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DOE OSTI2021

RhizoVision Explorer: open-source software for root image analysis and measurement standardization

Abstract Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

High-resolution ptychographic imaging enabled by high-speed multi-pass scanning

As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh’s criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1985

A First Look at Airborne Imaging Spectrometer (AIS) Data in an Area of Altered Volcanic Rocks and Carbonate Formations, Hot Creek Range, South Central Nevada

Three flight lines of Airborne Imaging Spectrometer (AIS) data were collected in 128 bands between 1.2 and 2.4 microns in the Hot Creek Range, Nevada on July 25, 1984. The flight lines are underlain by hydrothermally altered and unaltered Paleozoic carbonates and Tertiary rhyolitic to latitic volcanics in the Tybo mining district. The original project objectives were to discriminate carbonate rocks from other rock types, to distinguish limestone from dolomite, and to discriminate carbonate units from each other using AIS imagery. Because of high cloud cover over the prime carbonate flight line and because of the acquisition of another flight line in altered and unaltered volcanics, the study has been extended to the discrimination of alteration products. In an area of altered and unaltered rhyolites and latites in Red Rock Canyon, altered and unaltered rock could be discriminated from each other using spectral features in the 1.16 to 2.34 micron range. The altered spectral signatures resembled montmorillonite and kaolinite. Field samples were gathered and the presence of montmorillonite was confirmed by X-ray analysis.

Feldman, S. C.↗

NASA NTRS1993

Can cluster environment modify the dynamical evolution of spiral galaxies?

Over the past decade many effects of the cluster environment on member galaxies have been established. These effects are manifest in the amount and distribution of gas in cluster spirals, the luminosity and light distributions within galaxies, and the segregation of morphological types. All these effects could indicate a specific dynamical evolution for galaxies in clusters. Nevertheless, a more direct evidence, such as a different mass distribution for spiral galaxies in clusters and in the field, is not yet clearly established. Indeed, Rubin, Whitmore, and Ford (1988) and Whitmore, Forbes, and Rubin (1988) (referred to as RWF) presented evidence that inner cluster spirals have falling rotation curves, unlike those of outer cluster spirals or the great majority of field spirals. If falling rotation curves exist in centers of clusters, as argued by RWF, it would suggest that dark matter halos were absent from cluster spirals, either because the halos had become stripped by interactions with other galaxies or with an intracluster medium, or because the halos had never formed in the first place. Even if they didn't disagree with RWF, other researchers pointed out that the behaviour of the slope of the rotation curves of spiral galaxies (in Virgo) is not so clear. Amram, using a different sample of spiral galaxies in clusters, found only 10% of declining rotation curves (2 declining vs 17 flat or rising) in opposition to RWF who find about 40% of declining rotation curves in their sample (6 declining vs 10 flat or rising), we will hereafter briefly discuss the Amram data paper and compare it to the results of RWF. We have measured the rotation curves for a sample of 21 spiral galaxies in 5 nearby clusters. These rotation curves have been constructed from detailed two-dimensional maps of each galaxy's velocity field as traced by emission from the Ha line. This complete mapping, combined with the sensitivity of our CFHT 3.60 m. + Perot-Fabry + CCD observations, allows the construction of high-quality rotation curves. Details concerning the acquisition and reduction procedures of the data are given in Amram. We present and discuss our preliminary analysis and compare them with RWF's results.

Amram, P.↗

NASA NTRS2018

Results from One Year of Ka-Band Beacon Measurements at Svalbard

Since April 1, 2016, a Ka-band (20.198 GHz) propagation terminal has been installed and operating at the Svalsat facility in Longyearbyen, Norway. This campaign is a joint effort between the European Space Agency (ESA), Kongsberg Satellite Services (KSAT), the French Aerospace Laboratory (ONERA), the Centre National d'Etudes Spatiales (CNES), and NASA Glenn Research Center (GRC) to characterize atmospheric attenuation, scintillation, and depolarization in the Ka-band in high latitude regions at low elevation angles. The propagation terminal observes the Thor 7 20.198 GHz RHCP beacon at nominally 2.6 deg elevation angle. Simultaneous 10 Hz and 1 Hz sampling is performed and a total dynamic range of 35 dB is achieved. One year of propagation data has been collected and the preliminary results are presented in this paper. From the first year of measurements, it is observed that at these low elevation angles, strong scintillation/multi-path conditions, as well as significant depolarization events can occur which may impose difficulties in meeting mission link acquisition requirements at 5 deg elevation angle, such as those desired by the Joint Polar Satellite System (JPSS) mission. The design of the dual-polarized terminal with integrated digital radiometer, as well as the data processing techniques are described, along with the first year results and preliminary conclusions.

Nessel, James↗

DOE OSTI2022

The Edge of Exploration: An Edge Storage and Computing Framework for Ambient Noise Seismic Interferometry Using Internet of Things Based Sensor Networks

Recent technological advances have reduced the complexity and cost of developing sensor networks for remote environmental monitoring. However, the challenges of acquiring, transmitting, storing, and processing remote environmental data remain significant. The transmission of large volumes of sensor data to a centralized location (i.e., the cloud) burdens network resources, introduces latency and jitter, and can ultimately impact user experience. Edge computing has emerged as a paradigm in which substantial storage and computing resources are located at the “edge” of the network. In this paper, we present an edge storage and computing framework leveraging commercially available components organized in a tiered architecture and arranged in a hub-and-spoke topology. The framework includes a popular distributed database to support the acquisition, transmission, storage, and processing of Internet-of-Things-based sensor network data in a field setting. We present details regarding the architecture, distributed database, embedded systems, and topology used to implement an edge-based solution. Lastly, a real-world case study (i.e., seismic) is presented that leverages the edge storage and computing framework to acquire, transmit, store, and process millions of samples of data per hour.

58 GEOSCIENCES↗

NASA NTRS1992

Assessing spatial and seasonal variations in grasslands with spectral reflectances from a helicopter platform

The helicopter system data acquisition technique has shown to be a viable means of gathering surface data with spectral detail adequate for intersite, intrasite, and temporal characterizations and for assessing temporal and spatial variability throughout the FIFE 1987 IFCs. The successful employment of nadir measurements for grassland assessments is notable given the reflectance anisotropy (Middleton, 1992). Though only five sites were repetitively observed, the conclusions reached from this particular sample of sites agree well with assessments from other data sources (Sellars et al., 1990 and Kittel et al., 1990).

Walthall, Charles L.↗

NASA NTRS2011

PING Gamma Ray and Neutron Measurements of a Meter-Sized Carbonaceous Asteroid Analog

Determining the elemental composition of carbonaceous (spectral type C) asteroids is still one of the basic problems when studying these objects. The only main source of elemental composition information for asteroids is from their optical, NIR and IR properties, which include their spectral reflectance characteristics, albedo, polarization, and the comparison of optical spectroscopy with meteorite groups corresponding to asteroids of every spectral type. Unfortunately, these sources reflect observations from widely contrasting spatial scales that presently yield a void in the continuum of microscopic and macroscopic evidence, a lack of in situ measurement confirmation, and require deeper sensing techniques to discern the nature of these asteroids. The Probing In situ with Neutrons and Gamma rays (PING) instrument is ideally suited to address this problem because it can be used to determine the bulk elemental composition, H and C content, the average atomic weight and density of the surface and subsurface layers of C-type asteroids, and can provide measurements used to determine the difference between and distinguish between different types of asteroids. We are currently developing the PING instrument that combines gamma ray and neutron detectors with a 14 Me V pulsed neutron generator to determine the in-situ bulk elemental abundances and geochemistry of C-type asteroids with a spatial resolution of 1 m down to depths of tens of cm to 1 m. One aspect of the current work includes experimentally testing and optimizing PING on a known meter-sized Columbia River basalt C-type asteroid analog sample that has a similar composition and the same neutron response as that of a C-type asteroid. An important part of this effort focuses on utilizing timing measurements to isolate gamma rays produced by neutron inelastic scattering, neutron capture and delayed activation processes. Separating the gamma ray spectra by nuclear processes results in higher precision and sensitivity elemental composition measurements. Using gated data acquisition techniques allows for the unambiguous identification of gamma ray lines from different isotopes and nuclear processes, especially in situations when limited detector resolution results in overlapping gamma ray lines that cannot be individually resolved. In this paper, we will present the PING basalt layering experimental data, taken at the test facility at NASA Goddard Space Flight Center using the time tagged event-by-event data analysis technique, compared to our MCNPX computer simulation results for the C-type asteroid and basalt layering simulant models. Comparison of these data will show the advantages, validity, and measurement sensitivity of PING's nuclear interrogation methods to obtain more precise and sensitive in situ bulk elemental composition and density measurements of the subsurface of asteroids.

Bodnarik, J.↗

DOE OSTI2022

Machine Learning for Optical Scanning Probe Nanoscopy

Abstract The ability to perform nanometer‐scale optical imaging and spectroscopy is key to deciphering the low‐energy effects in quantum materials, as well as vibrational fingerprints in planetary and extraterrestrial particles, catalytic substances, and aqueous biological samples. These tasks can be accomplished by the scattering‐type scanning near‐field optical microscopy (s‐SNOM) technique that has recently spread to many research fields and enabled notable discoveries. Herein, it is shown that the s‐SNOM, together with scanning probe research in general, can benefit in many ways from artificial‐intelligence (AI) and machine‐learning (ML) algorithms. Augmented with AI‐ and ML‐enhanced data acquisition and analysis, scanning probe optical nanoscopy is poised to become more efficient, accurate, and intelligent.

Chen, Xinzhong↗

DOE OSTI2025

EGS Collab Experiment 2: Continuous Active Source Seismic Monitoring (CASSM)

The dataset contains continuous active-source seismic monitoring (CASSM) data collected during EGS Collab Experiment 2, conducted from February to September 2022 at the Sanford Underground Research Facility in Lead, South Dakota. This experiment aimed to investigate enhanced geothermal systems through high-pressure fluid injections at depths of 1200-1500 meters. The seismic monitoring system included 16 three-component piezoelectric accelerometers and 24 hydrophones installed in boreholes around the injection zones, recording signals from piezoelectric seismic sources. Data were acquired using both continuous and triggered recording systems, with sampling rates of up to 100 kHz. The raw data are organized by timestamps and stored in .dat format, with accompanying log files. Calibration certificates for selected accelerometers are provided to aid in correcting sensor responses, though users are advised to consider possible effects of enclosures and installation on sensor performance. Users are strongly advised to consult the accompanying report, which outlines the experimental setup, data acquisition, sensor specifications, and recording systems.

15 GEOTHERMAL ENERGY↗

NASA NTRS1984

Nuclear Science Symposium, 30th, and Symposium on Nuclear Power Systems, 15th, San Francisco, CA, October 19-21, 1983, Proceedings

The range of disciplines covered includes physics instrumentation, data acquisition, FASTBUS, radiation detectors, scintillators, photomultipliers and optical detectors, subnanosecond 2-D imaging, medical and health instrumentation, reactor instrumentation, and space instrumentation. Cerenkov detectors, the prevention and rate capability of breakdown processes in wire chambers, and an interactive parallel processor for data analysis are studied. Attention is also given to bismuth germanate's role in gamma-ray spectroscopy, and the construction of a broadband universal sampling head is described. Gamma-ray imaging with a rotating hexagonal uniform redundant array, and broadband X-ray astronomical spectrometry are considered.

Nakamura, M.↗

DOE OSTI2024

Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features

In the Antibody Mediated Prevention (AMP) trials (HVTN 704/HPTN 085 and HVTN 703/HPTN 081), prevention efficacy (PE) of the monoclonal broadly neutralizing antibody (bnAb) VRC01 (vs. placebo) against HIV-1 acquisition diagnosis varied according to the HIV-1 Envelope (Env) neutralization sensitivity to VRC01, as measured by 80% inhibitory concentration (IC80). Here, we performed a genotypic sieve analysis, a complementary approach to gaining insight into correlates of protection that assesses how PE varies with HIV-1 sequence features. We analyzed HIV-1 Env amino acid (AA) sequences from the earliest available HIV-1 RNA-positive plasma samples from AMP participants diagnosed with HIV-1 and identified Env sequence features that associated with PE. The strongest Env AA sequence correlate in both trials was VRC01 epitope distance that quantifies the divergence of the VRC01 epitope in an acquired HIV-1 isolate from the VRC01 epitope of reference HIV-1 strains that were most sensitive to VRC01-mediated neutralization. In HVTN 704/HPTN 085, the Env sequence-based predicted probability that VRC01 IC80 against the acquired isolate exceeded 1 µg/mL also significantly associated with PE. In HVTN 703/HPTN 081, a physicochemical-weighted Hamming distance across 50 VRC01 binding-associated Env AA positions of the acquired isolate from the most VRC01-sensitive HIV-1 strain significantly associated with PE. These results suggest that incorporating mutation scoring by BLOSUM62 and weighting by the strength of interactions at AA positions in the epitope:VRC01 interface can optimize performance of an Env sequence-based biomarker of VRC01 prevention efficacy. Future work could determine whether these results extend to other bnAbs and bnAb combinations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Tractometry of the Human Connectome Project: resources and insights

The Human Connectome Project (HCP) has become a keystone dataset in human neuroscience, with a plethora of important applications in advancing brain imaging methods and an understanding of the human brain. We focused on tractometry of HCP diffusion-weighted MRI (dMRI) data. We used an open-source software library (pyAFQ; https://yeatmanlab.github.io/pyAFQ) to perform probabilistic tractography and delineate the major white matter pathways in the HCP subjects that have a complete dMRI acquisition (n = 1,041). We used diffusion kurtosis imaging (DKI) to model white matter microstructure in each voxel of the white matter, and extracted tract profiles of DKI-derived tissue properties along the length of the tracts. We explored the empirical properties of the data: first, we assessed the heritability of DKI tissue properties using the known genetic linkage of the large number of twin pairs sampled in HCP. Second, we tested the ability of tractometry to serve as the basis for predictive models of individual characteristics (e.g., age, crystallized/fluid intelligence, reading ability, etc.), compared to local connectome features. To facilitate the exploration of the dataset we created a new web-based visualization tool and use this tool to visualize the data in the HCP tractometry dataset. Finally, we used the HCP dataset as a test-bed for a new technological innovation: the TRX file-format for representation of dMRI-based streamlines. We released the processing outputs and tract profiles as a publicly available data resource through the AWS Open Data program's Open Neurodata repository. We found heritability as high as 0.9 for DKI-based metrics in some brain pathways. We also found that tractometry extracts as much useful information about individual differences as the local connectome method. We released a new web-based visualization tool for tractometry—“Tractoscope” (https://nrdg.github.io/tractoscope). We found that the TRX files require considerably less disk space-a crucial attribute for large datasets like HCP. In addition, TRX incorporates a specification for grouping streamlines, further simplifying tractometry analysis.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Lessons Learned From Designing and Building Low Organic Outgassing Cleanrooms for NASA OSIRIS-REx and Hayabusa2 Curation Facility

NASA Johnson Space Center Astromaterials Acquisition and Curation Office completed construction and commissioning of the OSIRIS-REx and Hayabusa2 cleanroom laboratory suites along with new precision cleaning and advanced curation laboratories consisting of ISO Class 5, 6, and 7 cleanrooms. The new curation facilities are designed for initial receiving, basic characterization, curation processing, and preliminary examination of carbonaceous asteroidal material. The facilities are also designed to enable long-term pristine sample storage to preserve the scientific integrity of each sample to enable future research by the international science community. The scientific study of organics is critical for both missions. The OSIRIS-REx mission instituted a stringent contamination control plan for low organics. Given these mission requirements and long-term storage preservation requirements, cleanroom construction materials were carefully selected to not hinder the scientific search for amino acids and the study of organics in the samples. Cleanroom candidate construction materials were researched for the HVAC system, floors, walls, ceiling, and plenum areas. The team chose several candidate materials that were further tested for their specific outgassing characteristics using ASTM E-595 per ASTM E-2312. The information gained provided the foundation for the final design selection of the cleanroom materials. While material selection is important before and during the facility design phase, the construction phase is where these choices are implemented by the prime construction contractor through final product and material submittals. These submittals are the last check point and changes are often submitted due to engineering/construction conflicts, especially when renovating an existing building. Any new material or equipment/product change must be identified and scrutinized for low particulate shedding and outgassing properties. In some cases, quick testing of new material is required, and compromises must be made in real-time. Careful selection and implementation of cleanroom materials significantly reduced organic and inorganic contamination beyond normal cleanroom baselines.

astromaterials curation↗

NASA NTRSDate not supplied

Lessons Learned From Designing and Building Low Organic Outgassing Cleanrooms for NASA OSIRIS-REx and Hayabusa2 Curation Facility

astromaterials curation↗

DOE OSTI2020

3-D Radiological Data Acquisition, Visualization and Modeling - 20211

The U.S. Army Corps of Engineers (USACE) was tasked to investigate and remediate low activity radiological contamination from research and production of the nation's first nuclear weapons at the former DuPont Chambers Works Formerly Utilized Sites Remedial Action Program (FUSRAP) site (DuPont). The DuPont site had several buildings used for the Manhattan project that were demolished in the 1940's and 1950's apparently using heavy earthmoving equipment. Some of the contaminated rubble from the demolition appears to have been spread out by this equipment resulting in somewhat random scattering of radiologically contaminated soil and debris along with aqueous spills. Traditional investigative methods such as soil borings, test pits and 2-dimensional gamma walkovers were only partially successful in delineating the radiological contamination at the site. It was feared that even 'chasing' the contamination during remediation would miss contamination if the demolition resulted in discontinuous trails of radiologically contaminated soils. In evaluating the data generated over the interceding decades, the USACE determined that a better method to collect and process the remedial action radiological data was needed to enable the project team to optimize predictive planning and meet documentation expectations. The purpose of this paper is to provide an overview of the effort and progress to combine and organize radiological survey methods into a highly flexible sampling, modeling, and decision analysis approach that emphasizes the quality of decision-making during remediation. This innovative system blends multiple tools to develop a methodology that can extend MARRSIM [1] into the subsurface and provide tools that can be applied to other sites. (authors)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Comparison of Orientation Mapping in SEM and TEM

In this work, multiple experimental configurations for performing nanoscale orientation mapping are compared to determine their fidelity to the true 3D microstructure of a sample. Transmission Kikuchi Diffraction (TKD) experiments in an SEM and nanobeam diffraction (NBD) experiments in a TEM were performed on thin electrodeposited hard Au films with two different microstructures. The Au samples either have a grain size that is >50 nm or <20 nm. The same regions of the samples were measured with TKD apparatuses at 30 kV in an SEM with detectors in the horizontal and vertical configurations and in the TEM at 300 kV. Under the proper conditions, we demonstrate all three configurations can produce data of equivalent quality.Each method has strengths and challenges associated with its application and representation of the true microstructure. The conditions needed to obtain high-quality data for each acquisition method and the challenges associated with each will be discussed.

36 MATERIALS SCIENCE↗

NASA NTRS1982

A microprocessor-based one dimensional optical data processor for spatial frequency analysis

A high degree of accuracy was obtained in measuring the spatial frequency spectrum of known samples using an optical data processor based on a microprocessor, which reliably collected intensity versus angle data. Stray light control, system alignment, and angle measurement problems were addressed and solved. The capabilities of the instrument were extended by the addition of appropriate optics to allow the use of different wavelengths of laser radiation and by increasing the travel limits of the rotating arm to + or - 160 degrees. The acquisition, storage, and plotting of data by the computer permits the researcher a free hand in data manipulation such as subtracting background scattering from a diffraction pattern. Tests conducted to verify the operation of the processor using a 25 mm diameter pinhole, a 39.37 line pairs per mm series of multiple slits, and a microscope slide coated with 1.091 mm diameter polystyrene latex spheres are described.

Collier, R. L.↗