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DOE OSTI2018

Synchrotron-based X-ray Fluorescence Microscopy as a Technique for Imaging of Elements in Plants

Understanding the distribution of elements within plant tissues is important across a range of fields in plant science. In this review, we examine synchrotron-based X-ray fluorescence microscopy (XFM) as an elemental imaging technique in plant sciences, considering both its historical and current uses as well as discussing emerging approaches. XFM offers several unique capabilities of interest to plant scientists, including in vivo analyses at room temperature and pressure, good detection limits (ca. 1-100 mg/kg), and excellent resolution (down to 50 nm). This has permitted its use in a range of studies, including for functional characterization in molecular biology, examining the distribution of nutrients in food products, understanding movement of foliar fertilizers, investigating the behaviour of engineered nanoparticles, elucidating the toxic effects of metal(loid)s in agronomic plant species, and studying the unique properties of hyperaccumulating plants. We anticipate that continuing technological advances at XFM beamlines will also provide new opportunities moving into the future, such as for high-throughput screening in molecular biology, use of exotic metal tags for protein localization, and for enabling time-resolved, in vivo analyses of living plants. By examining current and potential future applications, we hope to encourage further XFM studies in plant sciences by highlighting the versatility of this approach.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

X-ray free-electron laser based dark-field X-ray microscopy: a simulation-based study

Dark-field X-ray microscopy (DFXM) is a nondestructive full-field imaging technique providing three-dimensional mapping of microstructure and local strain fields in deeply embedded crystalline elements. This is achieved by placing an objective lens in the diffracted beam, giving a magnified projection image. So far, the method has been applied with a time resolution of milliseconds to hours. In this work, the feasibility of DFXM at the picosecond time scale using an X-ray free-electron laser source and a pump–probe scheme is considered. Thermomechanical strain-wave simulations are combined with geometrical optics and wavefront propagation optics to simulate DFXM images of phonon dynamics in a diamond single crystal. Using the specifications of the XCS instrument at the Linac Coherent Light Source as an example results in simulated DFXM images clearly showing the propagation of a strain wave.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale molecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗

DOE OSTI2020

XTIP – the world's first beamline dedicated to the synchrotron X-ray scanning tunneling microscopy technique

In recent years, there have been numerous efforts worldwide to develop the synchrotron X-ray scanning tunneling microscopy (SX-STM) technique. Here, the inauguration of XTIP, the world's first beamline fully dedicated to SX-STM, is reported. The XTIP beamline is located at Sector 4 of the Advanced Photon Source at Argonne National Laboratory. It features an insertion device that can provide left- or right-circular as well as horizontal- and vertical-linear polarization. XTIP delivers monochromatic soft X-rays of between 400 and 1900 eV focused into an environmental enclosure that houses the endstation instrument. This article discusses the beamline system design and its performance.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

A variable X-ray chopper system for phase-sensitive detection in synchrotron X-ray scanning tunneling microscopy

An ultra-high-vacuum compatible X-ray chopper system has been designed, constructed and integrated into the XTIP beamline at the Advanced Photon Source at Argonne National Laboratory. The XTIP beamline can operate at soft X-ray energies from 400 eV to 1900 eV while providing a focused beam down to about 10 µm × 10 µm into the synchrotron X-ray scanning tunneling microscopy (SX-STM) endstation instrument. The X-ray chopper is a critical component for separating topographic information from chemical information in SX-STM through phase-sensitive current detection. Depending on the experimental needs, the modulation frequency can be controlled from 100 Hz to 10 kHz. In addition, the chopper system is fully bakeable and can achieve a base pressure of 10 -10 mbar. Facilities for active water cooling have been designed, but passive cooling through copper braids has been shown to be sufficient at standard chopping frequencies. Using an Fe/Al 2 O 3 /CoAl(111) sample, the separation of the SX-STM current into a chemical component and a stable feedback signal is demonstrated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Repeatability and sensitivity characterization of the far-field high-energy diffraction microscopy instrument at the Advanced Photon Source

In the last two decades, far-field high-energy diffraction microscopy (FF-HEDM) and similar non-destructive techniques have been actively developed at synchrotron light sources around the world. As these techniques (and associated analysis tools) are becoming more available for the general users of these light sources, it is important and timely to characterize their performance and capabilities. In this work, the FF-HEDM instrument implemented at the 1-ID-E endstation of the Advanced Photon Source (APS) is summarized. The set of measurements conducted to characterize the instrument's repeatability and sensitivity to changes in grain orientation and position are also described. When an appropriate grain matching method is used, the FF-HEDM instrument's repeatability is approximately 5 µm in translation, 0.02° in rotation, and 2 × 10 −4 in strain; the instrument sensitivity is approximately 5 µm in translation and 0.05° in rotation.

3DXRD↗

DOE OSTI2022

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

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 OSTI2025

High-resolution in-situ characterization of laser powder bed fusion via transmission X-ray microscopy at X-ray free electron lasers

In this work, we describe the instrumentation used to perform the first operando transmission X-ray microscopy (TXM) and simultaneous X-ray diffraction of laser melting simulating laser powder bed fusion on the XCS instrument at the Linac Coherent Light Source (LCLS) X-ray free-electron laser (XFEL). Our TXM with 40× magnification in the X-ray regime at 11 keV gave spatial resolutions down to 940 nm per line pair, with effective pixel sizes down to 206 nm, image integration times of <100 fs, and frame rates tunable between 2.1 and 119 ns for two probe frames (0.48 GHz to 8.4 MHz). Images were recorded on Zyla and Icarus (UXI) detectors to trade off between spatial resolution and time dynamics. A 1 kW CW IR laser was coupled into the interaction point to conduct pump–probe studies of laser melting and solidification dynamics. Our temporal and spatial resolution with attenuation-based contrast exceeds that currently possible with synchrotron-based high-speed radiography. This system was sensitive to feature velocities of 10–12000 m s −1 but we did not observe any motion in this range in the laser melting of Al6061 alloy. Shockwaves were not observed and hot cracking proceeded at velocities below the detection limits. Pore accumulation was observed between successive shots, indicating that bubble escape mechanisms were not active. With proper experimental design, the spatial resolution, contrast and field of view could be further improved or modified. The increased brightness and narrower bandwidth of the XFEL allowed for this imaging technique and it lays the groundwork for a wide range of operando techniques to study additive manufacturing.

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

Transmission Electron Microscopy Study on Microstructure of Degraded CdTe Mini-Modules

In this paper, we employ transmission electron microscopy coupled with energy-dispersive X-ray spectrometry (EDS) to study the structure and chemistry of cadmium telluride (CdTe) thin-film solar cells with different extents of degradation. The studied regions originate from the same photovoltaic mini-module, which was subjected to one-sun light exposure at a temperature of 100 degrees C for 400 h to induce light and heat degradation. EDS maps reveal a discontinuous CdS layer and particles rich in O and S but Te-depleted within the CdTe absorber layer after the light and heat stress. These features could act as enhanced recombination centers, resulting in decreased photovoltaic conversion efficiency. Additionally, the most degraded CdTe sample shows a strong accumulation of Na precisely localized in the discontinuous part of the CdS layer. The local Na concentration is determined to be ~16 at.%. In addition, appreciable Na accumulation is observed at the soda-lime glass/transparent conductive oxide interface in both degraded CdTe solar cells. The microstructure of the baseline CdTe mini-module with no stress was also investigated to demonstrate that the structure difference was caused by the light- and heat-induced degradation, instead of module fabrication. These results highlight the need to control the distribution of Na in fielded CdTe modules to sustain long-term high-power output.

14 SOLAR ENERGY↗

DOE OSTI2018

Tunable, Ultrafast Fiber-Laser between 1.15 μm and 1.35 μm for Harmonic Generation Microscopy in Human Skin

We demonstrate a fiber-optic ultrafast tunable source for harmonic generation microscopy (HGM) in human skin. The source is based on a 31-MHz Er-fiber laser followed by self-phase modulation enabled spectral selection (SESS). The resulting pulses are tunable between 1.15 and 1.35 μm with up to >10-nJ pulse energy and ~100-fs pulse duration. Here we employ this source to drive a scanning microscope for HGM imaging of ex vivo human skin. A systematic investigation on imaging depth versus excitation wavelength reveals that excitation wavelengths in the 1.15-1.25 μm range exhibit low optical attenuation within the tissue and allows larger imaging depth for HGM in human skin. HGM driven by fiber-based SESS sources constitutes an enabling tool for noninvasive virtual skin biopsy in clinical applications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

In Situ Transmission Electron Microscopy: Signal processing challenges and examples

Transmission electron microscopy (TEM) is a powerful tool for imaging material structure and characterizing material chemistry. Recent advances in data collection technology for TEM have enabled high-volume and high-resolution data collection at a microsecond frame rate. Here, taking advantage of these advances in data collection rates requires the development and application of data processing tools, including image analysis, feature extraction, and streaming data processing techniques. In this article, we highlight a few areas in materials science that have benefited from combining signal processing and statistical analysis with data collection capabilities in TEM and present a future outlook on opportunities of integrating signal processing with automated TEM data analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Transmission Electron Microscopy Study on Degradation Mechanism of CdTe Thin-Film Solar Cells

In this work, we used transmission electron microscopy in a structural and chemical study on CdTe thin-film solar cells with different degradation degrees from the same photovoltaic module. We found that in the most-degraded CdTe solar cell, the accumulation of Na is precisely localized in the discontinuous part of the CdS layer. The local concentration of Na is determined to be ~18 at.%. This could be the root-cause degradation mechanism in CdTe thin-film solar cells. In addition, the notable accumulation of Na at the TCO/SLG interface could be responsible for the delamination of the TCO layer from the SLG substrate.

14 SOLAR ENERGY↗

DOE OSTI2020

In-situ Microscopy Characterization of Cu(In,Ga)Se2 Potential-Induced Degradation

We report on the role of sodium in potentialinduced degradation (PID) of Cu(In, Ga)Se 2 (CIGS) solar cells. In-situ microscopy characterizations on AFM platform were performed on two stressed CIGS device under room temperature (RT) and high temperature (HT) at 85 degrees C. During PID stressing we observed depletion region gets wider as Na migrates, p-n junction becomes leaky at RT for over a month; and similar junction evolution was observed for HT-stressed sample, eventually the junction collapsed after 18 hours. The diode behaviors were confirmed by dark I-V measurement. Time-of Flight secondary-ion mass spectrometry reveals that the Na accumulates on ZnO and CdS side, as well as the upper layer of CIGS layer. The results indicate that Na drifted by the voltage applied on the soda-lime glass, then diffuse through the whole device. And the sodium profiles have different points of evolution due to the temperature differences between the two stressed samples. The consistent results unambiguously show how Na from substrate glass causes PID in CIGS solar cells.

14 SOLAR ENERGY↗

DOE OSTI2024

Exploring Local Ionic Motion in Perovskite Solar Cells at Nanoscale through Scanning Thermo-Ionic Microscopy

We investigate the local ionic motion in the absorber layer of perovskite solar cells using scanning thermo-ionic microscopy (STIM). STIM images of perovskite films show higher STIM amplitude at most of the grain boundaries due to higher ionic motion at those regions. The perovskite absorber layer of devices aged under blue (450 nm) light soaking shows higher amplitude in STIM signal compared to controls kept in dark storage. Such enhancement of STIM amplitude upon aging under light implies an increased concentration or diffusivity (or both) of mobile ionic species in stressed devices. Our results demonstrate the utilization of the STIM technique to assess and understand the intrinsic local ionic motion in perovskite absorbers for further advancement in device stability and functionality.

aging↗

DOE OSTI2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

3D alignment↗

DOE OSTI2020

In Situ Transmission Electron Microscopy Study of Conductive Filament Formation in Copper Oxides

The structural and electrical property changes of two types of copper oxides (CuO and Cu 2 O) under voltage bias are studied with in situ transmission electron microscopy (TEM). The phases of different materials are confirmed with electron diffraction. In both types of oxides, dynamic conductive path formation and dissolution are observed. The decrease in resistance of CuO film is found to be accompanied with the formation of Cu 4 O 3 phase where the electric field strength is highest. We also find that the decrease in resistivity of Cu 2 O film is more extensive and occurs in an area depending on the level of current compliance. In conclusion, the physical mechanisms responsible for the observations and their implications for the formation of conducting regions in copper oxide-based memristors are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Iterative Learning Control for Video-rate Atomic Force Microscopy

We present a control scheme for video-rate atomic force microscopy with rosette pattern. The controller structure involves a feedback internal-model-based controller and a feedforward iterative learning controller. The iterative learning controller is designed to improve tracking performance of the feedback-controlled scanner by rejecting the repetitive disturbances arising from the system nonlinearities. We investigate the performance of two inversion techniques for constructing the learning filter. We conduct tracking experiments using a two-degree-of-freedom microelectromechanical system (MEMS) nanopositioner at frame rates ranging from 5 to 20 frames per second. Furthermore, the results reveal that the algorithm converges rapidly and the iterative learning controller significantly reduces both the transient and steady-state tracking errors. We acquire and report a series of high-resolution time-lapsed video-rate AFM images with the rosette pattern.

42 ENGINEERING↗