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All sources NASA NTRS DOE OSTI

DOE OSTI2020

Real-time damage characterization for GFRCs using high-speed synchrotron X-ray phase contrast imaging

Here, we report the application of high-speed synchrotron X-ray phase contrast imaging (PCI) in real-time damage characterization for glass fiber reinforced composites (GFRCs) subjected to dynamic loading. Dynamic single-edge notched bending (DSENB) experiments on pre-notched S-2 GFRCs were performed on a modified Kolsky compression bar. During loading, the synchrotron X-ray beam penetrated through the composite specimen from the side to detect damage evolution inside the material. Entire dynamic events were recorded by a high-speed camera as image sequences.0° and 90° unidirectional and cross-ply composites were investigated. An optical imaging technique was also employed to capture similar dynamic events in comparison with the radiographic imaging. It is demonstrated that high-speed X-ray PCI had sufficient phase contrast to characterize a crack initiation at a 20-μm spatial resolution within 920 ns and track the crack geometry during propagation, thereby providing reliable data to quantify the dynamic damage resistance of GFRCs. Furthermore, being capable of recognizing microscopic damage-related features at a sub-10-μm resolution, high-speed X-ray PCI provided fundamental material failure mechanisms to reveal the essential of macroscale structural failure of composites. It can also track the damage evolution inside and between individual plies of laminated composites. However, current high-speed X-ray PCI technique only supports in-situ observation and the high timing and spatial resolutions are limited within a field of view of ~2.5 mm in square, preventing its application in the three-dimensional and larger-area damage detection for GFRC structures.

42 ENGINEERING↗

DOE OSTI2025

The construction of large-scale structure catalogs for the Dark Energy Spectroscopic Instrument

We present the technical details on how large-scale structure (LSS) catalogs are constructed from redshifts measured from spectra observed by the Dark Energy Spectroscopic Instrument (DESI). The LSS catalogs provide the information needed to determine the relative number density of DESI tracers as a function of redshift and celestial coordinates and, e.g., determine clustering statistics. We produce catalogs that are weighted subsamples of the observed data, each matched to a weighted `random' catalog that forms an unclustered sampling of the probability density that DESI could have observed those data at each location. Precise knowledge of the DESI observing history and associated hardware performance allows for a determination of the DESI footprint and the number of times DESI has covered it at sub-arcsecond level precision. This enables the completeness of any DESI sample to be modeled at this same resolution. The pipeline developed to create LSS catalogs has been designed to easily allow robustness tests and enable future improvements. We describe how it allows ongoing work improving the match between galaxy and random catalogs, such as including further information when assigning redshifts to randoms, accounting for fluctuations in target density, accounting for variation in the redshift success rate, and accommodating blinding schemes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Tomography of pions and kaons in the QCD vacuum: Transverse momentum dependent parton distribution functions

We evaluate the pion and kaon transverse momentum dependent parton distribution functions in the instanton liquid model, a model of the QCD vacuum at low resolution. The relevant transverse momentum distributions (TMDs) are factored into a constituent quark distribution times a rapidity dependent soft factor from staple-shaped Wilson lines, for fixed parton longitudinal momentum and transverse separation. The results are evolved to higher rapidities using the Collins-Soper kernel and higher resolution using renormalization group evolution. The comparison to existing extractions of pion TMDs from Drell-Yan data is briefly discussed.

classical solutions in field theory↗

DOE OSTI2020

MEP: Mobility Energy Productivity Metric

In response to the need to assess fundamental improvements in mobility as technology provides new modes, methods, and opportunities in urban areas to connect people with goods, services, and employment, a mobility-energy productivity score (MEPS) has been developed. The MEPS fundamentally measures the potential of a multi-modal system to connect a person to a variety of services and activities that define a high-quality of life. The MEPS is measured relative to the convenience and energy needed to provide connectivity. Fundamentally derived from accessibility theory, the MEPS advances practice by using readily available travel time data (either from web-based APIs or outputs from an urban transportation model) combined with established parameters that reflect the energy intensity of various travel modes, and relative frequency of activity engagement. The construction of the MEPS allows for aggregation and disaggregation to the appropriate spatial, modal, and trip purpose resolution, as analysis needs dictate. The MEPS could be used to compare alternative futures related to technology, infrastructure investment, or policy, providing a much needed tool for planners, researchers, and analysts. In other words, the metric measures how efficiently connected a place is.

Hou, Yi↗

DOE OSTI2020

Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS

The continental flood inundation mapping (CFIM) framework is a high-performance computing (HPC)-based computational framework for the Height Above Nearest Drainage (HAND)-based inundation mapping methodology. Using the 10m Digital Elevation Model (DEM) data produced by U.S. Geological Survey (USGS) 3DEP (the 3-D Elevation Program) and the NHDPlus hydrography dataset produced by USGS and the U.S. Environmental Protection Agency (EPA), a hydrological terrain raster called HAND is computed for HUC6 units in the conterminous U.S. (CONUS). The value of each raster cell in HAND is an approximation of the relative elevation between the cell and its nearest water stream. Derived from HAND, a hydraulic property table is established to calculate river geometry properties for each of the 2.7 million river reaches covered by NHDPlus (5.5 million kilometers in total length). This table is a lookup table for water depth given an input stream flow value. Such lookup is available between water depth 0m and 25m at 1-foot interval. The flood inundation map is then computed by using HAND and this lookup table based on the near real-time water forecast from the National Water Model (NWM) at the National Oceanic and Atmospheric Administration (NOAA). HAND and the Hydraulic Property Table version 0.2. is created to correspond to data updates in the USGS 1/3 arcsec DEM, the USGS National Hydrography Dataset, including its Water Boundary Dataset, and the NHDPlus medium resolution dataset. This dataset comprises 331 HUC6 units for CONUS (excluding the five great lakes units), each is a downloadable zip file. Version 0.1 was computed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urban-Champaign in 2016 and is currently hosted at the Texas Advanced Computing Center (TACC). Please cite this data DOI and the following publications and data DOIs when you use HAND and the hydraulic property table: Liu, Yan Y., David R. Maidment, David G. Tarboton, Xing Zheng, and Shaowen Wang. 'A CyberGIS integration and computation framework for high-resolution continental-scale flood inundation mapping.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 770-784. DOI: 10.1111/1752-1688.12660 Zheng, Xing, David G. Tarboton, David R. Maidment, Yan Y. Liu, and Paola Passalacqua. 'River channel geometry and rating curve estimation using height above the nearest drainage.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 785-806. DOI: 10.1111/1752-1688.12661 Liu, Y. (2018). Height Above Nearest Drainage (HAND) for CONUS - v0.1, HydroShare, https://doi.org/10.4211/hs.69f7d237675c4c73938481904358c789 LICENSE FOR USE -- MAPS AND DATA DISCLAIMER This resource is shared under the Creative Commons Attribution CC BY, http://creativecommons.org/licenses/by/4.0/ MAPS AND DATA DISCLAIMER The Oak Ridge National Laboratory (ORNL) shall not be held liable for improper or incorrect use of the data described or information contained on this map or associated series of maps. The data and related map graphics are not legal, land survey or engineering documents and are not intended to be used as such. ORNL gives no warranty, express or implied, as to the accuracy, reliability, utility or completeness of this information. The user of these maps and data assumes all responsibility and risk for the use of the maps and data. ORNL disclaims all warranties, representations or endorsements either express or implied, with regard to the information contained in this map product, including, but not limited to, all implied warranties of merchantability, fitness for a particular purpose or non-infringement. This preliminary map product is for research and review purposes only. It is not intended to be used for emergency management operational or life safety decisions at the local or regional governmental level or by the general public. Users requiring information regarding hazardous conditions or meteorological conditions for specific geographic areas should consult directly with their city or county emergency management office.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Open Source Visualization and Analysis Platform for 3D Reconstructions of Materials by Transmission Electron Microscopy

Three-dimensional characterization of materials at the nano- and meso-scale has become possible with transmission and scanning transmission electron microscopes (S/TEM). Its importance has extended to a wide class of nanomaterials such as hydrogen fuel cells, solar cells, industrial catalysts, new battery materials and semiconductor devices, as well as spanning high-tech industry, universities, and national labs. While capable instrumentation is abundant, this rapidly expanding demand for high-resolution tomography is bottlenecked by software that is instead tailored for lower-dose, biological applications and not optimized for higher-resolution materials applications. Existing tomography fails to utilize the chemical information provided by S/TEM spectrometers. To address this problem, this project delivered a scalable, fully functional, freely-distributable, open Source materials tomography package with a modern user interface that enables automated acquisition, alignment, and real-time reconstruction of raw tomography data, and provides advanced segmentation, three-dimensional chemical visualization and analysis optimized for materials applications. It has established an extendable framework capable of automation for high-throughput for the tomography of materials from data acquisition to visualization. Phase I and II delivered a full-featured, cross-platform, clean and integrated application for S/TEM materials tomography. It can read projection data from the microscope, with graphical tools for alignment of data, tomographic reconstruction, segmentation, and visualization of the reconstructed 3D volume. The entire pipeline can be saved to an XML state file, enabling fully reproducible data processing and analysis with a full Python environment for the development of custom algorithms, processing, and analysis requirements. Phase IIB extended the application to provide real-time tomographic reconstruction, "live updates" as data is processed, analysis of big data, and multi-channel tomography. Here, quantitative assessment of nanomaterials can occur as data is being recorded on a 3D visualization platform that accommodates additional information from multiple channels. We provide unmatched high-throughput tomography, where the complete tomographic pipeline from measurement to 3D visualization can occur rapidly. The project was extended to offer capabilities for micro-CT, X-ray, neutron, focused ion beam, atomic electron tomography and atom probe tomography. With over 600 transmission electron microscopes worldwide and approximately 50 coming online each year, the demand and impact of an open-source tomography tool is large. Significant opportunities exist in high-tech industry, universities, and national labs to enable or enhance three-dimensional imaging at the nanoscale and bring automated high-throughput approaches that will accelerate progress in materials characterization and metrology. The project supports a service based business model by enabling lab-specific acquisition and processing customization and integration-support and development that will be provided into Phase III and beyond.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Status of the ANNIE experiment

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a Gadolinium-loaded water Cherenkov detector located in the Booster Neutrino Beam at Fermilab. One of its primary physics goals is to measure the final state neutron multiplicity of neutrino-nucleus interactions. This measurement of the neutron yield as a function of the outgoing lepton kinematics will be useful to constrain systematic uncertainties and reduce biases in future long-baseline oscillation and cross-section experiments. ANNIE is also a testbed for innovative new detection technologies. It will make use of pioneering photodetectors called Large Area Picosecond Photodetectors (LAPPDs) with better than 100 picosecond time resolution, which will enhance its reconstruction capabilities and demonstrate the feasibility of this technology as a new tool in high energy physics. The status of the experiment is reported here in terms of the overall progress, the deployment of the first LAPPD and an overview of recently taken beam and calibration data. Additional future R\&D efforts and analysis opportunities involving the use of the novel detection medium of Water-based Liquid Scintillators (WbLS) are also briefly highlighted.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Progress Towards a Predictive Eagle Behavior and Risk Modeling Framework: Overview and Recent Validation Efforts

This presentation summarizes progress to date of the U.S. Department of Energy project, "Development of a computational framework for modeling golden eagles (Aquila chrysaetos) near wind farms," which focuses on stochastic behavioral modeling of soaring raptors across landscape, facility, and turbine spatiotemporal scales. This publicly available, open-source modeling framework includes behavioral models based on three different underlying principles: energy minimization at landscape scale, behavioral heuristics at landscape-facility scale, and data-driven behaviors at the facility-micro-scale. We will briefly overview the key advancements in the behavioral modeling state of the art, which leverages multiple high-resolution telemetry data sources combined with high-fidelity atmospheric flow modeling insights. We then present preliminary results from a validation study in Altamont, California. This new study involves a novel application of the Stochastic Soaring Raptor Simulator (SSRS), in a new geographic locale, to understand facility scale eagle movement patterns over time scales representative of a wind project's lifetime. For this desktop analysis (that does not depend on any high-performance computing resources), SSRS simultaneously considers a variety of wind conditions and eagle approach vectors toward a project site of interest. This work demonstrates the integration of publicly available landscape-scale atmospheric datasets, our recently improved engineering updraft models (see presentation from Thedin et al.), and our energy minimization behavioral models within the SSRS framework. While we only present results from a single behavioral model, the integration of these three modeling components forms the foundation for our more sophisticated behavioral models (see presentations from Brandes et al., Sandhu et al.) that are under active development. Results are presented in the form of presence maps, which may be applied to estimate risk to wildlife, augment ground survey data, inform wind-plant operations, or incorporated into wind-plant designs.

agent-based modeling↗

DOE OSTI2020

Improvement of Quantification in Non-Destructive Characterization of Radioactive Waste Packages -Introduction to the Ideas of a Currently Started Project - 20197

For the characterization of radioactive waste packages (e.g. 200-L drums) with inhomogeneous activity and density distributions preferably non-destructive methods like segmented gamma scanning and transmission measurements are applied. While the first is used for identification of the radioactive inventory, both are necessary for a reliable activity quantification. Although at nuclear facilities, segmented gamma scanner are state-of-the-art and are mostly equipped with a vertically moveable transmission source the combining of this data and further a-priori information improving accuracy in data estimation giving realistic, reliable and traceable uncertainty estimations are improvable. This challenge is tackled by a R and D project funded by the German Federal Ministry of Education and Research (BMBF). The boundary conditions for this project are (i) taking into account the typical instrumentation available at nuclear facilities, (ii) minimize the overall measurement time and (iii) combining data from emission and transmission measurements by Bayesian methods. For the R and D project, being still in its initial stage, the basic ideas, the data used for evaluation and the result of a preliminary investigation demonstrating the proof of principle are presented. Additionally, some first aspects on spatial resolution in emission and transmission measurements are addressed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

"Hierarchical Speed Planner for Automated Vehicles: A Framework for Lagrangian Variable Speed Limit in Mixed Autonomy Traffic"

This paper introduces a novel control framework for Lagrangian variable speed limits in hybrid traffic flow environments utilizing automated vehicles (AVs). The framework was validated using a fleet of 100 connected automated vehicles as part of the largest coordinated open-road test designed to smooth traffic flow. The framework includes two main components: a high-level controller deployed on the server side, named Speed Planner, and low-level controllers called vehicle controllers deployed on the vehicle side. The Speed Planner designs and updates target speeds for the vehicle controllers based on real-time Traffic State Estimation (TSE) [1]. The Speed Planner comprises two modules: a TSE enhancement module and a target speed design module. The TSE enhancement module is designed to minimize the effects of inherent latency in the received traffic information and to improve the spatial and temporal resolution of the input traffic data. The target speed design module generates target speed profiles with the goal of improving traffic flow. The vehicle controllers are designed to track the target speed meanwhile responding to the surrounding situation. The numerical simulation indicates the performance of the proposed method: the bottleneck throughput has increased by 5.01%, and the speed standard deviation has been reduced by a significant 34.36%. We further showcase an operational study with a description of how the controller was implemented on a field-test with 100 AVs and its comprehensive effects on the traffic flow.

Wang, Han↗

DOE OSTI2024

Efficient boundary-guided scanning for high-resolution X-ray ptychography

In the realm of X-ray ptychography experiments, a considerable amount of ptychography scans are typically performed within a field of view encompassing the target sample. While it is crucial to obtain overlapping scans in small increments over the region of interest for achieving high-resolution sample reconstruction, a significant number of these scans often redundantly measure the empty background within the wide field of view. To address this inefficiency, an innovative algorithm is proposed that introduces automatic guidance for data acquisition. The algorithm first directs the scan point to actively search for the object of interest within the field of view. Subsequently, it intelligently scans along the perimeter of the sample, strategically acquiring measurements exclusively within the boundary of the region of interest. By employing this approach, a reduction in the number of measurements required to obtain high-resolution reconstruction images is demonstrated, as compared with conventional raster scanning methods. Furthermore, the automatic guidance provided by the algorithm offers the added advantage of saving valuable time during the reconstruction process. Through practical implementation on real experiments, these findings showcase the efficacy of the proposed algorithm in enhancing the efficiency and accuracy of X-ray ptychography experiments. This novel approach holds immense potential for advancing sample analysis and imaging techniques in various scientific disciplines.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Characterization of Pinhole Collimators for High-Resolution Gamma Imaging of Irradiated Fuel

Post-irradiation examination (PIE) of nuclear fuels requires imaging tools capable of resolving isotopic and spatial features with high throughput. This project contributes to a proof-of-concept effort aimed at advancing gamma emission tomography (GET) by evaluating novel fine-aperture pinhole collimators. Two Rose’s metal collimators, 100 µm (20° acceptance angle) and 350 µm (30° acceptance angle), were prototyped and characterized for their effectiveness in transporting gamma rays through the pinhole aperture. To support data collection, a Python-based data acquisition system was developed to coordinate a rotation stage, linear stage, and CZT detector, reducing latency in high-rate gamma event logging to one second per acquisition. Queue-based file writing enabled seamless real-time data capture for count rates up to 35,000 counts per second (cps). List-mode parsing algorithms were implemented to differentiate single and simultaneous gamma interactions for future tomographic reconstruction. Detector response was evaluated in both spectroscopy and list mode acquisition methods across varying source distances to confirm absolute and collimator efficiencies. Preliminary efficiency figures suggest effective collimation of gamma-rays with energies below 700 keV, with ~4% residual intensity through the aperture for Cs-137. The impact of collimator geometry on image quality is currently being evaluated. This groundwork supports the ongoing development of a sub mm resolution cone-beam CT system for imaging fuel phantoms, an essential step toward improving GET efficiency and accelerating nuclear fuel qualification efforts.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗

DOE OSTI2022

A Conterminous USA-Scale Map of Relative Tidal Marsh Elevation

Abstract Tidal wetlands provide myriad ecosystem services across local to global scales. With their uncertain vulnerability or resilience to rising sea levels, there is a need for mapping flooding drivers and vulnerability proxies for these ecosystems at a national scale. However, tidal wetlands in the conterminous USA are diverse with differing elevation gradients, and tidal amplitudes, making broad geographic comparisons difficult. To address this, a national-scale map of relative tidal elevation ( Z * MHW ), a physical metric that normalizes elevation to tidal amplitude at mean high water (MHW), was constructed for the first time at 30 × 30-m resolution spanning the conterminous USA. Contrary to two study hypotheses, watershed-level median Z * MHW and its variability generally increased from north to south as a function of tidal amplitude and relative sea-level rise. These trends were also observed in a reanalysis of ground elevation data from the Pacific Coast by Janousek et al. (Estuaries and Coasts 42 (1): 85–98, 2019). Supporting a third hypothesis, propagated uncertainty in Z * MHW increased from north to south as light detection and ranging (LiDAR) errors had an outsized effect under narrowing tidal amplitudes. The drivers of Z * MHW and its variability are difficult to determine because several potential causal variables are correlated with latitude, but future studies could investigate highest astronomical tide and diurnal high tide inequality as drivers of median Z * MHW and Z * MHW variability, respectively. Watersheds of the Gulf Coast often had propagated Z * MHW uncertainty greater than the tidal amplitude itself emphasizing the diminished practicality of applying Z * MHW as a flooding proxy to microtidal wetlands. Future studies could focus on validating and improving these physical map products and using them for synoptic modeling of tidal wetland carbon dynamics and sea-level rise vulnerability analyses.

Holmquist, James R. (ORCID:0000000325466766)↗

DOE OSTI2022

Quantifying Dynamic Signal Spread in Real-Time High-Energy X-ray Diffraction

Abstract Measured intensity in high-energy monochromatic X-ray diffraction (HEXD) experiments provides information regarding the microstructure of the crystalline material under study. The location of intensity on an areal detector is determined by the lattice spacing and orientation of crystals so that changes in the heterogeneity of these quantities are reflected in the spreading of diffraction peaks over time. High temporal resolution of such dynamics can now be experimentally observed using technologies such as the mixed-mode pixel array detector (MM-PAD) which facilitates in situ dynamic HEXD experiments to study plasticity and its underlying mechanisms. In this paper, we define and demonstrate a feature computed directly from such diffraction time series data quantifying signal spread in a manner that is correlated with plastic deformation of the sample. A distinguishing characteristic of the analysis is the capability to describe the evolution from the distinct diffraction peaks of an undeformed alloy sample through to the non-uniform Debye–Scherrer rings developed upon significant plastic deformation. We build on our previous work modeling data using an overcomplete dictionary by treating temporal measurements jointly to improve signal spread recovery. We demonstrate our approach in simulations and on experimental HEXD measurements captured using the MM-PAD. Our method for characterizing the temporal evolution of signal spread is shown to provide an informative means of data analysis that adds to the capabilities of existing methods. Our work draws on ideas from convolutional sparse coding and requires solving a coupled convex optimization problem based on the alternating direction method of multipliers.

Engineering↗

DOE OSTI2020

Interactions Between the Amazonian Rainforest and Cumuli Clouds: A Large‐Eddy Simulation, High‐Resolution ECMWF, and Observational Intercomparison Study

Abstract The explicit coupling at meter and second scales of vegetation's responses to the atmospheric‐boundary layer dynamics drives a dynamic heterogeneity that influences canopy‐top fluxes and cloud formation. Focusing on a representative day during the Amazonian dry season, we investigate the diurnal cycle of energy, moisture and carbon dioxide at the canopy top, and the transition from clear to cloudy conditions. To this end, we compare results from a large‐eddy simulation technique, a high‐resolution global weather model, and a complete observational data set collected during the GoAmazon14/15 campaign. The overall model‐observation comparisons of radiation and canopy‐top fluxes, turbulence, and cloud dynamics are very satisfactory, with all the modeled variables lying within the standard deviation of the monthly aggregated observations. Our analysis indicates that the timing of the change in the daylight carbon exchange, from a sink to a source, remains uncertain and is probably related to the stomata closure caused by the increase in vapor pressure deficit during the afternoon. We demonstrate quantitatively that heat and moisture transport from the subcloud layer into the cloud layer are misrepresented by the global model, yielding low values of specific humidity and thermal instability above the cloud base. Finally, the numerical simulations and observational data are adequate settings for benchmarking more comprehensive studies of plant responses, microphysics, and radiation.

Vilà‐Guerau de Arellano, J.↗

DOE OSTI2023

Citizen and machine learning-aided high-resolution mapping of urban heat exposure and stress

Abstract Through conversion of land cover to more built-up, impervious surfaces, cities create hotter environments than their surroundings for urban residents, with large differences expected between different parts of the city. Existing measurements of ambient air temperature and heat stress, however, are often insufficient to capture the intra-urban variability in heat exposure. This study provides a replicable method for modeling air temperature, humidity, and moist heat stress over the urban area of Chapel Hill while engaging citizens to collect high-temporal and spatially-resolved air temperature and humidity measurements. We use low-cost, consumer-grade sensors combined with satellite remote sensing data and machine learning to map urban air temperature and relative humidity over various land-cover classes to understand intra-urban spatial variability of ambient heat exposure at a relatively high resolution (10 m). Our findings show that individuals may be exposed to higher levels of air temperature and moist heat stress than weather station data suggest, and that the ambient heat exposure varies according to land cover type, with tree-covered land the coolest and built-up areas the warmest, and time of day, with higher air temperatures observed during the early afternoon. Combining our resulting dataset with sociodemographic data, policymakers and urban planners in Chapel Hill can use data output from this method to identify areas exposed to high temperature and moist heat stress as a first step to design effective mitigation measures.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed X-ray radiography

Full-field ultra-high-speed (UHS) X-ray imaging experiments have been well established to characterize various processes and phenomena. However, the potential of UHS experiments through the joint acquisition of X-ray videos with distinct configurations has not been fully exploited. In this paper, we investigate the use of a deep learning-based spatio-temporal fusion (STF) framework to fuse two complementary sequences of X-ray images and reconstruct the target image sequence with high spatial resolution, high frame rate and high fidelity. We applied a transfer learning strategy to train the model and compared the peak signal-to-noise ratio (PSNR), average absolute difference (AAD) and structural similarity (SSIM) of the proposed framework on two independent X-ray data sets with those obtained from a baseline deep learning model, a Bayesian fusion framework and the bicubic interpolation method. The proposed framework outperformed the other methods with various configurations of the input frame separations and image noise levels. With three subsequent images from the low-resolution (LR) sequence of a four times lower spatial resolution and another two images from the high-resolution (HR) sequence of a 20 times lower frame rate, the proposed approach achieved average PSNRs of 37.57 dB and 35.15 dB, respectively. When coupled with the appropriate combination of high-speed cameras, the proposed approach will enhance the performance and therefore the scientific value of UHS X-ray imaging experiments.

deep learning↗

DOE OSTI2022

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.

transcription start and end sites↗