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Results for “correlative light and electron microscopy”

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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Identification and demonstration of roGFP2 as an environmental sensor for cryogenic correlative light and electron microscopy

Cryogenic correlative light and electron microscopy (cryo-CLEM) seeks to leverage orthogonal information present in two powerful imaging modalities. While recent advances in cryogenic electron microscopy (cryo-EM) allow for the visualization and identification of structures within cells at the nanometer scale, information regarding the cellular environment, such as pH, membrane potential, ionic strength, etc., which influences the observed structures remains absent. Fluorescence microscopy can potentially be used to reveal this information when specific labels, known as fluorescent biosensors, are used, but there has been minimal use of such biosensors in cryo-CLEM to date. Here we demonstrate the applicability of one such biosensor, the fluorescent protein roGFP2, for cryo-CLEM experiments. At room temperature, the ratio of roGFP2 emission brightness when excited at 425 nm or 488 nm is known to report on the local redox potential. When samples containing roGFP2 are rapidly cooled to 77 K in a manner compatible with cryo-EM, the ratio of excitation peaks remains a faithful indicator of the redox potential at the time of freezing. Using purified protein in different oxidizing/reducing environments, we generate a calibration curve which can be used to analyze in situ measurements. As a proof-of-principle demonstration, we investigate the oxidation/reduction state within vitrified Caulobacter crescentus cells. The polar organizing protein Z (PopZ) localizes to the polar regions of C. crescentus where it is known to form a distinct microdomain. Finally, by expressing an inducible roGFP2-PopZ fusion we visualize individual microdomains in the context of their redox environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗
DOE OSTI2022

Origin of organic matter and organic pores in the overmature Ordovician-Silurian Wufeng-Longmaxi Shale of the Sichuan Basin, China

Organic matter (OM)-hosted pores play important roles in controlling the porosity and gas content of gas shales. However, the control of organic pore development and preservation remains poorly understood, partly because of the inability to distinguish OM types under the scanning electron microscope (SEM). In this study, seven over-mature Wufeng-Longmaxi Shale samples (equivalent vitrinite reflectance 1.93%–3.07%) were investigated with organic petrography and scanning electron microscope to study the origin of OM and development of organic pores in this black shale succession. Correlative light and electron microscopy was employed to examine pore development in individual macerals. Organic petrographic observations show that OM in these over-mature black shales is dominated by pyrobitumen and graptolites (> 90 vol.% of total OM based on point counting). Pyrobitumen mainly occurs as matrix bitumen in the fine-grained matrix, and also as a mixture with clay minerals and fossil cavity infillings. Vitrinite-like particles are minor constituents of OM in the Wufeng-Longmaxi Shale, and their average reflectance, reflectance distribution, and morphology suggest that they may be derived from graptolite fragments lacking diagnostic features and acritarchs. OM type critically controls the development of organic pores. Here, organic pores primarily occur in pyrobitumen, whereas other macerals are mostly non-porous when examined under the SEM. Results of this study provided important insights into OM thermal evolution and organic pore development in source-rock reservoirs, calling for a critical appraisal of OM in black shales with organic petrography in addition to SEM.

03 NATURAL GAS↗
DOE OSTI2024

Correlative X-ray micro-nanotomography with scanning electron microscopy at the Advanced Light Source

Geological samples are inherently multi-scale. Understanding their bulk physical and chemical properties requires characterization down to the nano-scale. A powerful technique to study the three-dimensional microstructure is X-ray tomography, but it lacks information about the chemistry of samples. To develop a methodology for measuring the multi-scale 3D microstructure of geological samples, correlative X-ray micro- and nanotomography were performed on two rocks followed by scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS) analysis. The study was performed in five steps: (i) micro X-ray tomography was performed on rock sample cores, (ii) samples for nanotomography were prepared using laser milling, (iii) nanotomography was performed on the milled sub-samples, (iv) samples were mounted and polished for SEM analysis and (v) SEM imaging and compositional mapping was performed on micro and nanotomography samples for complimentary information. Correlative study performed on samples of serpentine and basalt revealed multiscale 3D structures involving both solid mineral phases and pore networks. Significant differences in the volume fraction of pores and mineral phases were also observed dependent on the imaging spatial resolution employed. This highlights the necessity for the application of such a multiscale approach for the characterization of complex aggregates such as rocks. Information acquired from the chemical mapping of different phases was also helpful in segmentation of phases that did not exhibit significant contrast in X-ray imaging. Adoption of the protocol used in this study can be broadly applied to 3D imaging studies being performed at the Advanced Light Source and other user facilities.

58 GEOSCIENCES↗
DOE OSTI2021

SEM petrography of dispersed organic matter in black shales: A review

Organic matter (OM)-hosted pores are important constituents of the pore system of black shales and play a crucial role in determining their methane adsorption capacity and porosity. OM-hosted pores are generally observed and described with scanning electron microscope (SEM) on Ar ion-milled surfaces. However, SEM imaging is not able to reliably distinguish OM types and relate the observed pores to specific macerals. Partly because of this inability to relate organic pores to macerals, the evolution of organic porosity during thermal maturation remains poorly understood. In this paper, we review the petrographic characteristics of dispersed organic matter (DOM) in black shales under the SEM. Organic petrographic classification of DOM developed for reflected-light microscopy is so far the most practical method when describing DOM in black shales under the SEM because this classification has information on the origin of DOM. Therefore, correlative microscopy (combination of reflected-light and electron microscopy) is the most effective method to identify both OM types and OM-hosted pores. This method, however, is not readily available to most researchers. Although identifying OM on the basis of SEM observations is a challenging task, it is achievable provided there is a good understanding of the studied shales, especially their thermal maturity and original OM composition. Therefore, the overall objective of this paper is to review petrographic characteristics of DOM in black shales under the SEM to provide some guidelines for identifying DOM from SEM observations. We also review factors that control the formation and preservation of OM-hosted pores. OM-hosted pores consist of primary and secondary organic pores. Primary organic pores are pores inherited from the biological structure of the original OM. Secondary organic pores develop during hydrocarbon generation and expulsion from oil-prone OM and are hosted by solid bitumen or pyrobitumen. The development of secondary organic pores is controlled by thermal maturity and OM type, and their preservation is subject to thermal maturity, OM content, and mineralogical composition. The presented view of the evolution of micropore and mesopore characteristics of OM with thermal maturity is based on data from the literature. The specific surface area and pore volume of OM in black shales follow a parabolic pattern with increasing thermal maturity (quantified via vitrinite reflectance, R o ). The initial increase reflects development of OM-hosted pores, and the subsequent decrease is due to denser stacking of aromatic units in the macromolecular structure of OM, with maximum values (specific surface area ~ 300 m 2 /g and pore volume ~ 0.3 cm 3 /g) reached at R o values in the 2.5-3.5% range. The contribution of OM-hosted pores to the pore characteristics of black shales depends on OM content, OM type, and thermal maturity.

03 NATURAL GAS↗
DOE OSTI2021

Multiscale X-ray phase contrast imaging of human cartilage for investigating osteoarthritis formation

The evolution of cartilage degeneration is still not fully understood, partly due to its thinness, low radio-opacity and therefore lack of adequately resolving imaging techniques. X-ray phase-contrast imaging (X-PCI) offers increased sensitivity with respect to standard radiography and CT allowing an enhanced visibility of adjoining, low density structures with an almost histological image resolution. This study examined the feasibility of X-PCI for high-resolution (sub-) micrometer analysis of different stages in tissue degeneration of human cartilage samples and compare it to histology and transmission electron microscopy. Ten 10%-formalin preserved healthy and moderately degenerated osteochondral samples, post-mortem extracted from human knee joints, were examined using four different X-PCI tomographic set-ups using synchrotron radiation the European Synchrotron Radiation Facility (France) and the Swiss Light Source (Switzerland). Volumetric datasets were acquired with voxel sizes between 0.7 × 0.7 × 0.7 and 0.1 × 0.1 × 0.1 µm 3 . Data were reconstructed by a filtered back-projection algorithm, post-processed by ImageJ, the WEKA machine learning pixel classification tool and VGStudio max. For correlation, osteochondral samples were processed for histology and transmission electron microscopy. X-PCI provides a three-dimensional visualization of healthy and moderately degenerated cartilage samples down to a (sub-)cellular level with good correlation to histologic and transmission electron microscopy images. X-PCI is able to resolve the three layers and the architectural organization of cartilage including changes in chondrocyte cell morphology, chondrocyte subgroup distribution and (re-)organization as well as its subtle matrix structures. X-PCI captures comprehensive cartilage tissue transformation in its environment and might serve as a tissue-preserving, staining-free and volumetric virtual histology tool for examining and chronicling cartilage behavior in basic research/laboratory experiments of cartilage disease evolution.

3D analysis↗
DOE OSTI2024

Microscopy modality transfer of steel microstructures: Inferring scanning electron micrographs from optical microscopy using generative AI

Scanning electron microscopy (SEM) is resource intensive, which limits its throughput in some applications. As an alternative, we propose applying computer vision and machine learning to generate high-quality synthetic SEM micrographs from micrographs obtained using light optical microscopy (LOM). Working with a correlated LOM/SEM dataset of dual-phase steel images, we test generative models of various architectures, including encoder-decoder networks, generative adversarial networks (GANs), and diffusion-based models. We find that the diffusion models significantly outperform other methods on both qualitative and quantitative assessments, while preserving key metallurgical meaning. This work establishes diffusion as the state-of-the-art for microscopy modality transfer and demonstrates the potential of AI-powered microscopy to enhance LOM with micron scale structural recreation.

Computer vision↗
DOE OSTI2021

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. Furthermore, the results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Spectral and polarization based imaging in deep-ultraviolet excited photoelectron microscopy

Using photoelectron emission microscopy, nanoscale spectral imaging of atomically thin MoS2 buried between Al2O3 and SiO2 is achieved by monitoring the wavelength and polarization dependence of the photoelectron signal excited by deep-ultraviolet light. Although photons induce the photoemission, images can exhibit resolutions below the photon wavelength as electrons sense the response. To validate this concept, the dependence of photoemission yield on the wavelength and polarization of the exciting light was first measured and then compared to simulations of the optical response quantified with classical optical theory. A close correlation between experiment and theory indicates that photoemission probes the optical interaction of UV-light with the material stack directly. The utility of this probe is then demonstrated when both the spectral and polarization dependence of photoemission observe spatial variation consistent with grains and defects in buried MoS2. Taken together, these new modalities of photoelectron microscopy allow mapping of optical property variation at length scales unobtainable with conventional light-based microscopy.

Beechem, Thomas E. (ORCID:0000000275360719)↗
DOE OSTI2026

Exploring the impact of nucleotide length on lipid nanoparticle structure and properties

Lipid nanoparticles (LNPs) are versatile carriers for nucleic acid (NA) therapeutics, including ASOs, siRNA, mRNA, and poly-IC. While lipid composition is known to influence LNP properties, the impact of NA length on morphology and internal structure is less understood, particularly during the stages of carrier–cargo assembly. Here, we examine NA length and lipid composition immediately after mixing using high-throughput SAXS, dynamic light scattering, and cryogenic electron microscopy. All LNPs form ordered NA/lipid compartments, with longer NAs promoting inverse hexagonal (H II ) phases and larger intercompartment distances. In contrast, short NAs, especially in formulations with SM102 ionizable lipid, favor lamellar phases. SAXS peak deconvolution quantifies ordered versus disordered phases via a Robustness of Ordered Phase factor, which correlates with particle size and encapsulation efficiency. Formulations with MC3 ionizable and DOPE helper lipids exhibit the most stable H II -phase packing, highlighting the role of helper-lipid curvature in compartment stabilization. Variations in NA compartmentalization indicate differences in payload capacity, offering a framework for rational LNP design across diverse nucleic acid cargos.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Multimode Characterization Approach for Understanding Cell-Level PV Performance and Degradation

Cell-level degradation processes impact the economic viability and large-scale deployment prospects for both established and emerging photovoltaic (PV) technologies. This project addresses the need to develop experimental and device-modeling approaches for studying cell-level degradation processes in photovoltaic (PV) devices using a variety of characterization techniques that provide access to complementary material and device properties. Our results demonstrate that by coupling characterization results with device modeling it is possible to develop comprehensive understanding of processes leading to performance limitations and degradation. This project developed a suite of novel measurement techniques including pulsed-light-bias operando X-ray and photoelectron spectroscopy (popXPS), light-biased scanning microwave impedance microscopy (sMIM), and near-field transport imaging (TI). In addition, operando characterization methodologies and in situ stressing capabilities have been developed and applied for techniques including electron-beam-induced current (EBIC), cathodoluminescence (CL), and Kelvin probe force microscopy (KPFM). Device-physics models were developed and applied to simulate correlative, multi-mode measurements to extract material and device parameters that control performance degradation. These characterization and modeling techniques were applied in a multi-mode approach to probe cell-level degradation mechanisms in Cd(Se,Te) and hybrid perovskite PV devices. Together these efforts contribute to foundational PV degradation science by establishing a framework for understanding PV performance degradation at the cell level and benefit the U.S. PV industry by providing resources in the form of novel experimental capabilities, knowledge gained, and available expertise that can accelerate research and development of improved PV device materials and architectures. The project provided a comprehensive understanding of degradation in baseline Cd(Se,Te) solar cells provided by our collaborators at Colorado State University (CSU). EBIC and CL-based measurements and revealed unusual collection and recombination profiles in these devices, which underwent significant changes with during stressing. KPFM and operando XPS measurements showed that device stressing permanently alters energy-band alignments at the (Mg,Zn)O/Cd(Se,Te) interface, which in turn account for an observed loss in fill factor. Studies on hybrid perovskite devices were hampered to a significant extent by delays related to the pandemic. Nevertheless, a set of hybrid perovskite devices (supplied through an NREL-industry partnership) were stress tested and characterized with techniques including EBIC, sMIM, popXPS/popUPS and optically excited TI. Available results from these measurements informed the device modeling effort and suggest that defects and related band offsets at the C60/LiF/hybrid perovskite interface are the primary source of degradation in these devices.

14 SOLAR ENERGY↗
DOE OSTI2024

Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Models and Measurements Quantify Photon Recycling, Charge-Carrier Diffusion and Photon Scattering Contributions to Photoluminescence in InP Nanowire Arrays

Nanowire arrays present many unique advantages for solar-to-chemical energy conversion. One possible advantage is that photon recycling between neighboring nanowires has the potential to increase solar energy conversion efficiencies. Here, in this work, we explore three underlying mechanisms of optical and electronic coupling between neighboring nanowires─incident photon scattering, photon recycling, and charge-carrier transport from the photoexcited nanowire to the neighboring nanowire via the underlying substrate─using single nanowire-level microscopy and spectroscopy measurements. We present a comprehensive analysis of light absorption and emission of a single nanowire at open circuit, and subsequent re-absorption and re-emission by a neighboring nanowire. We developed a novel correlated single nanowire microspectroscopy and widefield imaging methodology to spatially resolve photon communication pathways between neighboring nanowires and selectively image re-emitted and reflected photons. We developed unique multiphysics models to couple wave optics and semiconductor photophysics to especially isolate contributions from photon recycling and electronic transport to photon emission from neighboring nanowires. By systematically varying the morphologies of the nanowires modeled, we identified pathways to maximize photon recycling between neighboring nanowires. We concluded that the measured photoluminescence is more strongly influenced by the diffusion of charge carriers as compared to photon recycling in materials with moderate-to-large charge-carrier mobilities (>10 cm 2 V –1 s –1 ), and that photon recycling dictates photoluminescence intensity only when the charge-carrier mobility is low (<1 cm 2 V –1 s –1 ). The experimental and simulation platforms developed herein for photon management strategies can be leveraged by the semiconductor photocatalysis community to enhance solar-to-chemical conversion efficiencies in semiconductor nanowire arrays.

25 ENERGY STORAGE↗
DOE OSTI2023

Photoconversion in Disordered Semiconductors: Spatial, Spectral, and Temporal Insights through Nonlinear Microscopy (Final Technical Report)

Conversion of solar photons to useable energy requires two processes to occur successfully in a light-harvesting material: 1) the initial photoexcited state must efficiently produce excited states that are free to move, and 2) those states must be transported to a new location where they can do useful work before any potential is lost as heat. The core focus of this project examined the spatial and energetic dynamics of these two primary events of photoconversion in solution-processed semiconducting materials. The electronic properties of these systems are complex and strongly influenced by the cumulative interaction of local morphology and composition, along with defects, interfaces, and trap sites. It is therefore important to interrogate these systems at the local level, where structural and compositional heterogeneity can be precisely correlated to variation in functionality. Utilizing ultrafast laser spectroscopy coupled together with optical microscopy, this project examined how excited states and free charges spatially and energetically evolve on length scales between 10 nanometers and 10 microns and on timescales from 50 femtoseconds to 1 nanosecond. Insights gained from measurements made on these characteristic length and time scales provided new insight into how macroscopic functionality in disordered photovoltaic materials emerges from the interplay of nanoscale and mesoscale interactions.

14 SOLAR ENERGY↗
DOE OSTI2024

Correlating microstructure and mechanical properties of harvested high dose Zorita light water reactor internals

Here, in this study, microstructural studies and micro-mechanical testing of an ex-plant material harvested from the decommissioned pressurized water reactor (PWR) is carried out. Irradiated 304 stainless steel (SS) components were harvested by the Electric Power Research Institute, U.S. Nuclear Regulatory Commission, and members of the José Cabrera Nuclear Power Station (Zorita) in Spain. The bi-crystalline micro-tensile specimens, atom probe tomography (APT) tips, and transmission electron microscopy (TEM) lamellae were fabricated from the baffle plate materials irradiated to 0.05, 15 and 50 dpa to elucidate microstructural, microchemical, and local mechanical properties changes as a function of dose. TEM and APT studies reveal radiation induced Ni, Cr, and Si rich precipitates in the 15 dpa sample that become smaller and partially redissolve into the matrix of the 50 dpa sample (decreasing size and number density). Dislocation loop and cavity number density and size were quantified as a function of dose as well as swelling. Intergranular Ni and Si enrichments with concomitant Fe and Cr depletion were observed in the 15 dpa sample and were more pronounced in the 50 dpa sample. Micro-tensile testing performed in the scanning electron microscope (SEM) at room temperature and 300 °C shows that the material's local yield strength and ultimate tensile strength decreases with increased dose and elevated test temperature and provides further insights via localized strain mapping. Current and previous mechanical data was compared with calculated values using the dispersed barrier hardening model with inputs of dislocation loops, precipitates, and cavities from microstructural characterization.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Nanoscale-femtosecond dielectric response of Mott insulators captured by two-color near-field ultrafast electron microscopy

Characterizing and controlling the out-of-equilibrium state of nanostructured Mott insulators hold great promises for emerging quantum technologies while providing an exciting playground for investigating fundamental physics of strongly-correlated systems. Here, we use two-color near-field ultrafast electron microscopy to photo-induce the insulator-to-metal transition in a single VO 2 nanowire and probe the ensuing electronic dynamics with combined nanometer-femtosecond resolution (10 –21 m • s). We take advantage of a femtosecond temporal gating of the electron pulse mediated by an infrared laser pulse, and exploit the sensitivity of inelastic electron-light scattering to changes in the material dielectric function. By spatially mapping the near-field dynamics of an individual nanowire of VO 2 , we observe that ultrafast photo-doping drives the system into a metallic state on a timescale of ~150 fs without yet perturbing the crystalline lattice. Due to the high versatility and sensitivity of the electron probe, our method would allow capturing the electronic dynamics of a wide range of nanoscale materials with ultimate spatiotemporal resolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗