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DOE OSTI2024

RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs

Abstract Flatbed scanners are commonly used for root analysis, but typical manual segmentation methods are time-consuming and prone to errors, especially in large-scale, multi-plant studies. Furthermore, the complex nature of root structures combined with noisy backgrounds in images complicates automated analysis. Addressing these challenges, this article introduces RhizoNet, a deep learning-based workflow to semantically segment plant root scans. Utilizing a sophisticated Residual U-Net architecture, RhizoNet enhances prediction accuracy and employs a convex hull operation for delineation of the primary root component. Its main objective is to accurately segment root biomass and monitor its growth over time. RhizoNet processes color scans of plants grown in a hydroponic system known as EcoFAB, subjected to specific nutritional treatments. The root detection model using RhizoNet demonstrates strong generalization in the validation tests of all experiments despite variable treatments. The main contributions are the standardization of root segmentation and phenotyping, systematic and accelerated analysis of thousands of images, significantly aiding in the precise assessment of root growth dynamics under varying plant conditions, and offering a path toward self-driving labs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Lipid Informed Quantitation and Identification

LIQUID (Lipid Informed Quantitation and Identification) is a software program that has been developed to enable users to conduct both informed and high-throughput global liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based lipidomics analysis. This newly designed desktop application can quickly identify and quantify lipids from LC-MS/MS datasets while providing a friendly graphical user interface for users to fully explore the data. Informed data analysis simply involves the user specifying an electrospray ionization mode, lipid common name (i.e. PE(16:0/18:2)), and associated charge carrier. A stemplot of the isotopic profile and a line plot of the extracted ion chromatogram are also provided to show the MS-level evidence of the identified lipid. In addition to plots, other information such as intensity, mass measurement error, and elution time are also provided. Typically, a global analysis for 15,000 lipid targets.

Crowell, Kevin↗

DOE OSTI2025

Acoustic Tomography of the Atmosphere: A Large-Eddy Simulation Sensitivity Study

Accurate measurement of atmospheric turbulent fluctuations is critical for understanding environmental dynamics and improving models in applications such as wind energy. Advanced remote sensing technologies are essential for capturing instantaneous velocity and temperature fluctuations. Acoustic tomography (AT) offers a promising approach that utilizes sound travel times between an array of transducers to reconstruct turbulence fields. This study presents a systematic evaluation of the time-dependent stochastic inversion (TDSI) algorithm for AT using synthetic travel-time measurements derived from large-eddy simulation (LES) fields under both neutral and convective atmospheric boundary-layer conditions. Unlike prior work that relied on field observations or idealized fields, the LES framework provides a ground-truth atmospheric state, enabling quantitative assessment of TDSI retrieval reliability, sensitivity to travel-time measurement noise, and dependence on covariance model parameters and temporal data integration. A detailed sensitivity analysis was conducted to determine the best-fit model parameters, identify the tolerance thresholds for parameter mismatch, and establish a maximum spatial resolution. The TDSI algorithm successfully reconstructed large-scale velocity and temperature fluctuations with root mean square errors ( RMSE s) below 0.35 m/s and 0.12 K, respectively. Spectral analysis established a maximum spatial resolution of approximately 1.4 m, and reconstructions remained robust for travel-time measurement uncertainties up to 0.002 s. These findings provide critical insights into the operational limits of TDSI and inform future applications of AT for atmospheric turbulence characterization and system design.

17 WIND ENERGY↗

DOE OSTI2015

Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames

This dissertation presents research on addressing some of the contemporary challenges in the analysis of vector fields—an important type of scientific data useful for representing a multitude of physical phenomena, such as wind flow and ocean currents. In particular, new theories and computational frameworks to enable consistent feature extraction from vector fields are presented. One of the most fundamental challenges in the analysis of vector fields is that their features are defined with respect to reference frames. Unfortunately, there is no single “correct” reference frame for analysis, and an unsuitable frame may cause features of interest to remain undetected, thus creating serious physical consequences. This work develops new reference frames that enable extraction of localized features that other techniques and frames fail to detect. As a result, these reference frames objectify the notion of “correctness” of features for certain goals by revealing the phenomena of importance from the underlying data. An important consequence of using these local frames is that the analysis of unsteady (time-varying) vector fields can be reduced to the analysis of sequences of steady (timeindependent) vector fields, which can be performed using simpler and scalable techniques that allow better data management by accessing the data on a per-time-step basis. Nevertheless, the state-of-the-art analysis of steady vector fields is not robust, as most techniques are numerical in nature. The residing numerical errors can violate consistency with the underlying theory by breaching important fundamental laws, which may lead to serious physical consequences. This dissertation considers consistency as the most fundamental characteristic of computational analysis that must always be preserved, and presents a new discrete theory that uses combinatorial representations and algorithms to provide consistency guarantees during vector field analysis along with the uncertainty visualization of unavoidable discretization errors. Together, the two main contributions of this dissertation address two important concerns regarding feature extraction from scientific data: correctness and precision. The work presented here also opens new avenues for further research by exploring more-general reference frames and more-sophisticated domain discretizations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Impact of numerical choices on water conservation in the E3SM Atmosphere Model version 1 (EAMv1)

Abstract. The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1∘ horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model becomes negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors in early V1 versions decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in V1 results in a very thin model layer at the Earth's surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for V1.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Impact of numerical choices on water conservation in the E3SM Atmosphere Model Version 1 (EAM V1)

The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations for sea level rise projection. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model is negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in the new model results in a very thin model layer at the Earth’s surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for this model.

Zhang, Kai↗

DOE OSTI2016

Validation of a pretreatment delivery quality assurance method for the CyberKnife Synchrony system

Purpose: To evaluate the geometric and dosimetric accuracies of the CyberKnife Synchrony respiratory tracking system (RTS) and to validate a method for pretreatment patient-specific delivery quality assurance (DQA). Methods: An EasyCube phantom was mounted on the ExacTrac gating phantom, which can move along the superior–inferior (SI) axis of a patient to simulate a moving target. The authors compared dynamic and static measurements. For each case, a Gafchromic EBT3 film was positioned between two slabs of the EasyCube, while a PinPoint ionization chamber was placed in the appropriate space. There were three steps to their evaluation: (1) the field size, the penumbra, and the symmetry of six secondary collimators were measured along the two main orthogonal axes. Dynamic measurements with deliberately simulated errors were also taken. (2) The delivered dose distributions (from step 1) were compared with the planned ones, using the gamma analysis method. The local gamma passing rates were evaluated using three acceptance criteria: 3% local dose difference (LDD)/3 mm, 2%LDD/2 mm, and 3%LDD/1 mm. (3) The DQA plans for six clinical patients were irradiated in different dynamic conditions, to give a total of 19 cases. The measured and planned dose distributions were evaluated with the same gamma-index criteria used in step 2 and the measured chamber doses were compared with the planned mean doses in the sensitive volume of the chamber. Results: (1) A very slight enlargement of the field size and of the penumbra was observed in the SI direction (on average <1 mm), in line with the overall average CyberKnife system error for tracking treatments. (2) Comparison between the planned and the correctly delivered dose distributions confirmed the dosimetric accuracy of the RTS for simple plans. The multicriteria gamma analysis was able to detect the simulated errors, proving the robustness of their method of analysis. (3) All of the DQA clinical plans passed the tests, both in static and dynamic conditions. No statistically significant differences were found between static and dynamic cases, confirming the high degree of accuracy of the Synchrony RTS. Conclusions: The presented methods and measurements verified the mechanical and dosimetric accuracy of the Synchrony RTS. Their method confirms the fact that the RTS, if used properly, is able to treat a moving target with great precision. By combining PinPoint ion chamber, EBT3 films, and gamma evaluation of dose distributions, their DQA method robustly validated the effectiveness of CyberKnife and Synchrony system.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Demonstration of Dimensional and Microstructural Postirradiation Examination Capabilities on MiniFuel Disk Specimens

This work demonstrates two new MiniFuel postirradiation examination (PIE) capabilities, laser profilometry and serial sectioning, for future use on alpha-U specimens for the upcoming Mini-99 irradiation campaign. Representative U–Mo disk specimens—3 mm in diameter and approximately 0.75 mm in thickness—were subjected to dimensional measurements using standard calipers, as well as a new Keyence CL-3000 series laser profilometry system designed to measure the surface of both sides of the disk simultaneously. The laser profilometry system captured thickness gradients across the specimens as large as 0.2 mm. Additionally, because of the limitations inherent to the use of calipers, caliper measurements consistently overestimated the initial volume of MiniFuel disk specimens compared to the laser profilometry method by up to 5%. However, the results show that optimal data collection and analysis procedures are crucial to avoiding significant artifacts during data collection that can lead to large errors (approximately 10%). Serial sectioning using a combination of ion milling and electron imaging was also demonstrated for the analysis of micron-sized control volumes. Nanometer- to micron-scale porosity was resolved on a representative U–Mo specimen before irradiation, even when the surface of the specimen appeared free of porosity. Future efforts to relate microstructural features (porosity, fission product distributions, and so on) to macroscale effects (dimensional changes, thermal conductivity degradation) require accurate characterization methods such as those demonstrated in this work. These advanced PIE capabilities will be applied to optimized alpha-U specimens for the upcoming Mini-99 neutron irradiation campaign.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Merger identification through photometric bands, colours, and their errors

Aims. We present the application of a fully connected neural network (NN) for galaxy merger identification using exclusively photometric information. Our purpose is not only to test the method’s efficiency, but also to understand what merger properties the NN can learn and what their physical interpretation is. Methods. We created a class-balanced training dataset of 5860 galaxies split into mergers and non-mergers. The galaxy observations came from SDSS DR6 and were visually identified in Galaxy Zoo. The 2930 mergers were selected from known SDSS mergers and the respective non-mergers were the closest match in both redshift and r magnitude. The NN architecture was built by testing a different number of layers with different sizes and variations of the dropout rate. We compared input spaces constructed using: the five SDSS filters: u, g, r, i, and z; combinations of bands, colours, and their errors; six magnitude types; and variations of input normalization. Results. We find that the fibre magnitude errors contribute the most to the training accuracy. Studying the parameters from which they are calculated, we show that the input space built from the sky error background in the five SDSS bands alone leads to 92.64 ± 0.15% training accuracy. We also find that the input normalization, that is to say, how the data are presented to the NN, has a significant effect on the training performance. Conclusions. We conclude that, from all the SDSS photometric information, the sky error background is the most sensitive to merging processes. This finding is supported by an analysis of its five-band feature space by means of data visualization. Moreover, studying the plane of the g and r sky error bands shows that a decision boundary line is enough to achieve an accuracy of 91.59%.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Planning, design and logistics of a decision analysis study: The FBI/Ames study involving forensic firearms examiners

This paper describes design and logistical aspects of a decision analysis study to assess the performance of qualified firearms examiners working in accredited laboratories in the United States in terms of accuracy (error rate), repeatability, and reproducibility of decisions involving comparisons of fired bullets and cartridge cases. The purpose of the study was to validate current practice of the forensic discipline of firearms/toolmarks (F/T) examination. It elicited error rate data by counting the number of false positive and false negative conclusions. Preceded by the experimental design, decisions, and logistics described herein, testing was ultimately administered 173 qualified, practicing F/T examiners in public and private crime laboratories. The first round of testing evaluated accuracy, while two subsequent rounds evaluated repeatability and reproducibility of examiner conclusions. This project expands on previous studies by involving many F/T examiners in challenging comparisons and by executing the study in the recommended double-blind format.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2017

Dark Energy Survey Year 1 Results: Multi-Probe Methodology and Simulated Likelihood Analyses

We present the methodology for and detail the implementation of the Dark Energy Survey (DES) 3x2pt DES Year 1 (Y1) analysis, which combines configuration-space two-point statistics from three different cosmological probes: cosmic shear, galaxy-galaxy lensing, and galaxy clustering, using data from the first year of DES observations. We have developed two independent modeling pipelines and describe the code validation process. We derive expressions for analytical real-space multi-probe covariances, and describe their validation with numerical simulations. We stress-test the inference pipelines in simulated likelihood analyses that vary 6-7 cosmology parameters plus 20 nuisance parameters and precisely resemble the analysis to be presented in the DES 3x2pt analysis paper, using a variety of simulated input data vectors with varying assumptions. We find that any disagreement between pipelines leads to changes in assigned likelihood $\Delta \chi^2 \le 0.045$ with respect to the statistical error of the DES Y1 data vector. We also find that angular binning and survey mask do not impact our analytic covariance at a significant level. We determine lower bounds on scales used for analysis of galaxy clustering (8 Mpc$~h^{-1}$) and galaxy-galaxy lensing (12 Mpc$~h^{-1}$) such that the impact of modeling uncertainties in the non-linear regime is well below statistical errors, and show that our analysis choices are robust against a variety of systematics. These tests demonstrate that we have a robust analysis pipeline that yields unbiased cosmological parameter inferences for the flagship 3x2pt DES Y1 analysis. We emphasize that the level of independent code development and subsequent code comparison as demonstrated in this paper is necessary to produce credible constraints from increasingly complex multi-probe analyses of current data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Cloud Influence on ERA5 and AMPS Surface Downwelling Longwave Radiation Biases in West Antarctica

The surface downwelling longwave radiation component (LW?) is crucial for the determination of the surface energy budget and has significant implications for the resilience of ice surfaces in the polar regions. Accurate model evaluation of this radiation component requires knowledge about the phase, vertical distribution, and associated temperature of water in the atmosphere, all of which control the LW? signal measured at the surface. In this study, we examine the LW? model errors found in the Antarctic Mesoscale Prediction System (AMPS) operational forecast model and the ERA5 reanalysis model relative to observations from the AWARE campaign at McMurdo Station and the West Antarctic Ice Sheet (WAIS) Divide. The errors are calculated separately for observed clear sky conditions, ice cloud occurrences, and liquid-bearing cloud layer (LBCL) occurrences. The analysis results show a tendency (in both models at each site) to underestimate the LW? during clear sky conditions, high error variability (standard deviations > 20 W/m2) during any type of cloud occurrence, and negative LW? biases when LBCLs are observed (bias magnitudes > 15 W/m2 in tenuous LBCL cases; > 43 W/m2 in optically thick/opaque LBCLs instances). We suggest that a generally dry and liquid water-deficient atmosphere responsible for the identified LW? biases in both models is the result of excessive ice formation and growth, which could stem from model initial and lateral boundary conditions, microphysics scheme, aerosol representation, and/or limited vertical resolution.

Silber, Israel↗

DOE OSTI2019

Hybrid method simulations of a soft x-ray beamline

A wavefront propagation analysis of a soft X-ray beamline using the HYBRID method is reported. All elements of the beamline: the energy dependence of the insertion device emission, the beamline mirrors and their measured figure errors, the variable-line-spacing grating and its measured figure error, and several exit slit settings, are included in the simulations. The analysis of the propagated undulator radiation through the beamline at two slightly different deflection parameter values demonstrates that, within the beamline angular acceptance and when the monochromator is tuned to the same energy, the flux is higher when the undulator is tuned to slightly higher energy than that of the monochromator. The energy resolution determined from the FWHM of the energy bandwidth transmitted through the exit slit is narrower when the undulator is tuned to higher energy than the monochromator. This is not the case when the resolution is based on the standard deviation of the transmitted energy band. The diffraction effects due to the exit slit size and their consequence on the spot size at the sample position are investigated for a few photon energies.

beamline↗

DOE OSTI2018

Asymptotic analysis of the fluid flow with a pressure-dependent viscosity in a system of thin pipes

We consider the incompressible fluid with a pressure-dependent viscosity flowing through a multiple pipe system. The viscosity–pressure relation is given by the Barus law commonly used in the engineering applications. Assuming that the ratio between pipes thickness and its length is small, we propose a rigorous asymptotic approach based on the concept of the transformed pressure. As a result, we obtain new macroscopic model describing the effective behavior of the fluid in the system. In particular, the generalized version of the Kirchhoff’s law is derived giving the explicit formula for the junction pressure. The error estimate for the asymptotic approximation is also provided. Mathematical analysis presented here can be applied to a general viscosity–pressure relation satisfied by other empiric laws.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Optimized mirror shape tuning using beam weightings based on distance, angle of incidence, reflectivity, and power

For glancing-incidence optical systems, such as short-wavelength optics used for nano-focusing, incorporating physical factors in the calculations used for shape optimization can improve performance. Wavefront metrology, including the measurement of a mirror's shape or slope, is routinely used as input for mirror figure optimization on mirrors that can be bent, actuated, positioned, or aligned. Modeling shows that when the incident power distribution, distance from focus, angle of incidence, and the spatially varying reflectivity are included in the optimization, higher Strehl ratios can be achieved. Following the works of Maréchal and Mahajan, optimization of the Strehl ratio (for peak intensity with a coherently illuminated system) occurs when the expectation value of the phase error's variance is minimized. We describe an optimization procedure based on regression analysis that incorporates these physical parameters. This approach is suitable for coherently illuminated systems of nearly diffraction-limited quality. Mathematically, this work is an enhancement of the methods commonly applied for ex situ alignment based on uniform weighting of all points on the surface (or a sub-region of the surface). It follows a similar approach to the optimization of apodized and non-uniformly illuminated optical systems. Significantly, it reaches a different conclusion than a more recent approach based on minimization of focal plane ray errors.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

On the Speed-up of Wave-like Dark Matter Searches with Entangled Qubits

Qubit-based sensing platforms offer promising new directions for wave-like dark matter searches. Recent proposals demonstrate that entangled qubits can achieve quadratic scaling of the signal in the number of qubits. In this work we expand on these proposals to analyze the bandwidth and scan rate performance of entangled qubit protocols across different error regimes. We find that the phase-based readout of entangled protocols preserves the search bandwidth independent of qubit number, in contrast to power-based detection schemes, thereby achieving a genuine scan-rate advantage. We derive coherence time and error rate requirements for qubit systems to realize this advantage. Applying our analysis to dark photon searches, we find that entangled states of approximately 100 qubits can become competitive with benchmark photon-counting cavity experiments for masses $\gtrsim 30{-}40~μ{\rm eV}$, provided sufficiently low error rates are achieved. The advantage increases at higher masses where cavity volume scaling becomes less favorable.

Bodas, Arushi [Fermilab; Chicago U.] (ORCID:000000↗

DOE OSTI2022

Case studies in bias reduction and inference for electronic health record data with selection bias and phenotype misclassification

Electronic health records (EHR) are not designed for population‐based research, but they provide easy and quick access to longitudinal health information for a large number of individuals. Many statistical methods have been proposed to account for selection bias, missing data, phenotyping errors, or other problems that arise in EHR data analysis. However, addressing multiple sources of bias simultaneously is challenging. We developed a methodological framework (R package, SAMBA ) for jointly handling both selection bias and phenotype misclassification in the EHR setting that leverages external data sources. These methods assume factors related to selection and misclassification are fully observed, but these factors may be poorly understood and partially observed in practice. As a follow‐up to the methodological work, we demonstrate how to apply these methods for two real‐world case studies, and we evaluate their performance. In both examples, we use individual patient‐level data collected through the University of Michigan Health System and various external population‐based data sources. In case study (a), we explore the impact of these methods on estimated associations between gender and cancer diagnosis. In case study (b), we compare corrected associations between previously identified genetic loci and age‐related macular degeneration with gold standard external summary estimates. These case studies illustrate how to utilize diverse auxiliary information to achieve less biased inference in EHR‐based research.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

RADAR: Runtime Asymmetric Data-access Driven Scientific Data Replication

Efficient I/O on large-scale spatiotemporal scientific data requires scrutiny of both the logical layout of the data (e.g., row-major vs. column-major) and the physical layout (e.g., distribution on parallel filesystems). For increasingly complex datasets, hand optimization is a difficult matter prone to error and not scalable to the increasing heterogeneity of analysis workloads. Given these factors, we present a partial data replication system called RADAR. We capture datatype- and collective-aware I/O access patterns (indicating logical access) via MPI-IO tracing and use a combination of coarse-grained and fine-grained performance modeling to evaluate and select optimized physical data distributions for the task at hand. Unlike conventional methods, we store all replica data and metadata, along with the original untouched data, under a single file container using the object abstraction in parallel filesystems. Our system results in manyfold improvements in some commonly used subvolume decomposition access patterns.Moreover, the modeling approach can determine whether such optimizations should be undertaken in the first place.

access pattern↗