GeoNEX↗

NASA NTRS2012

The Kepler End-to-End Data Pipeline: From Photons to Far Away Worlds

The Kepler mission is described in overview and the Kepler technique for discovering exoplanets is discussed. The design and implementation of the Kepler spacecraft, tracing the data path from photons entering the telescope aperture through raw observation data transmitted to the ground operations team is described. The technical challenges of operating a large aperture photometer with an unprecedented 95 million pixel detector are addressed as well as the onboard technique for processing and reducing the large volume of data produced by the Kepler photometer. The technique and challenge of day-to-day mission operations that result in a very high percentage of time on target is discussed. This includes the day to day process for monitoring and managing the health of the spacecraft, the annual process for maintaining sun on the solar arrays while still keeping the telescope pointed at the fixed science target, the process for safely but rapidly returning to science operations after a spacecraft initiated safing event and the long term anomaly resolution process.The ground data processing pipeline, from the point that science data is received on the ground to the presentation of preliminary planetary candidates and supporting data to the science team for further evaluation is discussed. Ground management, control, exchange and storage of Kepler's large and growing data set is discussed as well as the process and techniques for removing noise sources and applying calibrations to intermediate data products.

data archiving↗

DOE OSTI2021

A data engineering approach for sustainable chemical end-of-life management

The presence of chemicals causing significant adverse human health and environmental effects during end-of-life (EoL) stages is a challenge for implementing sustainable management efforts and transitioning towards a safer circular life cycle. Conducting chemical risk evaluation and exposure assessment of potential EoL scenarios can help understand the chemical EoL management chain for its safer utilization in a circular life-cycle environment. However, the first step is to track the chemical flows, estimate releases, and potential exposure pathways. Hence, this work proposes an EoL data engineering approach to perform chemical flow analysis and screening to support risk evaluation and exposure assessment for designing a safer circular life cycle of chemicals. This work uses publicly-available data to identify potential post-recycling scenarios (e.g., industrial processing/use operations), estimate inter-industry chemical transfers, and exposure pathways to chemicals of interest. Furthermore, a case study demonstration shows how the data engineering framework identifies, estimates, and tracks chemical flow transfers from EoL stage facilities (e.g., recycling and recovery) to upstream chemical life cycle stage facilities (e.g., manufacturing). Also, the proposed framework considers current regulatory constraints on closing the recycling loop operations and provides a range of values for the flow allocated to post-recycling uses associated with occupational exposure and fugitive air releases from EoL operations.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2011

Dynamic Black-Level Correction and Artifact Flagging for Kepler Pixel Time Series

Methods applied to the calibration stage of Kepler pipeline data processing [1] (CAL) do not currently use all of the information available to identify and correct several instrument-induced artifacts. These include time-varying crosstalk from the fine guidance sensor (FGS) clock signals, and manifestations of drifting moire pattern as locally correlated nonstationary noise, and rolling bands in the images which find their way into the time series [2], [3]. As the Kepler Mission continues to improve the fidelity of its science data products, we are evaluating the benefits of adding pipeline steps to more completely model and dynamically correct the FGS crosstalk, then use the residuals from these model fits to detect and flag spatial regions and time intervals of strong time-varying black-level which may complicate later processing or lead to misinterpretation of instrument behavior as stellar activity.

Kolodziejczak, J. J.↗

DOE OSTI2025

Computer Vision Pipeline for Image Analysis for Freeze‐Fracture Electron Microscopy: Rosette Cellulose Synthase Complexes Case

In materials science, plant biology, agriculture, and environmental research, the automated analysis of high-magnification, complex microscopy images, such as those generated by freeze-fracture electron microscopy (FF-TEM), remains a critical challenge that limits the scalability of data interpretation. We present a deep learning computer vision pipeline for high-throughput detection and morphological characterization analysis of cellulose synthase complexes (CSCs, or rosettes) in FF-TEM images. The pipeline integrates preprocessing, detection, human-in-the-loop verification, and semantic segmentation to quantify features such as rosette diameter and inter-lobe spacing. The approach was trained and tested on a curated dataset of high-resolution FF-TEM micrographs of Physcomitrium patens, expanded via strategic tiling and augmentation to over 650 images. We compare YOLOv8 and YOLOv9 architectures and demonstrate that YOLOv9 achieves superior performance in both localization accuracy (mAP50-95 = 0.854) and inference speed. The resulting distributions revealed biological variability consistent with prior manual studies, validating the approach for high-throughput applications. Our results show that the pipeline achieves human-expert level accuracy while dramatically reducing analysis time, enabling scalable, reproducible structural characterization of intramembrane protein complexes. The pipeline is broadly applicable to other domains requiring precise interpretation of complex microscopy data and establishes a foundation for future artificial intelligence (AI)-assisted workflows in biological imaging.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2023

Uncovering Unique Molecular Adaptations in the Arabidopsis Thaliana Cvi-0 Ecotype

This research proposal aims to investigate the unique molecular adaptations exhibited by Arabidopsis Thaliana, specifically focusing on the Cape Verde Islands (Cvi-0) ecotype, in response to microgravity conditions. The study examines data from NASA’s Open Science Data Repository and applies a multifaceted RNAseq analysis pipeline using tools in the UseGalaxy.org open platform. Through transcriptomic analysis, differential gene expression patterns were identified in Cvi-0, revealing an absence of heat shock protein (HSP) upregulation and an upregulation of Rubisco Activase (RCA) and chloroplast-related pathways. To test the hypothesis that these adaptations may contribute to Cvi-0’s increased adaptability in microgravity, a three-fold experimental design is proposed. Four experimental groups will be cultivated under simulated microgravity and ground control conditions, including Cvi-0, Col-0, and genetically modified Col-0 with silenced HSP genes, and genetically modified Col-0 with upregulated RCA gene. Growth parameters will be measured to assess plant resilience, and RNA sequencing will provide transcriptomic data for pathway analysis. Anticipated outcomes include improved markers of plant health (mass, growth, etc.) of Cvi-0 in simulated microgravity and enhanced resilience in genetically altered Col-0 variants, providing insights into potential mechanisms of adaptation. This research would bear significance for space agriculture, nutrition for extended space missions, and sustainable terrestrial crop enhancement. Moreover, the insights gained could reshape crop engineering on Earth, enhancing robustness to climate induced stresses and bolstering global food security. The proposal’s trajectory blends scientific curiosity with practical applicability, forging a path towards sustainable food production and improving human exploration beyond our planet.

GL4HS↗

DOE OSTI2023

The Target-selection Pipeline for the Dark Energy Spectroscopic Instrument

Abstract In 2021 May, the Dark Energy Spectroscopic Instrument (DESI) began a 5 yr survey of approximately 50 million total extragalactic and Galactic targets. The primary DESI dark-time targets are emission line galaxies, luminous red galaxies, and quasars. In bright time, DESI will focus on two surveys known as the Bright Galaxy Survey and the Milky Way Survey. DESI also observes a selection of “secondary” targets for bespoke science goals. This paper gives an overview of the publicly available pipeline ( desitarget ) used to process targets for DESI observations. Highlights include details of the different DESI survey targeting phases, the targeting ID ( TARGETID ) used to define unique targets, the bitmasks used to indicate a particular type of target, the data model and structure of DESI targeting files, and examples of how to access and use the desitarget code base. This paper will also describe “supporting” DESI target classes, such as standard stars, sky locations, and random catalogs that mimic the angular selection function of DESI targets. The DESI target-selection pipeline is complex and sizable; this paper attempts to summarize the most salient information required to understand and work with DESI targeting data.

47 OTHER INSTRUMENTATION↗

NASA NTRS2002

Uncertainty estimation and propagation in SIRTF pipelines

Explore the source record for details and available documents.

calibrated science products estimating uncertainti↗

NASA NTRSDate not supplied

Science Yield Estimates and Sensitivities With the AstroPIC Integrated Photonic Coronagraph for the Habitable Worlds Observatory

The Habitable Worlds Observatory (HWO) flagship has a goal to survey ~100 of the nearest stellar systems and their habitable zones in order to detector and spectroscopically characterize ~25 potentially “Earth-like planets” (or “Exoearths”). The HWO telescope will feature a >6-m diameter aperture and a coronagraph that will suppress starlight by ten orders of magnitude to enable the detection and characterization of Earth analogues in the habitable zone. Three Exploratory Analytic Cases (EACs) are currently considering different aperture configurations for HWO including on-axis and off-axis apertures and both different hexagonal and keystone segmentation configurations. Photonic Integrated Circuits (PICs) offer a path to miniaturize traditional, bulk optics coronagraph functionality reducing risk margins and increasing mission science exoearth yields for the HWO mission. We have developed a simulation pipeline that enables evaluation of the AstroPIC photonic integrated coronagraph through to estimates mission yields. We present sensitivities to aberrations for different types of segmentation and low-order aberrations for HWO EACs demonstrating that AstroPIC is suitable for both on-axis and off-axis configurations. We perform a parametric sweep of the exoearth science yield sensitivities in terms of key coronagraph parameters including coronagraphic end-to-end throughput, inner working angle, robustness to aberrations, and bandwidth. We consider both a hybrid and a pure photonic architecture; a pure integrated photonic architecture provides the greatest potential in science yield improvements, although a hybrid PIC limited in its numbers of modes can provide complementary science to a traditional, bulk-optic coronagraph and increasing the estimated science yield when operated jointly.

Photonics↗

DOE OSTI2025

Language models for materials discovery and sustainability: Progress, challenges, and opportunities

Significant advancements have been made in one of the most critical branches of artificial intelligence: natural language processing (NLP). These advancements are exemplified by the remarkable success of OpenAI’s GPT-3.5/4 and the recent release of GPT-4.5, which have sparked a global surge of interest akin to an NLP gold rush. Here, in this article, we offer our perspective on the development and application of NLP and large language models (LLMs) in materials science. We begin by presenting an overview of recent advancements in NLP within the broader scientific landscape, with a particular focus on their relevance to materials science. Next, we examine how NLP can facilitate the understanding and design of novel materials and its potential integration with other methodologies. To highlight key challenges and opportunities, we delve into three specific topics: (i) the limitations of LLMs and their implications for materials science applications, (ii) the creation of a fully automated materials discovery pipeline, and (iii) the potential of GPT-like tools to synthesize existing knowledge and aid in the design of sustainable materials.

36 MATERIALS SCIENCE↗