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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy

High-resolution scanning transmission electron microscopy (S/TEM) is an indispensable tool for characterizing the structure and properties of materials down to the atomic scale. Conventional S/TEM imaging, however, is limited by the phase problem, whereby the phase of the electron exit wave is lost upon detection. Recent advances in diffractive imaging and 4D-STEM have enabled a range of phase-retrieval techniques that computationally reconstruct the missing information encoded in the phase of the transmission function. These approaches offer improved dose efficiency and enhanced sensitivity to weakly scattering signals, extending quantitative imaging to beam-sensitive materials composed of light elements. In this work, we introduce the phase problem in electron microscopy and survey the diverse landscape of phase-retrieval techniques used in the field. Despite their many acronyms and algorithmic variations, these techniques share a common physical and mathematical foundation. We present a unified framework that connects these seemingly distinct methods, from parallax imaging and tilt-corrected bright-field (tcBF-STEM), to aberration-corrected bright-field (acBF-STEM), optimum bright-field (OBF-STEM) and single-sideband (SSB) ptychography, as well as first-moment integrated center of mass techniques (iCOM) and iterative ptychographic algorithms. Based on these insights, we discuss the opportunities and practical limitations of applying these methods across different materials systems, detector designs, and microscope configurations.Graphical abstractRepresentative electron microscopy configurations used for phase retrieval and diffractive imaging in S/TEM: (a) Zernike phase-contrast transmission electron microscopy (TEM), (b) small-convergence-angle four-dimensional scanning transmission electron microscopy (4D-STEM) for nanobeam-based phase reconstruction methods, and (c) large-convergence-angle 4D-STEM for ptychographic and related diffractive imaging techniques reviewed in this work.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Understanding Degradation Mechanisms in SrIrO 3 Oxygen Evolution Electrocatalysts: Chemical and Structural Microscopy at the Nanoscale

Designing acid-stable oxygen evolution reaction electrocatalysts is key to developing sustainable energy technologies such as polymer electrolyte membrane electrolyzers but has proven challenging due to the high applied anodic potentials and corrosive electrolyte. This work showcases advanced nanoscale microscopy techniques supported by complementary structural and chemical characterization to develop a fundamental understanding of stability in promising SrIrO 3 thin film electrocatalyst materials. Cross-sectional high-resolution transmission electron microscopy illustrates atomic-scale bulk and surface structure, while secondary ion mass spectrometry imaging using a helium ion microscope provides the nanoscale lateral elemental distribution at the surface. After accelerated degradation tests under anodic potential, the SrIrO 3 film thins and roughens, but the lateral distribution of Sr and Ir remains homogeneous. A layer-wise dissolution mechanism is hypothesized, wherein anodic potential causes the IrO x -rich surface to dissolve and be regenerated by Sr leaching. Finally, the characterization approaches utilized herein and mechanistic insights into SrIrO 3 are translatable to a wide range of catalyst systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Review of Advanced Characterization Methods and Techniques for Amorphous and Poorly Crystalline Materials Applicable to Cementitious Waste Forms

This review covers advanced characterization methods of cementitious materials. The particular focus is to understand cementitious compositions with amorphous content because conventional techniques such as X-ray diffraction are more applicable to materials with long range order. Also of interest is advanced characterization that provides deeper insights into properties such as porosity. There are five groups of characterization methods discussed in this review which are: electron beam/microscopy, X-ray, neutron diffraction and scattering, nuclear magnetic resonance, and optical techniques. The techniques can be further grouped by the categories of nanoscale structural understanding (transmission electron microscopy and pair distribution function), microscale structural understanding (focused ion beam and x-ray tomography), microscopic elemental distributions (energy dispersive spectroscopy and X-ray fluorescence), and chemical binding information (electron energy loss spectroscopy, x-ray absorption spectroscopy, nuclear magnetic resonance, Raman spectroscopy, and infrared spectroscopy), with advantages and disadvantages of each method discussed. The recommendation for further research is to begin with techniques that are easier to prepare samples for, measure, and analyze, such as the optical techniques of Raman and infrared spectroscopy. If more information is needed, pursue collaborations, other techniques, or proposals for beam time at the synchrotron sources.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Realignment and suppression of charge density waves in the rare-earth tritellurides 𝑅⁢Te 3 (𝑅 = La, Gd, Er)

The rare-earth tritellurides have a rich phase diagram that includes charge density waves (CDWs), superconductivity, and magnetic order, offering a platform to study the interplay between these phases on a square-net system. Prior studies have shown that defects can affect the CDW characteristics in these materials, yet coupling between the CDW order and the underlying microstructure has not been studied at the nanoscale. Here we use scanning transmission electron microscopy at cryogenic temperatures to directly visualize the effects of defects on the CDW order and provide a spatially resolved microscopic correlation between the CDW transition and structural defects. Here, we show that in the presence of extended defects, such as dislocations and stacking faults, the weak orthorhombicity of the rare-earth tritellurides is lost and the material becomes pseudotetragonal. Since the orthorhombicity acts as a symmetry breaking field for the CDW transitions in rare-earth tritellurides, the presence of these extended defects modulates the energetics of the CDWs and suppresses the ground-state CDW phase at low temperature.

Charge density waves↗
DOE OSTI2020

Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction

Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Mechanisms of Skyrmion and Skyrmion Crystal Formation from the Conical Phase

Real-space topological magnetic structures such as skyrmions and merons are promising candidates for information storage and transport. However, the microscopic mechanisms that control their formation and evolution are still unclear. In this work, using in situ Lorentz transmission electron microscopy, we demonstrate that skyrmion crystals (SkXs) can nucleate, grow, and evolve from the conical phase in the same ways that real nanocrystals form from vapors or solutions. More intriguingly, individual skyrmions can also “reproduce” by division in a mitosis-like process that allows them to annihilate SkX lattice imperfections, which is not available to crystals made of mass-conserving particles. Combined string method and micromagnetic calculations show that competition between repulsive and attractive interactions between skyrmions governs particle-like SkX growth, but nonconservative SkX growth appears to be defect mediated. Our results provide insights toward manipulating magnetic topological states by applying established crystal growth theory, adapted to account for the new process of skyrmion mitosis.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Non-equilibrium insertion of lithium ions into graphite

Graphite has been regarded as the most important anode material for currently used lithium-ion batteries due to its two-dimensional (2D) nature hosting ionic intercalations. However, the kinetic insertion of Li ions is still not well known microscopically. In this work, we investigate the real-time intercalation process of Li ions using in situ transmission electron microscopy. We observe the lithium insertion process at the atomic scale, in which the graphite layers undergo expansion, forming wrinkles and finally inhomogeneous cracks as the Li ions accumulate, different from the proposed models. Leveraging on theoretical simulations, Li-ion migration driven by an external electrical field is suggested to be induced into the irreversible wrinkled structures. This non-equilibrium behavior that occur in lithium-ion batteries can be more pronounced at a high charging rate, which will practically degrade the capacity of graphite. Furthermore, this work unveils the reaction scenario of the non-equilibrium Li-ion insertion, which benefits the understanding of the performance of graphite-based energy-storage devices.

25 ENERGY STORAGE↗
DOE OSTI2023

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Abstract Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Corrosion Resistance of an AlCeMg/Stainless-Steel Reactive Bond

A major issue for metal components in many industries is corrosion as it can substantially reduce their lifetime. This issue is especially problematic for materials used in heat exchanger applications. Al–Ce–Mg alloys, which exhibit corrosion resistance and can reactively bond with other metals, may be a viable solution to this problem. This investigation studied the corrosion behavior of Al–2Ce–6Mg (atomic percent)/stainless-steel (SS) reactive bond interfaces after full immersion in nitric, sulfuric, formic, and mixed acid for 267 h. This particular Al–Ce–Mg alloy was chosen due to its good castability. The results of scanning electron microscope characterization showed that reactive bond formations repeatedly occurred throughout the length of the casting in the as-cut samples and that these formations maintained a secure bonding between the alloy and the stainless-steel tubes. Transmission electron microscopy results showed that there was a clear compositional and microstructural transition across the reactive bond. The results of the immersion tests indicated that the nitric, sulfuric, and the mixed acid did not have an observably negative effect on the reactive bond structure. As for the sample exposed to formic acid only, noticable changes were seen in both the microstructural appearance and the elemental profile across the bond, suggesting that oxide formation occurred.

Brechtl, Jamieson [ORNL] (ORCID:0000000217394283)↗
NASA NTRS1990

Vestibular receptor cells and signal detection: bioaccelerometers and the hexagonal sampling of two-dimensional signals

The inner ear contains sensory organs which signal changes in head movement. The vestibular sacs, in particular, are sensitive to linear accelerations. Electron microscopic images have revealed the structure of tiny sensory hair bundles, whose mechanical deformation results in the initiation of neuronal activity and the transmission of electrical signals to the brain. The structure of the hair bundles is shown in this paper to be that of the most efficient two-dimensional phased-array signal processors.

NASA Program Space Physiology and Countermeasures↗
DOE OSTI2021

Ultrafast electron microscopy for probing magnetic dynamics

Abstract The spatial features of ultrafast changes in magnetic textures carry detailed information on microscopic couplings and energy transport mechanisms. Electrons excel in imaging such picosecond or shorter processes at nanometer length scales. We review the range of physical interactions that produce ultrafast magnetic contrast with electrons, and specifically highlight the recent emergence of ultrafast Lorentz transmission electron microscopy. From the fundamental processes involved in demagnetization at extremely short timescales to skyrmion-based devices, we show that ultrafast electron imaging will be a vital tool in solving pressing problems in magnetism and magnetic materials where nanoscale inhomogeneity, microscopic field measurement, non-equilibrium behavior or dynamics are involved. Graphic abstract

36 MATERIALS SCIENCE↗
DOE OSTI2023

Machine learning for automated experimentation in scanning transmission electron microscopy

Abstract Machine learning (ML) has become critical for post-acquisition data analysis in (scanning) transmission electron microscopy, (S)TEM, imaging and spectroscopy. An emerging trend is the transition to real-time analysis and closed-loop microscope operation. The effective use of ML in electron microscopy now requires the development of strategies for microscopy-centric experiment workflow design and optimization. Here, we discuss the associated challenges with the transition to active ML, including sequential data analysis and out-of-distribution drift effects, the requirements for edge operation, local and cloud data storage, and theory in the loop operations. Specifically, we discuss the relative contributions of human scientists and ML agents in the ideation, orchestration, and execution of experimental workflows, as well as the need to develop universal hyper languages that can apply across multiple platforms. These considerations will collectively inform the operationalization of ML in next-generation experimentation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Probing Electron Beam Induced Transformations on a Single-Defect Level via Automated Scanning Transmission Electron Microscopy

A robust approach for real-time analysis of the scanning transmission electron microscopy (STEM) data streams, based on ensemble learning and iterative training (ELIT) of deep convolutional neural networks, is implemented on an operational microscope, enabling the exploration of the dynamics of specific atomic configurations under electron beam irradiation via an automated experiment in STEM. Combined with beam control, this approach allows studying beam effects on selected atomic groups and chemical bonds in a fully automated mode. Here, in this study, we demonstrate atomically precise engineering of single vacancy lines in transition metal dichalcogenides and the creation and identification of topological defects in graphene. The ELIT-based approach facilitates direct on-the-fly analysis of the STEM data and engenders real-time feedback schemes for probing electron beam chemistry, atomic manipulation, and atom by atom assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Morphometrics of cellular damage in mice testis receiving X-ray and high-energy particle irradiation

Murine tests were exposed to single, low doses of either X-ray, helium, or argon radiation. Animals were sacrificed seventy-two hours later. Testes were fixed for transmission electron microscopy (TEM) and sectioned at either 60 nm for TEM observation or at 2 micron for counting using routine light microscope methods. Counts of the total population of surviving spermatogonia, including all type A cells, intermediate, and type B cells, were taken from tubule cross sections identified as Stage 6 and Stage 1 according to spermatogonial configuration. The surviving fraction of spermatogonia as compared to control, S/S sub o, was calculated for each dose. For both ions and X-rays, there was a rapid decline in survival at dose levels of .10 to .15 Gy in Stage 6 tubules. This was followed by a more gradual decrease in population. At higher doses, 0.30 Gy for argon and 0.80 Gy for helium and X-rays, the cell survival rates declined rapidly. Pre-leptotene spermatocytes in Stage 1 tubules exhibited a different survival curve indicating the extreme radio-sensitivity of type B spermatogonia. Data verify that the seminiferous tubules are composed of a heterogeneous population of cells with different radio-sensitivities and that these differences are manifested even at very low doses.

Sapp, Walter J.↗
DOE OSTI2024

Morphological and molecular characterization of a Sarcocystis bovifelis-like sarcocyst in American beef

Abstract Background Parasites in the apicomplexan genusSarcocystisinfect cattle worldwide. Assessing the economic importance of each such parasite species requires proper diagnosis.Sarcocystiscruzi,a thin-walled species, infects virtually all cattle. The prevalence of the other thin-walled parasite,Sarcocystisheydorni, remains less well established. The remaining six species all have thick (> 3 µm) cyst walls (Sarcocystishirsuta,S.hominis,S.bovifelis,S.bovini,S.sigmoideus, andS.rommeli). Thick-walled sarcocysts often induce inflammation in striated muscles (causing bovine eosinophilic myositis), leading to condemnation of carcasses at slaughter. One of these,S.hirsuta, can be seen macroscopically and lead to condemnation of beef. TwoSarcocystisspecies,S.hominisandS.heydorni, are zoonotic. AlthoughS.hominishas been reported as prevalent in Europe, the occurrence of thick-walled species in the US remains poorly known. Here, for the first time to our knowldge, we characterize a thick-walledSarcocystisspecies from a sample of beef from a local grocery store in Maryland. By morphological and genetic criteria, it closely, but not perfectly, resembles parasites previously ascribed toS.bovifelis. Methods Beef samples were examined forSarcocystisinfection, using acid-pepsin digestion to search for bradyzoites, microscopically by compression between a glass slide and coverslip, by histology of paraffin embedded sections stained with hematoxylin and eosin, and by transmission electron microscopy (TEM). Molecular characterization was attempted employing genetic markers:18SrRNA,28SrRNA,cox1,ITS1,gapdh1,ron3, andrpoB. Results Molecular evaluation revealed 100% identity withS.bovifelis-like sarcocysts from naturally infected cattle from Germany and Argentina; although the condition of the frozen material precludes complete characterization by TEM, we noted morphological features which differed from theS.bovifelisoriginally described from experimentally infected cattle from Germany. Conclusions A novelSarcocystisspecies is described from beef from the USA but not named until further evaluation. Graphical Abstract

Parasitology↗
DOE OSTI2023

Multimodal Few-Shot Segmentation of Electron Micrographs

Scanning transmission electron microscopy (STEM) is one of the most used methods of analyzing the chemistry and composition of materials. By analyzing microstructures, these microscopes can help scientists better understand the molecular underpinnings of microelectronics, batteries, and more. However, STEM data can be difficult to interpret, so recent developments have been made in applications of machine learning to analyze these images. The PNNL-developed pyCHIP Classifier has achieved results in segmenting STEM these images via few-shot learning, a method which requires little data and human input, perfect for quickly analysis. In my internship I (Eli Meyers) investigated a multimodal improvement of this classifier by incorporating energy dispersive x-ray spectroscopy (EDS) data into the classification process for a more accurate segmentation. Furthermore, I encoded the spectral data by training a mass spectrometry encoder on the EDS data to extract a more meaningful representation of the data.

36 MATERIALS SCIENCE↗
NASA NTRS2007

Microscopic Observation of Self-Propagation of Calcifying Nanoparticles (Nanobacteria)

Biologists typically define living organisms as carbon and water-based cellular forms with :self-replication" as the fundamental trait of the life process. However, this standard dictionary definition of life does not help scientists to categorize self-replicators like viruses, prions, proteons and artificial life. CNP also named nanobacteria were discovered in early 1990s as about 100 nanometer-sized bacteria-like particles with unique apatite mineral-shells around them, and found to be associated with pathological-calcification related diseases. Although CNP have been isolated and cultured from mammalian blood and diseased calcified tissues, and their biomineralizing properties well established, their biological nature and self-replicating capability have always been severely challenged. The terms "self-replication", "self-assembly" or "self-propagation" have been widely used for all systems including nanomachines, crystals, computer viruses and memes. In a simple taxonomy, all biological and non-biological "self replicators", have been classified into "living" or "nonliving" based on the properties of the systems and the amount of support they require to self-replicate. To enhance our understanding about self-replicating nature of CNP, we have investigated their growth in specific culture conditions using conventional inverted light microscope and BioStation IM, Nikon s latest time-lapse imaging system. Their morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, all concomitantly validate CNP as living self-replicators.

Mathew, Grace↗
NASA NTRS1972

Some surface characteristics and gas interactions of Apollo 14 fines and rock fragments.

Comprehensive survey of the physical surface characteristics of Apollo 14 fines, two fragments of a breccia (14321), and a crystalline rock (14310). The survey was carried out with optical and both scanning and transmission electron microscopy and by studying the adsorption of a variety of gases including nitrogen, hydrogen, and water vapor. Our objective in the optical microscope study was to relate the visible geological and petrological features to the surface properties. Electron microscopy particularly helped relate surface roughness and particle fusion to gas adsorption and pore structure. The fine sample (14163,111) had a surface area of 0.210 sq m/g and a helium density of 2.9 g/cc. Similar values have been observed with breccia fragments. Other observations include physical adsorption of molecular hydrogen at low temperatures and of water vapor at ambient temperatures. It is concluded that these particular lunar materials, while capable of adsorbing water vapor, do not retain it for any significant time at low pressures, nor, under lunar conditions, is there any indication of absorption or penetration.

Cadenhead, D. A.↗