Search NASA⌕ Search

SEARCH · Search NASA

Results for “data reconstruction”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genome-resolved metagenomics and metatranscriptomics of microbial communities in three meander-bound floodplain soils along the East River, Colorado.

This dataset comprises paired environmental and genomic data for soil samples collected across meander-bound floodplains G (ERMG), L (ERML) and Z (ERMZ). A total of 96 soil samples (32 per floodplain) from the ~ 10-25 cm layer were collected in September 2015, during base flow conditions. An additional 32 soil samples were collected from ERML in September 2016, including three samples from a depth just above the water table. A subset of samples (14) collected in 2016 were used for metatranscriptomics as well as metagenomics. The data package includes: 1) A spread sheet with sample names, location and depth by meander-bound floodplain. 2) Total organic carbon (TOC), total inorganic carbon (TIC), total carbon (TC = TOC + TIC), total nitrogen (TN), and the TOC to TN ratio (TOC:N) from 2015 subsamples. 3) Soil chemistry for 2016 subsamples. 4) A spread sheet with elevation, Easting, Northing, and topographic position index (TPI) for each site sampled in 2015. 5) A kml file, which can be viewed in Google Earth, with the locations of the 96 soil sampling sites along the East River Watershed Floodplain in Colorado. Metagenomics and metatranscriptomics data, as well as reconstructed genomes, are available elsewhere (see data package methods and bioRxiv preprint for links to the data). 6) Two sets of reconstructed genomes with overlapping members (see bioRxiv preprint for description and associated data). Metagenomes and metatranscriptomes are available elsewhere (see data package methods and bioRxiv preprint). To view tar.gz files, the following software can be used: https://www.gnu.org/software/tar/, https://www.7-zip.org/.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reconstructing patchy reionization with deep learning

The precision anticipated from next-generation cosmic microwave background (CMB) surveys will create opportunities for characteristically new insights into cosmology. Secondary anisotropies of the CMB will have an increased importance in forthcoming surveys, due both to the cosmological information they encode and the role they play in obscuring our view of the primary fluctuations. Quadratic estimators have become the standard tools for reconstructing the fields that distort the primary CMB and produce secondary anisotropies. While successful for lensing reconstruction with current data, quadratic estimators will be suboptimal for the reconstruction of lensing and other effects at the expected sensitivity of the upcoming CMB surveys. In this paper we describe a convolutional neural network, ResUNet-CMB, that is capable of the simultaneous reconstruction of two sources of secondary CMB anisotropies, gravitational lensing and patchy reionization. Furthermore, we show that the ResUNet-CMB network significantly outperforms the quadratic estimator at low noise levels and is not subject to the lensing-induced bias on the patchy reionization reconstruction that would be present with a straightforward application of the quadratic estimator.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Toward Real-Time Analysis of Synchrotron Micro-Tomography Data: Accelerating Experimental Workflows with AI and HPC

ynchrotron light sources are routinely used to perform imaging experiments. In this paper, we review the relevant computational stages, identify bottlenecks, and highlight future opportunities to streamline data acquisition for experimental microscopy workflows. We demonstrate our preliminary exploration with an end-to-end scientific workflow on Summit based on micro-computed tomography data. Computational elements include: 1) reconstruction of volumetric image data; 2) denoising with deep neural networks; and 3) non-local means based segmentation and quantitative analysis.

Mcclure, James↗
DOE OSTI2025

Doppler Backscattering Data Analysis and Integrated Modeling with OMFIT

One Modeling Framework for Integrated Tasks (OMFIT) is a widely used software tool in the magnetic fusion research community. OMFIT provides magnetic fusion energy researchers with a framework for the development of special-purpose physics modules. This paper describes an OMFIT physics module pertaining to the Doppler Backscattering (DBS) fusion plasma diagnostic. DBS measures density fluctuations and flow velocity through plasma scattering of electromagnetic waves. The OMFIT DBS module was developed to analyze experimental DBS data and facilitate modeling of DBS systems installed on multiple tokamak devices. The OMFIT DBS module is designed to support several analysis workflows: detailed analysis of experimental data, experimental planning, and theory-based synthetic diagnostic modeling. The DBS module uses integrated modeling by leveraging other OMFIT physics modules to perform tasks related to DBS, e.g. ray/beam–tracing simulations, edge-localized mode–synchronized data analysis, magnetic equilibrium reconstruction, and fitting kinetic profile data. Furthermore, this paper describes several supported workflows and serves a reference for the OMFIT DBS module.

Doppler backscattering↗
DOE OSTI2021

Simulations of Events for the LUX-ZEPLIN (LZ) Dark Matter Experiment

The LUX-ZEPLIN dark matter search aims to achieve a sensitivity to the WIMP-nucleon spin-independent cross-section down to (1–2) ×10−12 pb at a WIMP mass of 40 GeV/ c 2 . This paper describes the simulations framework that, along with radioactivity measurements, was used to support this projection, and also to provide mock data for validating reconstruction and analysis software. Of particular note are the event generators, which allow us to model the background radiation, and the detector response physics used in the production of raw signals, which can be converted into digitized waveforms similar to data from the operational detector. Inclusion of the detector response allows us to process simulated data using the same analysis routines as developed to process the experimental data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Abstract While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer ( Pty chographic G PU(multipl e )-based r econstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Neural network for 3D inertial confinement fusion shell reconstruction from single radiographs

In inertial confinement fusion (ICF), x-ray radiography is a critical diagnostic for measuring implosion dynamics, which contain rich three-dimensional (3D) information. Traditional methods for reconstructing 3D volumes from 2D radiographs, such as filtered backprojection, require radiographs from at least two different angles or lines of sight (LOS). In ICF experiments, the space for diagnostics is limited, and cameras that can operate on fast timescales are expensive to implement, limiting the number of projections that can be acquired. To improve the imaging quality as a result of this limitation, convolutional neural networks (CNNs) have recently been shown to be capable of producing 3D models from visible light images or medical x-ray images rendered by volumetric computed tomography. Here, we propose a CNN to reconstruct 3D ICF spherical shells from single radiographs. We also examine the sensitivity of the 3D reconstruction to different illumination models using preprocessing techniques such as pseudo-flatfielding. To resolve the issue of the lack of 3D supervision, we show that training the CNN utilizing synthetic radiographs produced by known simulation methods allows for reconstruction of experimental data as long as the experimental data are similar to the synthetic data. We also show that the CNN allows for 3D reconstruction of shells that possess low mode asymmetries. Further comparisons of the 3D reconstructions with direct multiple LOS measurements are justified.

3D Reconstruction↗
DOE OSTI2023

Optimal sensor placement for reconstructing wind pressure field around buildings using compressed sensing

Deciding how to optimally deploy sensors in a large, complex, and spatially extended structure is critical to ensure that the surface pressure field is accurately captured for subsequent analysis and design. In some cases, reconstruction of missing data is required in downstream tasks such as the development of digital twins. Here, this paper presents a data-driven sparse sensor selection algorithm, aiming to provide the most information contents for reconstructing aerodynamic characteristics of wind pressures over tall building structures parsimoniously. The algorithm first fits a set of basis functions to the training data, then applies a computationally efficient QR algorithm that ranks existing pressure sensors in order of importance based on the state reconstruction to this tailored basis. The findings of this study show that the proposed algorithm successfully re- constructs the aerodynamic characteristics of tall buildings from sparse measurement locations, generating stable and optimal solutions across a range of conditions. As a result, this study serves as a promising first step toward leveraging the success of data-driven and machine learning algorithms to supplement traditional genetic algorithms currently used in wind engineering.

42 ENGINEERING↗
DOE OSTI2020

A three-dimensional reconstruction algorithm for scanning transmission electron microscopy data from thick samples

Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data and transcends the prevalent structure retrieval algorithm assumption of a very thin specimen homogenous along the optic axis. We demonstrate this approach by reconstructing the different layers of a lead iridate (Pb$_2$Ir$_2$O$_7$) and yttrium-stabilized zirconia (Y$_{0.095}$Zr$_{0.905}$O$_2$) heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction.

Brown, Hamish G↗
DOE OSTI2022

Joint iterative reconstruction and 3D rigid alignment for X-ray tomography

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Unsupervised classification for region of interest in X-ray ptychography

X-ray ptychography offers high-resolution imaging of large areas at a high computational cost due to the large volume of data provided. To address the cost issue, we propose a physics-informed unsupervised classification algorithm that is performed prior to reconstruction and removes data outside the region of interest (RoI) based on the multimodal features present in the diffraction patterns. The preprocessing time for the proposed method is inconsequential in contrast to the resource-intensive reconstruction process, leading to an impressive reduction in the data workload to a mere 20% of the initial dataset. This capability consequently reduces computational time dramatically while preserving reconstruction quality. Through further segmentation of the diffraction patterns, our proposed approach can also detect features that are smaller than beam size and correctly classify them as within the RoI.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Lossy compression of statistical data using quantum annealer

Abstract We present a new lossy compression algorithm for statistical floating-point data through a representation learning with binary variables. The algorithm finds a set of basis vectors and their binary coefficients that precisely reconstruct the original data. The optimization for the basis vectors is performed classically, while binary coefficients are retrieved through both simulated and quantum annealing for comparison. A bias correction procedure is also presented to estimate and eliminate the error and bias introduced from the inexact reconstruction of the lossy compression for statistical data analyses. The compression algorithm is demonstrated on two different datasets of lattice quantum chromodynamics simulations. The results obtained using simulated annealing show 3–3.5 times better compression performance than the algorithm based on neural-network autoencoder. Calculations using quantum annealing also show promising results, but performance is limited by the integrated control error of the quantum processing unit, which yields large uncertainties in the biases and coupling parameters. Hardware comparison is further studied between the previous generation D-Wave 2000Q and the current D-Wave Advantage system. Our study shows that the Advantage system is more likely to obtain low-energy solutions for the problems than the 2000Q.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Microstructure reconstruction of battery polymer separators by fusing 2D and 3D image data for transport property analysis

A new approach to generate high-fidelity 3D microstructure reconstructions by leveraging resolution and sample volume characteristics from 2D and 3D microscopy methods is presented here. This approach is employed to model the microstructure of a highly orthotropic polypropylene separator used in lithium-ion batteries, which have challenging multi-scale features of fibrils (<100 nm) and lamellae (>100 nm) to resolve in 3D. Phase contrast nano X-ray computed tomographic data are used to reconstruct the lamellae phase, while 2D scanning electron microscopy data are used to characterize sub-100 nm microstructure features such as the thin fibrils that are beyond the effective resolution of X-ray computed tomography. Fibril geometries are reconstructed stochastically based on the 2D higher resolution data, and integrated with the lamellae geometries in 3D space. Transport property analyses are performed to investigate the bias of microstructure models without considering the fibrils. A sensitivity study is also conducted to facilitate understanding of the relationship between microstructure characteristics and transport properties.

25 ENERGY STORAGE↗
DOE OSTI2022

A Three-Dimensional Reconstruction Algorithm for Scanning Transmission Electron Microscopy Data from a Single Sample Orientation

Abstract Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, PbIrO, and yttrium-stabilized zirconia, YZrO, heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb–Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Data associated with Quaternary Research manuscript Latest Pleistocene glacial chronology and paleoclimate reconstruction for the East River watershed, Colorado, USA

The data here are associated with Quaternary Research manuscript Latest Pleistocene glacial chronology and paleoclimate reconstruction for the East River watershed, Colorado, USA and include data associated with cosmogenic exposure and depth profile dating as well as glacier-climate numerical modeling. Reconstructing Pleistocene glaciation timing and extent is vital for understanding paleoclimate. While late Pleistocene glaciation has been studied extensively in western North American mountain ranges, the glacial history of the western Elk Range in Colorado remains understudied, particularly in the East River watershed, a site of intense scientific focus. Here we use cosmogenic nuclide exposure and depth–profile dating methods to determine the timing of glaciation in the East River watershed. We use glacier modeling to reconstruct paleoglacier extents and quantify past climate conditions. Our findings indicate that the East River glacier retreated from its maximum position approximately 17–18 ka, moving to recessional positions between 13–15 ka, before experiencing more substantial retreat to high-elevation cirques around 12.9 ka. Glacier modeling suggests that the maximum ice extents at 17–18 ka could have been sustained by temperature depressions of approximately −6.5°C compared to modern conditions, assuming consistent precipitation. Additionally, the ice position at 13–15 ka could have been supported by temperature depressions of around −4.0°C. These results offer insights into the deglaciation timeline in the East River watershed and broader western Elk Range as well as paleoclimate conditions during the late Pleistocene, which may aid future research on critical zone evolution in the East River watershed.The data files include: 1. Table 1 In situ-produced 10Be sample data (.pdf, .csv, .xlsx)2. Table 2 In situ-produced 10Be exposure age results (.pdf, .csv, .xlsx)3. S1_A CRONUS calculator input assuming no erosion (.csv)4. S1_B CRONUS calculator input assuming erosion (.csv)5. S1_C CRONUS calculator results and comparison (.csv)6. S2_A In situ-produced 10Be sample data for depth profile (.csv)7. S2_B In situ-produced 10Be depth profile model input (.csv)8. S2_C In situ-produced 10Be depth profile model results (.csv)9. S3 Monthly cloudiness, rH, and windspeed data used in glacier climate model (.csv)10. S4 Glacier climate model results (.csv)

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Applying the Kalman filter particle method to strange and open charm hadron reconstruction in the STAR experiment

Here, we apply KF Particle, a Kalman Filter package for secondary vertex finding and fitting, to strange and open charm hadron reconstruction in heavy-ion collisions in the STAR experiment. Compared to the conventional helix swimming method used in STAR, the KF Particle method improves the reconstructed Λ, Ω and $D$ 0 significance considerably. At the same time, we demonstrate that Monte Carlo simulation with the STAR detector responses can well reproduce the topological variable distributions reconstructed in real data using the KF Particle method, therefore retaining good control on the reconstruction efficiency uncertainties for strange and open charm hadrons measurements in heavy-ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗