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DOE OSTI2023

Advanced techniques in automated high-resolution scanning transmission electron microscopy

Scanning transmission electron microscopy is a common tool used to study the atomic structure of materials. It is an inherently multimodal tool allowing for the simultaneous acquisition of multiple information channels. Despite its versatility, however, experimental workflows currently rely heavily on experienced human operators and can only acquire data from small regions of a sample at a time. Here, we demonstrate a flexible pipeline-based system for high-throughput acquisition of atomic-resolution structural data using an all-piezo sample stage applied to large-scale imaging of nanoparticles and multimodal data acquisition. As a result, the system is available as part of the user program of the Molecular Foundry at Lawrence Berkeley National Laboratory.

4D-STEM↗

DOE OSTI2026

Development and implementation of high-throughput proteomic and metabolomics assays by using advanced chromatographic and mass spectrometric systems (CRADA Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOFMS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Overall, the project advanced rapid metabolomics by combining liquid chromatography, ion mobility spectrometry, and data-independent mass spectrometry with machine learning. This multidimensional approach uses retention time, collision cross-section, precursor mass, and fragment-ion information to distinguish chemically similar metabolites that can be difficult to resolve using conventional liquid- or gas-chromatography methods. The resulting workflow also provided automated metabolite-identification error estimates, addressing a recognized need for statistical confidence measures in metabolomics.

Petzold, Christopher [Lawrence Berkeley National L↗

DOE OSTI2023

The fast camera (Fastcam) imaging diagnostic systems on the DIII-D tokamak

Two camera systems are installed on the DIII-D tokamak at the toroidal positions of 90° (90° system) and 225° (225° system), respectively. The cameras have two types of relay optics, namely, a coherent optical fiber bundle and a periscope system. The periscope system provides absolute intensity calibration stability while sacrificing resolution (10 lp/mm), while the fiber system provides high resolution (16 lp/mm) while sacrificing calibration stability. The periscope is available only for the 90° system. The optics of the 225° system were designed for view stability, repeatability, and easy maintenance. The cameras are located inside optimized neutron, x ray and magnetic shielding in order to reduce electronics damage, reboots, and magnetic and neutron interference, increasing the overall system reliability. An automated filter wheel, providing remote filter change, allows for remote wavelength selection. A software suite automates camera acquisition and data storage, allowing for remote operation and reduced operator involvement. System metadata is used to streamline the data analysis workflow, particularly for intensity calibration. Here, the spatial calibration uses multiple observable wall features, resulting in a reconstruction accuracy ≤2 cm.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Agilent AgileBioFoundry CRADA (Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Automated Integration of Continental-Scale Observations in Near-Real Time for Simulation and Analysis of Biosphere–Atmosphere Interactions

The National Ecological Observatory Network (NEON) is a continental-scale observatory with sites across the US collecting standardized ecological observations that will operate for multiple decades. To maximize the utility of NEON data, we envision edge computing systems that gather, calibrate, aggregate, and ingest measurements in an integrated fashion. Edge systems will employ machine learning methods to cross-calibrate, gap-fill and provision data in near-real time to the NEON Data Portal and to High Performance Computing (HPC) systems, running ensembles of Earth system models (ESMs) that assimilate the data. For the first time gridded EC data products and response functions promise to offset pervasive observational biases through evaluating, benchmarking, optimizing parameters, and training new machine learning parameterizations within ESMs all at the same model-grid scale. Leveraging open-source software for EC data analysis, we are already building software infrastructure for integration of near-real time data streams into the International Land Model Benchmarking (ILAMB) package for use by the wider research community. We will present a perspective on the design and integration of end-to-end infrastructure for data acquisition, edge computing, HPC simulation, analysis, and validation, where Artificial Intelligence (AI) approaches are used throughout the distributed workflow to improve accuracy and computational performance.

Durden, David J.↗

DOE OSTI2022

Experimental discovery of structure–property relationships in ferroelectric materials via active learning

Emergent functionalities of structural and topological defects in ferroelectric materials underpin an extremely broad spectrum of applications ranging from domain wall electronics to high dielectric and electromechanical responses. Many of these functionalities have been discovered and quantified via local scanning probe microscopy methods. However, the search has until now been based on either trial and error, or using auxiliary information such as the topography or domain wall structure to identify potential objects of interest on the basis of the intuition of operator or pre-existing hypotheses, with subsequent manual exploration. Here we report the development and implementation of a machine learning framework that actively discovers relationships between local domain structure and polarization-switching characteristics in ferroelectric materials encoded in the hysteresis loop. The hysteresis loops and their scalar descriptors such as nucleation bias, coercive bias and the hysteresis loop area (or more complex functionals of hysteresis loop shape) and corresponding uncertainties are used to guide the discovery of these relationships via automated piezoresponse force microscopy and spectroscopy experiments. As such, this approach combines the power of machine learning methods to learn the correlative relationships between high-dimensional data, as well as human-based physics insights encoded into the acquisition function. For ferroelectric materials, this automated workflow demonstrates that the discovery path and sampling points of on- and off-field hysteresis loops are largely different, indicating that on- and off-field hysteresis loops are dominated by different mechanisms. Here, the proposed approach is universal and can be applied to a broad range of modern imaging and spectroscopy methods ranging from other scanning probe microscopy modalities to electron microscopy and chemical imaging.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Real‐time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis

X‐ray scattering experiments using free electron lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID‐19 viral proteins). XFEL experiments are a challenge to computing in two ways: (i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; (ii) data‐collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min—sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS‐NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis within 10 min is a first for XFEL experiments and an important milestone if we are to keep up with data‐collection trends.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Real-Time XFEL Data Analysis at SLAC and NERSC: a Trial Run of Nascent Exascale Experimental Data Analysis

X-ray scattering experiments using Free Electron Lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID-19 viral proteins). XFEL experiments are a challenge to computing in two ways: i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; ii) data collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min -- sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS-NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Furthermore, completing data analysis with 10 mins is a first for XFEL experiments and an important milestone if we are to keep up with data collection trends.

Blaschke, Johannes P.↗

DOE OSTI2026

Toward Unified Autonomous Scattering Experiments: A Cross-Facility Case Study at ALS and PETRA III

Autonomous experiments rely on the integration of control, data acquisition, analysis, and decision-making frameworks. While such systems have been demonstrated at individual facilities, adapting them to additional instruments remains challenging due to differences in local infrastructure. We present a modular workflow that connects existing open-source tools for data access (Tiled), workflow orchestration (Prefect), analysis and visualization (pyFAI, Plotly Dash), and Gaussian-process-based adaptive sampling (gpCAM) into a unified framework for autonomous scattering experiments. The same configuration operates across two synchrotron beamlines (ALS 7.3.3 and PETRA III P03) with only minimal facility-specific adjustments, as shown in proof-of-concept demonstrations. This validates that a consistent design emphasizing modularity and shared interfaces can ease deployment across diverse experimental environments. The resulting framework provides a flexible foundation for extending autonomous control and analysis capabilities beyond a single beamline or instrument.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Transport Simulations on Scanning Transmission Electron Microscope Images of Nanoporous Shale

Digital rock physics is an often-mentioned approach to better understand and model transport processes occurring in tight nanoporous media including the organic and inorganic matrix of shale. Workflows integrating nanometer-scale image data and pore-scale simulations are relatively undeveloped, however. In this paper, a workflow is demonstrated progressing from sample acquisition and preparation, to image acquisition by Scanning Transmission Electron Microscopy (STEM) tomography, to volumetric reconstruction to pore-space discretization to numerical simulation of pore-scale transport. Key aspects of the workflow include (i) STEM tomography in high angle annular dark field (HAADF) mode to image three-dimensional pore networks in µm-sized samples with nanometer resolution and (ii) lattice Boltzmann method (LBM) simulations to describe gas flow in slip, transitional, and Knudsen diffusion regimes. It is shown that STEM tomography with nanoscale resolution yields excellent representation of the size and connectivity of organic nanopore networks. In turn, pore-scale simulation on such networks contributes to understanding of transport and storage properties of nanoporous shale. Interestingly, flow occurs primarily along pore networks with pore dimensions on the order of tens of nanometers. Smaller pores do not form percolating pathways in the sample volume imaged. Apparent gas permeability in the range of 10−19 to 10−16 m2 is computed.

42 ENGINEERING↗

NASA NTRS2019

2018 NISAR Applications Workshop: Agriculture and Soil Moisture

Agricultural lands cover the globe and play an essential role in not only sustaining a growing global population, but can have significant implications on the Earth system through land use change (e.g., deforestation, grazing, etc.). As such, countries around the world have dedicated programs for managing these lands. Accurate and timely information concerning the status of agricultural crops (soil moisture, crop health, crop type, etc.) is essential to those nations’ anthropogenic and ecological health as well as economy. The joint NASA/US Department of Agriculture Agricultural Research Service (USDA-ARS) workshop focused on advancing agriculture and soil moisture applications by using remote sensing data from the NASA-ISRO Synthetic Aperture Radar (NISAR) mission (expected launch 2022). Participants included representatives from the international agriculture community that are key players in facilitating integration of Earth Observations into decision support workflows including US Federal Agencies, nonprofits, and private sector. They included scientists, technicians, and program managers with a responsibility for data acquisition and exploitation such as product development, delivery, and use, as well as capacity building. Discussions were held over two and a half days to convey the broader agriculture and soil moisture community information needs, the mission and procedures for various representative participants and programs involved in the delivery of geospatial products, and the capabilities and status of the NISAR mission. Case studies were presented to demonstrate the current state of practice in the use of SAR remote sensing for applications of direct importance for the agriculture and soil moisture communities. Eleven organizations presented their information requirements in response to a set of questions provided by the NASA team, then the NASA team responded by describing the degree to which NISAR could meet these requirements. Discussion ensued about needed data product specifications to increase utility (e.g., projection, latency, etc.), tools and capacity building.

Stavros, Natasha↗

DOE OSTI2026

The Art of Automation: Translating Electron Microscopy Workflows Into Automated Processes

Acquiring data using a scanning transmission electron microscope (STEM) is a complex, multi-step process. The intricacy of the process depends on the type of sample, composition of the material, desired results of the experiment, resolution requirement and other experimental factors. Each experiment presents unique complications, such as sample drift and contamination, that the microscopist must consider when acquiring data. All these challenges are handled fluidly and expertly by experienced microscopists, but to reach new levels of innovation in material development, including greater reproducibility, throughput, and precision, the automation of these workflows is essential. The initial phase of this work involved translating intuition-based workflows into discrete, programmable steps. Some common key stages in STEM workflows are the initial tuning, scanning the sample for areas of interest, and then acquiring the data. Each stage can be broken further into specific parameter adjustments, such as aberration correction and dwell time optimization, depending on the experiment. When deconstructing various experiments each step was assessed for automation feasibility based on the amount of real time operator decisions. There are steps that lend themselves to automation more readily than others, such as course focusing and sample screening, but there is potential for full automation of all stages with time. As an initial step, an automated montage routine was developed, allowing for the efficient acquisition of large portions of the sample without requiring continuous intervention from the operator. The automation of this small process of the procedure demonstrates the value of this capability. A major challenge in automation arises from discrepancies between commanded, reported and actual stage movements. Using systematic tests, stage movement was quantified. This error can be corrected algorithmically for more accurate workflows in the future. Expanding automation capabilities would result in larger, more efficient data acquisition which allows for more robust statistical analysis. Additionally, this work lays the groundwork for a closed loop system where machine learning algorithms would intake automatically acquired data and make real time decisions. By progressively automating this instrument, this work establishes the foundation for fully automated experimentation in transmission electron microscopy.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Data supporting the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure"

This dataset contains atomic force microscopy images associated with the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure" by Maria Kelly, Emily R. Dunn, Ellis A. Spickermann, Josephine N. Gruber, César A. Lasalde-Ramírez, P. N. Romero Zavala, Éowyn Lucas, Ankur Gupta, Harry A. Atwater, and Wilson A. Smith. The dataset contains both raw images as well as segmented images produced by the image processing workflow described in the manuscript. A readme file and meta data file are included to provide additional details regarding the sample identity, image acquisition parameters, and file naming scheme.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Lithium–Sulfur Batteries: 3D Printed Tools and Assembly Techniques for Repeatable Lab-Scale Coin Cell Manufacturing

The coin cell form factor has become a standard in energy storage research owing to its relatively low cost, low quantity of requisite electroactive material, fast experimental turnover, and capability to generate publishable quality data. Coin cell assembly at the lab-scale requires precise manual alignment of the many internal components of a cell to yield a properly functioning device. Truly repeatable device assembly presents a significant challenge to the acquisition of reliable data. In this report, we present a three-dimensional (3D) printable design for a coin cell alignment device and describe techniques for a generalized workflow to achieve reproducible coin cell assembly of lithium-based batteries. Standardized assembly techniques using readily accessible, purpose-built tools were demonstrated for labscale production of lithium−sulfur (Li−S) coin cells. Li−S batteries fabricated using the alignment device as well as conductive adhesive incorporated workflows afforded coin cells with up to 35% reduction of assembly times, comparable or better functional cell yields, and improved electrochemical device performance with more consistent and up to 150 mAh/g higher average discharge capacities coupled with Coulombic efficiency increases of up to 2.0% over manually aligned cell assembly techniques.

Batteries↗

DOE OSTI2023

High-Resolution Image Products Acquired from Mid-Sized Uncrewed Aerial Systems for Land–Atmosphere Studies

We assess the viability of deploying commercially available multispectral and thermal imagers designed for integration on small uncrewed aerial systems (sUASs, <25 kg) on a mid-size Group-3-classification UAS (weight: 25–600 kg, maximum altitude: 5486 m MSL, maximum speed: 128 m/s) for the purpose of collecting a higher spatial resolution dataset that can be used for evaluating the surface energy budget and effects of surface heterogeneity on atmospheric processes than those datasets traditionally collected by instrumentation deployed on satellites and eddy covariance towers. A MicaSense Altum multispectral imager was deployed on two very similar mid-sized UASs operated by the Atmospheric Radiation Measurement (ARM) Aviation Facility. This paper evaluates the effects of flight on imaging systems mounted on UASs flying at higher altitudes and faster speeds for extended durations. We assess optimal calibration methods, acquisition rates, and flight plans for maximizing land surface area measurements. We developed, in-house, an automated workflow to correct the raw image frames and produce final data products, which we assess against known spectral ground targets and independent sources. We intend this manuscript to be used as a reference for collecting similar datasets in the future and for the datasets described within this manuscript to be used as launching points for future research.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Protocols for x-ray transient grating pump/optical probe experiments at x-ray free electron lasers

Abstract Transient grating spectroscopy is a specialized application of the four-wave-mixing methodology and constitutes a versatile technique for investigating the dynamics of vibrational, magnetic and electronic degrees of freedom of matter in a background-free fashion. Recent developments in free-electron laser sources have enabled the extension of this technique into the extreme ultraviolet range. Ongoing efforts to expand transient grating spectroscopy into the x-ray regime promise numerous advantages: (1) substantial penetration depths that allow for probing bulk material properties, (2) element specificity via specific core-excited states, and (3) short wavelengths that allow for excitation gratings with higher momentum transfer and improved spatial resolution. In this study, we comprehensively outline the procedures for conducting x-ray transient grating pump/optical probe experiment. The process encompasses the design and alignment of the experimental setup, as well as the subsequent steps involved in data acquisition and analysis. This paper is intended as a comprehensive guide for researchers interested in implementing x-ray transient grating spectroscopy, providing valuable insights into the intricacies of the experimental workflow required for this novel technique. Furthermore, we discuss the potential for extending this methodology to an x-ray pump/x-ray probe scheme, envisioning a future direction that holds promise for enhancing the capabilities and scope of x-ray transient grating spectroscopy, opening new opportunities for studying ultrafast processes with unprecedented temporal and spatial resolutions.

Optics↗

DOE OSTI2025

nmRanalysis: An Open-Source Web Application for Semi-automated NMR Metabolite Profiling

Though data acquisition and initial signal pre-processing of nuclear magnetic resonance (NMR) spectra have achieved high degrees of automation, downstream processing - specifically the profiling of spectra - has bottlenecked the overall NMR analysis workflow. Several efforts have been made to mitigate this bottleneck, but these solutions often trade an increase in automation for limitations elsewhere. Here, in this technical note, we introduce nmRanalysis, a user-friendly web-application that integrates the strengths of existing profiling tools for a more automated profiling workflow. nmRa-nalysis additionally incorporates novel features, including a machine-learning-driven recommender system for me-tabolite identification, further increasing the utility of nmRanalysis over the individual tools that it incorporates.

Flores, Javier E. [Pacific Northwest National Labo↗

DOE OSTI2024

CLAS12 remote data-stream processing using ERSAP framework

Implementing a physics data processing application is relatively straightforward with the use of current containerization technologies and container image runtime services, which are prevalent in most high-performance computing (HPC) environments. However, the process is complicated by the challenges associated with data provisioning and migration, impacting the ease of workflow migration and deployment. Transitioning from traditional file-based batch processing to data-stream processing workflows is suggested as a method to streamline these workflows. This transition not only simplifies file provisioning and migration but also significantly reduces the necessity for extensive disk space. Data-stream processing is particularly effective for real-time processing during data acquisition, thereby enhancing data quality assurance. This paper introduces the integration of the JLAB CLAS12 event reconstruction application within the ERSAP data-stream processing framework that facilitates the execution of streaming event reconstruction at a remote data center and enables the return streaming of reconstructed events to JLAB while circumventing the need for temporary data storage throughout the process.

Gyurjyan, Vardan↗