Results for “pipeline data processing” — Page 14

NASA NTRSDate not supplied

The NASA Open Science Data Repository: Biomedical Fair Data, Analysis Tools, User Communities, Publications, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

space biology↗

NASA NTRSDate not supplied

NASA Open Science Data Repository: Biomedical FAIR Data, Analysis Tools, User Communities, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

open access↗

NASA NTRSDate not supplied

AN INTRODUCTION TO THE GEONEX LEVEL-1G PRODUCTS: TOP-OF-ATMOSPHERE REFLECTANCE AND BRIGHTNESS TEMPERATURE

This paper introduces the GeoNEX (Geostationary-NASA Earth eXchange) Level-1G products of top-of-atmosphere (TOA) reflectance and brightness temperature. The products use data streams from the latest geostationary (GEO) sensors including the GOES-16/17 ABI and the Himawari-8/9 AHI. The GeoNEX processing pipeline starts by converting digital numbers to physical quantities with the latest radiometric calibration information. It integrates algorithms to automatically detect and remove residual geolocation errors, to estimate the pixel-wise data-acquisition time, and to accurately calculate the solar illumination angles for each pixel in the domain at every time step. The outputs are reprojected to a globally tiled common grid in geographic coordinates designed to facilitate inter-comparisons and/or synergies between the GeoNEX products and existing Earth observation datasets from polar-orbiting satellites. Therefore, the GeoNEX L1G products provide accurate and consistent TOA reflectance and brightness temperature datasets for scientific analyses and downstream product development.

Geostationary satellite, GOES-16, Himawari-8, NASA↗

DOE OSTI2024

Laminography as a tool for imaging large-size samples with high resolution

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

47 OTHER INSTRUMENTATION↗

NASA NTRS1986

Convolver for Pipelined-Image Processor

3 x 3 convolver produces weighted sum of nine contiguous picture elements in square. Data processed through convolver at video scanning rate of current raster line. Two previous lines stored in external buffers (N-3)element delays. Specific choice of convolution weights determines whether convolver performs smoothing, spatial-frequency filtering, edge detection, or other forms of image processing.

Wilcox, B.↗

DOE OSTI2025

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI‐driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS‐based multiomics data. While centered on MS‐based omics, this holistic AI‐driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI‐driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems‐level understanding of biological processes and accelerating a myriad of biodiscoveries.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Integrative SP3 Workflow for Multi-PTM Proteomics Profiling (TZ-DP0)

The goal of the experiment was to demonstrate that the optimized multiplexed multi-PTM profiling workflow can comprehensively and quantitatively capture dynamic changes in protein abundance, cysteine oxidation, phosphorylation, and acetylation in cytokine-induced inflammatory stress in mouse pancreatic ß-cells. Global proteomic, redox proteomic, phosphoproteomic, and acetylomic were data collected from mouse Beta-TC-6 pancreatic Beta-cells, untreated (mock) and cytokine-treated Beta-cells at 4, 8, and 24 hours with 4 biological replicates. Samples were digested with trypsin and Lys-C, then analyzed by LC-MS/MS. Data were searched with MS-GF+, MASIC, and MaxQuant using PNNL's DMS processing pipeline.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1981

Real-time image enhancement

Pipelined system with "vision" algorithm is implemented on LSI chip that processes input digital image data to produce image-edge map. System contains 3 input adder, difference and absolute value cells, and adder and comparator. Data store for 1 to 2 ms, and are easily transmitted or isolated; design has reduced package count and number of interconnections for increased reliability. Applications include locating objects on moving belt, deep-sea and coal mining, and control of robotic rovers.

Wong, V. S.↗

NASA NTRS1993

A comparison of multiprocessor scheduling methods for iterative data flow architectures

A comparative study is made between the Algorithm to Architecture Mapping Model (ATAMM) and three other related multiprocessing models from the published literature. The primary focus of all four models is the non-preemptive scheduling of large-grain iterative data flow graphs as required in real-time systems, control applications, signal processing, and pipelined computations. Important characteristics of the models such as injection control, dynamic assignment, multiple node instantiations, static optimum unfolding, range-chart guided scheduling, and mathematical optimization are identified. The models from the literature are compared with the ATAMM for performance, scheduling methods, memory requirements, and complexity of scheduling and design procedures.

Storch, Matthew↗

NASA NTRS2021

Automated Data Accountability for Missions in Mars Rover Data

As the Mars Curiosity Rover transmits data to the JPL Ground Data System (GDS), it frequently observes data loss and corruption, requiring re-transmits from the rover and Ground Data System Analysts (GDSA) to monitor the downlink process. As new missions are launched, the GDSA team redistributes analysts to these new missions, causing shortages in previous missions. The GDSA team can significantly benefit from the automation and optimization of the downlink process of telemetry data. In fact, there is a need for a better understanding of why the data is corrupted, so that the GDSA team can best determine the root cause of the issues in the GDS. This paper presents machine learning and deep learning based approaches to automate and optimize the detection of data loss. We first created a pipeline to automatically accumulate data from the telemetry databases (MAROS, Telemetry Data Storage, and GDS Elastic Search Database) in the downlink process. With our newly created datasets, we perform feature selection to supplement the GDSA understanding of the downlink process and provide supplemental analysis on the importance of different features. We implement various machine learning and deep learning based models, including support vector machines, ensemble methods, and deep neural networks and evaluate their accuracies in identifying whether a downlink process is complete or incomplete. We utilize fast hyperparameter optimization methods that allow our models to quickly be re-trained, allowing them to quickly be tuned and optimized on daily incoming data in real time. This hyperparameter optimization also allows our methods to be quickly integrated into other JPL missions. Our results show that our best-performing machine learning and deep learning based models outperform the existing GDSA detection software by 6 accuracy points and can aid analysts by providing insights into the data accountability problem. Since these various machine learning and deep learning approaches vary significantly in interpretability, we provide a discussion on the tradeoffs between their performance and trustworthiness in helping detect issues in data transmission.

Divsalar, Dariush↗

DOE OSTI2024

Fostering Geothermal Machine Learning Success: Elevating Big Data Accessibility and Automated Data Standardization in the Geothermal Data Repository: Preprint

The Department of Energy's (DOE) Geothermal Data Repository (GDR) has implemented improvements to both its data lakes and its data standards and automated data pipelines. The GDR data lakes have reduced storage and compute-related barriers to using large geothermal datasets, enabling these large datasets to be accessed by anyone with a modern computer and internet access. More recently, the GDR has been working to further reduce barriers through streamlining the data intake process, educating users on the process and requirements, and aiding users in accessing data from the data lakes. These improvements have augmented the quantity of datasets the GDR is able to accept into its data lakes and have enabled users who are new to cloud tools to access these datasets more easily, overall increasing the accessibility of big geothermal data for use in machine learning and other projects. In addition, the GDR now has built-in data standards and pipelines for drilling data, geospatial data, and distributed acoustic sensing (DAS) data. These standardization efforts aim to enhance the real-world applicability of geothermal machine learning outcomes by improving the quality of training data. Specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, thus allowing more time for actual research. By automating this process, the burden of standardization is lifted from the user, ultimately increasing the availability of standardized data.

accessibility↗

NASA NTRS1992

Implementation and performance of the Magellan digital correlator subsystem

The Magellan synthetic aperture radar (SAR) produces Venus surface images from data collected by the SAR carried on board the Magellan spacecraft. The core of the primary Magellan SAR processor is the digital correlator subsystem (DCS). The pipeline DSC architecture enables the Magellan primary SAR processor (PSP) to achieve real-time data processing capability. The implementation and performance of the DSC are described. Hardware (H/W) constraints that influenced the processing algorithm design are highlighted.

Chen, M.↗

NASA NTRS1997

Joint US-Japan Observations with the Infrared Space Observatory (ISO): Deep Surveys and Observations of High-Z Objects

Several important milestones were passed during the past year of our ISO observing program: (1) Our first ISO data were successfully obtained. ISOCAM data were taken for our primary deep field target in the 'Lockman Hole'. Thirteen hours of integration (taken over 4 contiguous orbits) were obtained in the LW2 filter of a 3 ft x 3 ft region centered on the position of minimum HI column density in the Lockman Hole. The data were obtained in microscanning mode. This is the deepest integration attempted to date (by almost a factor of 4 in time) with ISOCAM. (2) The deep survey data obtained for the Lockman Hole were received by the Japanese P.I. (Yoshi Taniguchi) in early December, 1996 (following release of the improved pipeline formatted data from Vilspa), and a copy was forwarded to Hawaii shortly thereafter. These data were processed independently by the Japan and Hawaii groups during the latter part of December 1996, and early January, 1997. The Hawaii group made use of the U.S. ISO data center at IPAC/Caltech in Pasadena to carry out their data reduction, while the Japanese group used a copy of the ISOCAM data analysis package made available to them through an agreement with the head of the ISOCAM team, Catherine Cesarsky. (3) Results of our LW2 Deep Survey in the Lockman Hole were first reported at the ISO Workshop "Taking ISO to the Limits: Exploring the Faintest Sources in the Infrared" held at the ISO Science Operations Center in Villafranca, Spain (VILSPA) on 3-4 February, 1997. Yoshi Taniguchi gave an invited presentation summarizing the results of the U.S.-Japan team, and Dave Sanders gave an invited talk summarizing the results of the Workshop at the conclusion of the two day meeting. The text of the talks by Taniguchi and Sanders are included in the printed Workshop Proceedings, and are published in full on the Web. By several independent accounts, the U.S.-Japan Deep Survey results were one of the highlights of the Workshop; these data showed conclusively that the ISOCAM S/N continues to decrease as the square root of time for periods as long as 13 hours.

Sanders, David B.↗

DOE OSTI2025

DMTN-277: The Monster: A reference catalog with synthetic ugrizy-band fluxes for the Vera C. Rubin observatory

In order to facilitate bootstrap photometric calibrations of early Rubin Observatory data we have created an all sky reference catalog called The Monster. This reference catalog uses a rank-ordered set of other reference catalogs to generate synthetic ugrizy-band fluxes that can be used calibrate images processed with the LSST science pipelines. This document describes the methodology used to create The Monster, documents the input external reference catalogs, and performs basic data validation of the first version of The Monster.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Datum: A Scientific Metadata Catalog

The data catalog market is currently flooded with a myriad of different products, but none serve the scientific community well. There are cloud-native tools like Databricks, Snowflake,to on-premise solutions like Collibra and Datahub. The common failing of all these tools however, is their inability to serve the scientific data community directly. Most catalogs are targeted towards financial, health, or user data - not sensor or scientific domain data. They also prioritize integrations that often don’t exist or are just starting to be used in the scientific realm - all while ignoring common scientific tools and file types. Datum is a catalog which targets the scientific data directly, including the tools and networks in which those tools are used. We work with the producers and consumers of the data where they are, targeting cloud and on-premise with a focus on classified networks. Datum is an Erlang/Elixir application. Technical Features Note: The features listed below are still under development and may change, slightly, upon final delivery of the product. File Formats - Datum has the ability to read additional metadata and provides processing pipelines for the following file formats: Plain Text, PDF, LaTeX, HTML, Open Document Format (.odt), XML, CSV/TSV (and other standard delimiters), OpenDocument Database and Spreadsheets, Geo-Referenced TIFF, Common Data Format, HDF/HDF5, LabView TDMS, Excel, DeltaTables, Parquet, Apache Iceberg, Apache Hudi and many others. Metadata Collection - Scanners for the local and networked file systems and cloud storage providers. Network integration with common databases such as MSSQL and MySQL. User Plugin System - Users are able to provide either file processing, metadata extraction, or sampling plugins in the programming language of their choice. Authentication/Authorization -: OIDC integration, SCIM provisioning and EntraID integration out of the box. Full user and group management system with a “least privilege” operating mode. Governance - Customizable data governance platform; dictate and enforce required metadata, enforce data embargos, and enforce user agreements and NDAs before data access. Ability to create health checks on data, rejecting abandoned or poorly curated data and automatically removing it from the search index. Ability for users to submit corrections. Search - Semantic search is a first class citizen. No licenses to expensive, external software required. Integrated use of vectors and vector-based search allows for AI agent integration at all levels of operation. Metadata Model - Display and control data’s lineage and connections to other data and data directories. Data is modeled after a filesystem - an organization instantly recognizable and navigable by most any user. CLI and SDK - Ships with a Command Line Interface (CLI) tool and with a fully-featured Python SDK. This allows for rapid and programmatic use of Datum by every level of user. Minimal Infrastructure - Datum ships as a single executable file and can be run on any operating system and most CPU architectures. Datum has no reliance on external databases, search indexing tools, or other outside services - and it runs equally well on edge computing devices, cloud services, or in a clustered HPC environment.

darrington, john↗

NASA NTRS1992

Alaska SAR processor implementation of E-ERS-1

The synthetic aperture radar (SAR) data processing algorithm used by the Alaska SAR Facility (ASF) for the European Space Agency's first Remote-Sensing Satellite (E-ERS-1) SAR data are examined. Preprocessing highlights two features: signal measurement, which includes signal-to-noise ratio, replica measurement, and noise measurement; and Doppler measurement, which includes clutter lock and autofocus. The custom pipeline architecture performs the main processing with controls at the input interface, range correlator, corner-turn memory, azimuth correlator, and multi-look memory. The control software employs a flexible control scheme. The Committee on Earth Observation Satellites (CEOS) format encapsulates the ASF products. System performance for SAR image processing of E-ERS-1 data is reviewed.

Cuddy, David↗

NASA NTRS2022

Characterization of Response Times based on Voice Communication and Traffic Surveillance Data

A barrier to the integration of remotely piloted aircraft operations in the U.S. National Airspace System is the latency of voice communications between the air traffic controller and the remote pilot, and the latency of communication between the aircraft and the remote pilot. The latency can be substantial especially when satellite-based beyond-radio-line-of-sight communication and relay through the aircraft are employed. This study uses voice recordings of controller-pilot communications and aircraft track data to establish a baseline of pilot readback latencies and maneuver detection delays in the current piloted operations. A machine learning pipeline was developed to parse the contents of the air traffic control clearances including the callsigns using natural language processing. After manually validating the results obtained using the pipeline, the average pilot readback latency was found to be about 0.6 seconds. The average latency between the end of maneuver (inferred from track data), initiated by the pilot in response to the clearance, and the end of clearance was found to be about 176 seconds for altitude change commands, 69 seconds for heading change commands, and 182 seconds for speed change commands. The average latency between the beginning of maneuver and the end of clearance was found to be about 17 seconds for altitude change commands, 17seconds for heading change commands, and 25 seconds for speed change commands.

controller-pilot communication, communication late↗

NASA NTRS2022

Characterization of Response Times Based on Voice Communication and Traffic Surveillance Data

A barrier to the integration of remotely piloted aircraft operations in the U.S. National Airspace System is the latency of voice communications between the air traffic controller and the remote pilot, and the latency of communication between the aircraft and the remote pilot. The latency can be substantial especially when satellite-based beyond-radio-line-of-sight communication and relay through the aircraft are employed. This study uses voice recordings of controller-pilot communications and aircraft track data to establish a baseline of pilot readback latencies and maneuver detection delays in the current piloted operations. A machine learning pipeline was developed to parse the contents of the air traffic control clearances including the callsigns using natural language processing. After manually validating the results obtained using the pipeline, the average pilot readback latency was found to be about 0.6 seconds. The average latency between the end of maneuver (inferred from track data), initiated by the pilot in response to the clearance, and the end of clearance was found to be about 176 seconds for altitude change commands, 69 seconds for heading change commands, and 182 seconds for speed change commands. The average latency between the beginning of maneuver and the end of clearance was found to be about 17 seconds for altitude change commands, 17seconds for heading change commands, and 25 seconds for speed change commands.

controller-pilot communication↗