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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.

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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Characterization of an imploding cylindrical plasma for electron transport studies using x-ray emission spectroscopy

We report here on the characterization of the conditions of an imploding cylindrical plasma by time-resolved x-ray emission spectroscopy. Knowledge about this implosion platform can be applied to studies of particle transport for inertial confinement fusion schemes or to astrophysical plasmas. A cylindrical Cl-doped CH foam within a tube of solid CH was irradiated by 36 beams (I total ~5×10 14 W/cm 2 , 1.5ns square pulse, and E total ~ 16.2kJ) of the OMEGA-60 laser to radially compress the CH toward the axis. The analysis of the time-resolved spectra showed that the compression can be described by four distinct phases, each presenting different plasma conditions. First the ablation of the cylinder is dominant; second, the foam is heated and induces a significant jump in emission intensities; third, the temperature and density of the foam reaches a maximum; and finally, the plasma expands. Ranges for the plasma temperature were inferred with the atomic physics code SCRAM (Spectroscopic Collisional-Radiative Atomic Model) and the experimental data have been compared to hydrodynamic simulations performed with the 2D code FLASH, which showed a similar implosion dynamic over time.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Implementing High-Performance Geometric Multigrid Solver with Naturally Grained Messages

Structured-grid linear solvers often require manually packing and unpacking of communication data to achieve high performance.Orchestrating this process efficiently is challenging, labor-intensive, and potentially error-prone.In this paper, we explore an alternative approach that communicates the data with naturally grained messagesizes without manual packing and unpacking. This approach is the distributed analogue of shared-memory programming, taking advantage of the global addressspace in PGAS languages to provide substantial programming ease. However, its performance may suffer from the large number of small messages. We investigate theruntime support required in the UPC ++ library for this naturally grained version to close the performance gap between the two approaches and attain comparable performance at scale using the High-Performance Geometric Multgrid (HPGMG-FV) benchmark as a driver.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

D-Guaranteed Discrimination of Statistical Hypotheses: a Review of Results and Unsolved Problems

We compare two sequential d-guaranteed tests and an optimal d-guaranteed test based on a fixed number of observations with respect to the average number of observations within the most accepted practical applications of Bayesian probabilistic models. We consider the sequential “first skipping” test, the sequential locally efficient test based on the score statistic, and the test based on a fixed number of observations that minimizes the necessary sample size. We study various characteristics of these tests connected with the number of observations within three probabilistic models, namely, the normal (ϑ, σ{sup 2}) distribution of the observed random variable and the normal a priori distribution of ϑ with fixed σ{sup 2}; the exponential distribution with the intensity parameter ϑ and the a priori gamma distribution of ϑ; and the Bernoulli sampling with the success probability ϑ and the a priori beta distribution of ϑ. We discuss the connection of the d-posterior approach with the compound decision problem as applied to the analysis of data provided by microchips (when the false discovery rate, or FDR, for short, is treated as the d-risk of the first kind). We present the vast data on characteristics of the mentioned tests obtained by the method of mathematical modeling in several tables. We discuss unsolved problems of the d-guaranteed discrimination of hypotheses with the minimal number of observations and approaches to their solution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Physics-Informed Machine Learning Model for Ceramic Matrix Composite Creep

A physics-informed recurrent neural network (RNN) based surrogate model is developed to emulate the nonlinear, time-dependent constitutive behavior of ceramic matrix composites (CMCs) driven by matrix damage and constituent creep at the microscale. Physics-informed constraints are introduced into the surrogate model through regularization to ground the prediction in physics and improve its predictive capabilities. Training data is generated using the high-fidelity generalized method of cells (HFGMC) approach which calls appropriate creep and damage models for each of the constituents. This coupling permits simulating the nonlinear behavior of CMCs based on constituent response at the microscale along with microstructural features such as fiber and porosity volume fraction and fiber radius. The microscale repeating unit cell is loaded under creep fatigue conditions to replicate the material loading experienced in a turbine engine. Therefore, the RNN-based surrogate model is tasked with predicting, as a function of variable input stress sequence, temperature, and microstructural features, the resulting strain history response while satisfying physical constraints related to creep rate, isochoric inelastic deformation, and strain energy density. The trained surrogate model is shown to effectively match the strain history over quantified distributions of microstructural features and relevant loading regimes and temperatures. Neural network based surrogate models can offer efficient alternatives to running computationally intensive multiscale material models to simulate the nonlinear response of large structural models. Therefore, the presented work provides evidence towards the feasibility of developing, training, and running such models for CMCs with complex microstructures, nonlinear time-dependent material response, and under non-monotonic loading conditions.

ceramic matrix composites↗
DOE OSTI2023

Porting the WAVEWATCH III (v6.07) wave action source terms to GPU

Abstract. Surface gravity waves play a critical role in several processes, including mixing, coastal inundation, and surface fluxes. Despite the growing literature on the importance of ocean surface waves, wind–wave processes have traditionally been excluded from Earth system models (ESMs) due to the high computational costs of running spectral wave models. The development of the Next Generation Ocean Model for the DOE’s (Department of Energy) E3SM (Energy Exascale Earth System Model) Project partly focuses on the inclusion of a wave model, WAVEWATCH III (WW3), into E3SM. WW3, which was originally developed for operational wave forecasting, needs to be computationally less expensive before it can be integrated into ESMs. To accomplish this, we take advantage of heterogeneous architectures at DOE leadership computing facilities and the increasing computing power of general-purpose graphics processing units (GPUs). This paper identifies the wave action source terms, W3SRCEMD, as the most computationally intensive module in WW3 and then accelerates them via GPU. Our experiments on two computing platforms, Kodiak (P100 GPU and Intel(R) Xeon(R) central processing unit, CPU, E5-2695 v4) and Summit (V100 GPU and IBM POWER9 CPU) show respective average speedups of 2× and 4× when mapping one Message Passing Interface (MPI) per GPU. An average speedup of 1.4× was achieved using all 42 CPU cores and 6 GPUs on a Summit node (with 7 MPI ranks per GPU). However, the GPU speedup over the 42 CPU cores remains relatively unchanged (∼ 1.3×) even when using 4 MPI ranks per GPU (24 ranks in total) and 3 MPI ranks per GPU (18 ranks in total). This corresponds to a 35 %–40 % decrease in both simulation time and usage of resources. Due to too many local scalars and arrays in the W3SRCEMD subroutine and the huge WW3 memory requirement, GPU performance is currently limited by the data transfer bandwidth between the CPU and the GPU. Ideally, OpenACC routine directives could be used to further improve performance. However, W3SRCEMD would require significant code refactoring to make this possible. We also discuss how the trade-off between the occupancy, register, and latency affects the GPU performance of WW3.

58 GEOSCIENCES↗
DOE OSTI2019

Textural analysis on contrast-enhanced CT in pancreatic neuroendocrine neoplasms: association with WHO grade

Purpose: Grades of pancreatic neuroendocrine neoplasms (PNENs) are associated with the choice of treatment strategies. Texture analysis has been used in tumor diagnosis and staging evaluation. In this study, we aim to evaluate the potential ability of texture parameters in differentiation of PNENs grades. Materials and methods: 37 patients with histologically proven PNENs and underwent pretreatment dynamic contrast-enhanced computed tomography examinations were retrospectively analyzed. Imaging features and texture features at contrast-enhanced images were evaluated. Receiver operating characteristic curves were used to determine the cut-off values and the sensitivity and specificity of prediction. Results: There were significant differences in tumor margin, pancreatic duct dilatation, lymph nodes invasion, size, portal enhancement ratio (PER), arterial enhancement ratio (AER), mean grey-level intensity, kurtosis, entropy, and uniformity among G1, G2, and pancreatic neuroendocrine carcinoma (PNEC) G3 (p < 0.01). Similar results were found between pancreatic neuroendocrine tumors (PNETs) G1/G2 and PNEC G3. AER and PER showed the best sensitivity (0.86–0.94) and specificity (0.92–1.0) for differentiating PNEC G3 from PNETs G1/G2. Mean grey-level intensity, entropy, and uniformity also showed acceptable sensitivity (0.73–0.91) and specificity (0.85–1.0). Mean grey-level intensity was also showed acceptable sensitivity (91% to 100%) and specificity (82% to 91%) in differentiating PNET G1 from PNET G2. Conclusions: Our data indicated that texture parameters have potential in grading PNENs, in particular in differentiating PNEC G3 from PNETs G1/G2.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Desalination metamodels and a framework for cross-comparative performance simulations

There is an opportunity to save energy and reduce operational expenses when choosing a suitable desalination method aided by computational modeling. Existing models are not conducive to generalized comparisons between different desalination methods. Therefore, the work in this study developed metamodels for six desalination methods, grouped them into thermal and molecular transport families, and validated their predictive performance within 9% difference from published data. This validated framework allowed comparisons of desalination methods at their prescribed ranges of operational conditions that they were designed for. These conditions specify feed salinity ranges of 1.6 to 2.4 g/kg for Capacitive Deionization and Reverse Osmosis (RO), 2.8 to 4.2 g/kg for Electrodialysis, 28 to 42 g/kg for Thermovapor Compression and Humidification-Dehumidification, and 37 to 55 g/kg for Multi-Effect Distillation (MED). Despite different operational conditions, all models exhibit non-linear, positive correlation between energy consumption and system size in response to feed salinity and production rate. The framework is also employed in a cross-comparative analysis between MED and RO whose results suggest that energy intensity for MED is an order of magnitude greater than RO for the same operational conditions, but actual operational costs are comparable. Overall, the framework is ready for deployment in case studies of actual desalination plants.

42 ENGINEERING↗
DOE OSTI2020

Development of a Comprehensive Two-Phase Flow Database for the Validation of NEK-2P

Three-dimensional (3-D) two-phase Computational Fluid Dynamics (CFD) codes are emerging as a powerful and potentially practical tool for applications in which detailed local flow information is needed. However, two-phase flow models and associated closure relations are not well established for CFD applications, which is partly due to the lack of high-quality validation data. The main objective of this work is to develop a comprehensive database of two-phase flows that can be used to validate two-phase CFD codes such as NEK-2P. In this project, four advanced local measurement systems, including Particle Image Velocimetry and Planar Laser-Induced Fluorescence (PIV-PLIF), high-speed imaging, x-ray densitometry, and multi-sensor conductivity probe are employed to measure the local two-phase flow parameters of both gas and liquid phases. By combining these techniques, the local void fraction, bubble velocity, interfacial area concentration, bubble frequency, liquid velocity, turbulence intensity, etc., in various two-phase flow regimes can be obtained. These local measurement techniques are first used in a 25.4 mm circular pipe test section. Seven air-water two-phase flow conditions spanning the bubbly, slug, churn-turbulent, and annular flow regimes are measured in this facility. The obtained database contains the radial profiles of both gas- and liquid-phase parameters at three axial locations along the test section. The second facility used in this work contains a 30 mm × 10 mm rectangular test section, in which three two-phase flow and two single-phase flow conditions are measured. Two-dimensional distributions of local two-phase flow parameters in the cross-sectional plane are measured in this facility at three axial locations as well. A facility featuring a 3×3 electrically heated rod bundle is also designed and being constructed in this project. This facility is specially designed for optical measurements and is expected to provide high-quality boiling data in the future. Preliminary analyses have been performed for the data taken in the 25.4 mm circular pipe. Both center-peaked and wall-peaked void fraction profiles have been observed in the data depending on the two-phase flow conditions and/or developing lengths. The 1-D drift-flux model was evaluated with the newly obtained datasets, in which both gas- and liquid-phases data were directly measured. The distribution parameter model has been optimized based on a new void-profile classification method proposed in this study. The optimized drift-flux model shows a significant improvement in predicting both gas velocity and void fraction. The measured liquid-phase turbulence was used to benchmark Sato’s turbulence model considering the bubble-induced shear stress for the three tested bubbly flows. The benchmark results showed good agreement between the PIV measurements and model predictions. In the bubbly flows tested that have low void fractions less than 3%, the effect of the bubble-induced turbulence was found not significant. However, the bubble-induced shear stress becomes important with the increase of the void fraction. The Conjugate Heat Transfer (CHT) model was developed and implemented in NEK-2P. This model allows the coupled simulation of the solid domain and two-phase fluid domain, allowing the specification of realistic boundary conditions. The CHT implementation was verified first with non-boiling simulations. The predicted temperatures in the fluid domain were shown to be identical in simulations with or without the CHT model. The CHT model was then validated through simulations of three Becker benchmark CHF tests performed under both Dryout (DO) and Departure from Nucleate Boiling (DNB) conditions. Reasonably good agreement was obtained between calculated wall temperatures and corresponding experimental data.

42 ENGINEERING↗
DOE OSTI2026

Resilience Metrics Framework for Solar Photovoltaics

This presentation was given at the Photovoltaic Specialist Conference (PVSC) 54 in New Orleans, Louisiana. Photovoltaic (PV) systems are routinely exposed to extreme weather, including wind and hail storms. Historically, most systems have proven to be resilient to such events, but some storms have damaged PV systems, leading to physical and financial loss. Storm hardening measures and specific system attributes can reduce this risk. This work introduces a set of resilience metrics and a framework for quantifying, comparing, and predicting PV system resilience. The framework is divided into two parts: 1) predictive, attribute metrics based on site and component characteristics, and 2) impact metrics that assess post-storm performance. Metrics are weighted and aggregated, producing hazard-specific resilience scores. We derive damage functions from storm-impacted PV systems, establishing a baseline against which post-storm performance can be compared. This damage was widely variable across hail and wind intensities, and field hail damage was less than predicted by laboratory tests, suggesting that system features - in addition to storm conditions - influence damage likelihood. Finally, the metrics framework is demonstrated using three case studies of storm damaged PV systems. Although additional data are needed to create attribute specific damage functions and establish metric weights, this study presents a methodology for evaluating PV resilience and contributes new damage functions to the literature.

14 SOLAR ENERGY↗
DOE OSTI2016

Benchmark Generation and Simulation at Extreme Scale

The path to extreme scale high-performance computing (HPC) poses several challenges related to power, performance, resilience, productivity, programmability, data movement, and data management. Investigating the performance of parallel applications at scale on future architectures and the performance impact of different architectural choices is an important component of HPC hardware/software co-design. Simulations using models of future HPC systems and communication traces from applications running on existing HPC systems can offer an insight into the performance of future architectures. This work targets technology developed for scalable application tracing of communication events. It focuses on extreme-scale simulation of HPC applications and their communication behavior via lightweight parallel discrete event simulation for performance estimation and evaluation. Instead of simply replaying a trace within a simulator, this work promotes the generation of a benchmark from traces. This benchmark is subsequently exposed to simulation using models to reflect the performance characteristics of future-generation HPC systems. This technique provides a number of benefits, such as eliminating the data intensive trace replay and enabling simulations at different scales. The presented work features novel software co-design aspects, combining the ScalaTrace tool to generate scalable trace files, the ScalaBenchGen tool to generate the benchmark, and the xSim tool to assess the benchmark characteristics within a simulator.

Lagadapati, Mahesh↗
DOE OSTI2016

A method for normalizing pathology images to improve feature extraction for quantitative pathology

Purpose: With the advent of digital slide scanning technologies and the potential proliferation of large repositories of digital pathology images, many research studies can leverage these data for biomedical discovery and to develop clinical applications. However, quantitative analysis of digital pathology images is impeded by batch effects generated by varied staining protocols and staining conditions of pathological slides. Methods: To overcome this problem, this paper proposes a novel, fully automated stain normalization method to reduce batch effects and thus aid research in digital pathology applications. Their method, intensity centering and histogram equalization (ICHE), normalizes a diverse set of pathology images by first scaling the centroids of the intensity histograms to a common point and then applying a modified version of contrast-limited adaptive histogram equalization. Normalization was performed on two datasets of digitized hematoxylin and eosin (H&E) slides of different tissue slices from the same lung tumor, and one immunohistochemistry dataset of digitized slides created by restaining one of the H&E datasets. Results: The ICHE method was evaluated based on image intensity values, quantitative features, and the effect on downstream applications, such as a computer aided diagnosis. For comparison, three methods from the literature were reimplemented and evaluated using the same criteria. The authors found that ICHE not only improved performance compared with un-normalized images, but in most cases showed improvement compared with previous methods for correcting batch effects in the literature. Conclusions: ICHE may be a useful preprocessing step a digital pathology image processing pipeline.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2018

Central and Eastern North America Ground-Motion Characterization (NGA-East)

This document is the final project report of the Next Generation Attenuation for Central and Eastern North America (CENA) project (NGA-East). The NGA-East objective was to develop a new ground-motion characterization (GMC) model for the CENA region. The GMC model consists of a set of new ground-motion models (GMMs) for median and standard deviation of ground motions and their associated weights to be used with logic-trees in probabilistic seismic hazard analyses (PSHA). NGA-East is a large multidisciplinary project coordinated by the Pacific Earthquake Engineering Research Center (PEER), at the University of California. The project has two components: (1) a set of scientific research tasks, and (2) a model-building component following the framework of the “Seismic Senior Hazard Analysis Committee (SSHAC) Level 3” (Budnitz et al. 1997; NRC 2012). Component (2) is built on the scientific results of component (1) of the NGA-East project. This report documents the tasks under component (2) of the project. Under component (1) of NGA-East, several scientific issues were addressed, including: (a) development of a new database of ground motion data recorded in CENA; (b) development of a regionalized ground-motion map for CENA, (c) definition of the reference site condition; (d) simulations of ground motions based on different methodologies; and (e) development of numerous GMMs for CENA. The scientific tasks of NGA-East were all documented as a series of PEER reports. The scope of component (2) of NGA-East was to develop the complete GMC. This component was designed as a SSHAC Level 3 study with the goal of capturing the ground motions’ center, body, and range of the technically defensible interpretations in light of the available data and models. The SSHAC process involves four key tasks: evaluation, integration, formal review by the Participatory Peer Review Panel (PPRP), and documentation (this report). Key tasks documented in this report include review and evaluation of the empirical groundmotion database, the regionalization of ground motions, and screening sets of candidate GMMs. These are followed by the development of new median and standard deviation GMMs, the development of new analyses tools for quantifying the epistemic uncertainty in ground motions, and the documentation of implementation guidelines of the complete GMC for PSHA computations. Appendices include further documentation of the relevant SSHAC process and additional supporting technical documentation of numerous sensitivity analyses results. The PEER reports documenting component (1) of NGA-East are also considered “attachments” to the current report and are all available online on the PEER website (https://peer.berkeley.edu/). The final NGA-East GMC model includes a set of 17 GMMs defined for 24 ground-motion intensity measures, applicable to CENA in the moment magnitude range of 4.0 to 8.2 and covering distances up to 1500 km. Standard deviation models are also provided for site-specific analysis (single-station standard deviation) and for general PSHA applications (ergodic standard deviation). Adjustment factors are provided for consideration of source-depth effects and hanging-wall effects, as well as for hazard computations at sites in the Gulf Coast region.

58 GEOSCIENCES↗
DOE OSTI2016

DEEP WIDEBAND SINGLE POINTINGS AND MOSAICS IN RADIO INTERFEROMETRY: HOW ACCURATELY DO WE RECONSTRUCT INTENSITIES AND SPECTRAL INDICES OF FAINT SOURCES?

Many deep wideband wide-field radio interferometric surveys are being designed to accurately measure intensities, spectral indices, and polarization properties of faint source populations. In this paper, we compare various wideband imaging methods to evaluate the accuracy to which intensities and spectral indices of sources close to the confusion limit can be reconstructed. We simulated a wideband single-pointing (C-array, L-Band (1–2 GHz)) and 46-pointing mosaic (D-array, C-Band (4–8 GHz)) JVLA observation using a realistic brightness distribution ranging from 1 μ Jy to 100 mJy and time-, frequency-, polarization-, and direction-dependent instrumental effects. The main results from these comparisons are (a) errors in the reconstructed intensities and spectral indices are larger for weaker sources even in the absence of simulated noise, (b) errors are systematically lower for joint reconstruction methods (such as Multi-Term Multi-Frequency-Synthesis (MT-MFS)) along with A-Projection for accurate primary beam correction, and (c) use of MT-MFS for image reconstruction eliminates Clean-bias (which is present otherwise). Auxiliary tests include solutions for deficiencies of data partitioning methods (e.g., the use of masks to remove clean bias and hybrid methods to remove sidelobes from sources left un-deconvolved), the effect of sources not at pixel centers, and the consequences of various other numerical approximations within software implementations. This paper also demonstrates the level of detail at which such simulations must be done in order to reflect reality, enable one to systematically identify specific reasons for every trend that is observed, and to estimate scientifically defensible imaging performance metrics and the associated computational complexity of the algorithms/analysis procedures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Laue-DIALS: Open-source software for polychromatic x-ray diffraction data

Most x-ray sources are inherently polychromatic. Polychromatic (“pink”) x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure—ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Nuclear and in-source laser spectroscopy with the ISAC yield station

A new decay station has been built for the ISAC facility at TRIUMF for the rapid and reliable characterization of radioactive ion beam (RIB) compositions and intensities with the capability of simultaneously collecting α, β, and γ decay data from RIB with intensities between a few and ≈10{sup 11} ions per second. It features user-friendly control, data acquisition, and analysis software. The analysis of individual decay time structures allows the unambiguous assignment of α and γ lines even with substantial isobaric contamination present. The capability for accurate half-life measurements is demonstrated with the example of {sup 46}K. The coupling of the yield station to the laser ion source, TRILIS, allows the correlation of radiometric data with automated laser frequency scans. First results of in-source laser spectroscopy measurements on astatine are discussed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

"Experimental Research at the Energy Frontier in High Energy Physics" (Final Technical Report)

Recent developments in particle physics and cosmology raise the exciting prospect that we are on the threshold of a major step forward in our understanding of the universe. This proposal describes a research program at the University of Illinois in experimental high-energy physics on the ATLAS experiment at CERN’s Large Hadron Collider (LHC). Our group actively collaborates with the Theory Group and other experimental efforts within the Office of Science frontiers (energy, intensity, and cosmic) to search broadly in the ATLAS data to maximize our potential for scientifc discovery. The thrust of this proposal is to search for new physics using ATLAS data. Emphasis is placed on novel use of the Higgs boson as a tool to search for new particles and interactions and development of fast particle tracking systems for use in triggering. We propose to continue our strong role in FTK commissioning and operations. To maximize the impact and vitality of the proposed physics program through the HL-LHC running, we will lead firmware efforts in the HWTT Phase-II TDAQ upgrade, leveraging our expertise acquired through development of fast tracking hardware and firmware for the FTK system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

High-Throughput Field Plant Phenotyping: A Self-Supervised Sequential CNN Method to Segment Overlapping Plants

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used. The first step in this process is typically plant segmentation, which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants. However, preparing such training data is both time and labor intensive. To solve this problem, we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems. This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages. The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed. We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes. We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques. This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

Significance Single-particle diffraction is an emerging technique in which diffraction images are collected from individual particles, and is used to study molecular structure from multiple conformational states that may be inaccessible through other methods. However, determining structure from these experiments is challenging, since orientations and states of imaged particles are unknown and images are highly contaminated with noise. Furthermore, the number of useful images is often limited by achievable single-particle hit rates, currently around 0.1%. We introduce an iterative projection framework to simultaneously determine orientations, states, and molecular structure from limited single-particle data by leveraging structural constraints throughout the reconstruction. This framework offers a potential pathway to increasing the amount of information that can be extracted from single-particle diffraction.

97 MATHEMATICS AND COMPUTING↗