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All sourcesNASA NTRSDOE OSTI
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

Stroboscopic ultrafast imaging using RF strip-lines in a commercial transmission electron microscope

The development of ultrafast electron microscopy (UEM), specifically stroboscopic imaging, has brought the study of structural dynamics to a new level by overcoming the spatial limitations of ultrafast spectroscopy and the temporal restrictions of traditional TEM simultaneously. Combining the concepts governing both techniques has enabled direct visualization of dynamics with spatiotemporal resolutions in the picosecond-nanometer regime. Here, in this study, we push the limits of imaging using a pulsed electron beam via RF induced transverse deflection based on the newly developed 200 keV frequency-tunable strip-line pulser. We demonstrate 0.2 nm spatial resolution at high magnifications and elucidation of Lorentz imaging using the phase-microscopy method. We also present beam coherence measurements and expand our study using the breathing modes of a silicon interdigitated comb under RF excitation which achieves improved temporal synchronization between the electron pulse-train and electric field. A new RF holder has also been developed with impedance matching to the RF signal to minimize transmission power loss to samples and its performance is compared with a conventional sample holder.

47 OTHER INSTRUMENTATION↗
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↗
NASA NTRS1995

Transmission electron microscope studies of extraterrestrial materials

Transmission Electron Microscopy, X-Ray spectrometry and electron-energy-loss spectroscopy are used to analyse carbon in interplanetary dust particles. Optical micrographs are shown depicting cross sections of the dust particles embedded in sulphur. Selected-area electron diffraction patterns are shown. Transmission Electron Microscope specimens of lunar soil were prepared using two methods: ion-milling and ultramicrotomy. A combination of high resolution TEM imaging and electron diffraction is used to characterize the opaque assemblages. The opaque assemblages analyzed in this study are dominated by ilmenite with lesser rutile and spinel exsolutions, and traces of Fe metal.

Keller, Lindsay P.↗
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↗
DOE OSTI2023

Resolving Nanoscale Processes during Carbon Mineralization Using Identical Location Transmission Electron Microscopy

Basalt reservoirs offer the potential for carbon mineralization, aiding in achieving net-zero emissions. However, debates persist about microscopic crystallization mechanisms due to limited characterization techniques under high-temperature and pressure conditions. By using Identical Location Transmission Electron Microscopy (IL-TEM) and cryo-TEM, this study reveals nanoscale interfacial carbonation processes of forsterite and diopside nanoparticles in water-saturated supercritical carbon dioxide under realistic reservoir conditions. Further, both minerals undergo preferential metal cation dissolution into a thin water film, forming porous Si-rich amorphous layers, supporting the leached layer mechanism as the dominant mineral reactivity process. Diopside’s amorphous layer has lower porosity and growth rate relative to forsterite, likely related to the connectivity of silicate tetrahedra. Kinetically favorable nesquehonite and aragonite nanocrystals form on the amorphous layers. These findings support the development of accurate reservoir simulations and help enable commercial-scale carbon storage deployment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
NASA NTRS2015

Compositional and Microstructural Evolution of Olivine During Pulsed Laser Irradiation: Insights Based on a FIB/Field-Emission TEM Study

Introduction: The use of pulsed laser irradiation to simulate the short duration, high-energy conditions characteristic of micrometeorite impacts is now an established approach in experimental space weathering studies. The laser generates both melt and vapor deposits that contain nanophase metallic Fe (npFe(sup 0)) grains with size distributions and optical properties similar to those in natural impact-generated melt and vapor deposits. There remains uncertainty, however, about how well lasers simulate the mechanical work and internal (thermal) energy partitioning that occurs in actual impacts. We are currently engaged in making a direct comparison between the products of laser irradiation and experimental/natural hypervelocity impacts. An initial step reported here is to use analytical TEM is to attain a better understanding of how the microstructure and composition of laser deposits evolve over multiple cycles of pulsed laser irradiation. Experimental Methods: We irradiated pressed-powder pellets of San Carlos olivine (Fo(sub 90)) with up to 99 rastered pulses of a GAM ArF excimer laser. The irradiated surface of the sample were characterized by SEM imaging and areas were selected for FIB cross sectioning for TEM study using an FEI Quanta dual-beam electron/focused ion beam instrument. FIB sections were characterized using a JEOL2500SE analytical field-emission scanning transmission electron microscope (FE-STEM) optimized for quantitative element mapping at less than 10 nm spatial resolutions. Results: In the SEM the 99 pulse pressed pellet sample shows a complex, inhomogeneous, distribution of laser-generated material, largely concentrated in narrow gaps and larger depressions between grains. Local concentrations of npFe0 spherules 0.1 to 1 micrometers in size are visible within these deposits in SEM back-scatter images. Fig. 1 shows bright-field STEM images of a FIB cross-section of a one of these deposits that continuously covers the top and sloping side of an olivine grain. The deposit has 3 microstructurally distinct sub-layers composed of silicate glass with varying modal fractions and size distributions of npFe( sup 0) spherules, along with nanocrystalline silicate material. A relatively thin (50-300 nm) topmost surface layer has a high-concentration of npFe0 spherules 5-20 nm in size. Element mapping shows the layer to be enriched in Fe by a factor of 2.5 relative to the olivine substrate, with Mg and Si depleted by 20% and 10% respectively. This is compositionally complementary to the underlying, middle layer of the deposit that is depleted in Fe, enriched in Mg and has a much lower npFe0 concentration. A third layer of nanocrystalline olivine occurs at the substrate interface. Discussion: The FE-STEM results suggest the topmost layer is a vapor deposit, underlain by a thicker microstructurally complex melt-generated layer. The compositional relations suggest the melt layer was partially vaporized, preferentially losing more volatile elements (e.g., Fe). The vaporized material re-condensed to form the thin, npFe(sup 0)-rich surface deposit during or immediately after the scan cycle. Nanocrystalline olivine that grew within the melt layer as it formed and cooled is similar in volume and microstructure to what we have observed in the impact melt lining of a micrometeorite impact crater in olivine. This suggest the time-temperature relations attained in the laser sample may not be too different from a micrometeorite impact. Our TEM observations, however, do not show evidence for the same level of mechanical dam-age (e.g., fracturing) seen around the natural micrometeorite crater.

Christoffersen, R.↗
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↗
NASA NTRS1991

Low-pressure clathrate-hydrate formation in amorphous astrophysical ice analogs

In modeling cometary ice, the properties of clathrate hydrates were used to explain anomalous gas release at large radial distances from the Sun, and the retention of particular gas inventories at elevated temperatures. Clathrates may also have been important early in solar system history. However, there has never been a reasonable mechanism proposed for clathrate formation under the low pressures typical of these environments. For the first time, it was shown that clathrate hydrates can be formed by warming and annealing amorphous mixed molecular ices at low pressures. The complex microstructures which occur as a result of clathrate formation from the solid state may provide an explanation for a variety of unexplained phenomena. The vacuum and imaging systems of an Hitachi H-500H Analytical Electron Microscope was modified to study mixed molecular ices at temperatures between 12 and 373 K. The resulting ices are characterized by low-electron dose Transmission Electron Microscopy (TEM) and Selected Area Electron Diffraction (SAED). The implications of these results for the mechanical and gas release properties of comets are discussed. Laboratory IR data from similar ices are presented which suggest the possibility of remotely observing and identifying clathrates in astrophysical objects.

Blake, D. F.↗
DOE OSTI2020

Atomic Resolution Imaging of Light Elements in a Crystalline Environment using Dynamic Hollow-Cone Illumination Transmission Electron Microscopy

Multiple electron scattering and the nonintuitive nature of image formation with coherent radiation complicate the interpretation of conventional transmission electron microscopy images. Precession of the illuminating beam in transmission electron microscopy (TEM) can lead to more robust and interpretable images with some penalty to image contrast, a technique known as dynamic hollow-cone illumination TEM. Here, we demonstrate direct and robust imaging of light and heavy atoms in a crystalline environment with this technique. This method is similar to the annular bright-field technique in scanning transmission electron microscopy, via the principle of reciprocity. Dynamic hollow-cone illumination TEM is challenging in practice due to sensitivity to the misalignment of the precession axis, microscope objective aperture, and crystal zone axis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1984

A study of tetrataenite

The tetrataenite in Dayton was examined using conventional transmission (TEM) and analytical electron microscopy (AEM). Tetrataenite was also simulated in terrestrial Fe-Ni alloys through electron irradiation of thin-foil specimens on the high voltage electron microscope (HVEM). The purpose was to correlate the results of the TEM, AEM and HVEM studies on Dayton and on terrestrial iron-nickel alloys to the low temperature iron-nickel phase diagram. Oxide forms spontaneously on the surfaces of thin-foil iron-nickel specimens. By determining the metal/oxide orientation relationships the reflections due to the oxide and the superlattice are distinguished. In Dayaton, the clear taenite (I) is fully ordered until near the cloudy zone interface. The ordered domains ranged in size from 30 to 650 nm with the largest domains corresponding to the highest Ni content and the smallest domain size corresponding to the lowest Ni content. In terrestrial alloys irradiated on the HVEM, the extent of electron irradiation induced ordering was determined as a function of temperature and composition. Ordering occurred in every specimen irradiated.

Reuter, K. B.↗
NASA NTRSDate not supplied

SURFACE EXOSURE TIMESCALES OF APOLLO CORE SAMPLE 73002 SPACE WEATHERED GRAINS

Introduction: Space weathering causes the surface regolith on airless bodies like the Moon to be morphologically, microstructurally, and chemically altered due to micrometeoroid bombardment and solar wind irradiation[1]. These processes produce a multitude of microstructural and chemical changes in individual soil grains that accumulate as grains are exposed on the surface over time. One microstructural feature produced by exposure to the solar wind is the development of ion-damaged rims on regolith grains via H+ and He+ ion irradiation. Also present are solar energetic particle (SEP) tracks, which are nanoscale lineations of ionization damage within grain interiors formed by high energy solar flare ions(primarily Fe group nuclei) which penetrate millimeters below the surface [2]. Recent work has confirmed that the thickness of solar wind-damaged amorphous rims on anorthite grains, nanocrystalline rims on olivine grains, and their respective SEP track densities are correlated with their surface exposure ages [3].Core sample 73002, recently released under the Apollo Next Generation Sample Analysis (ANGSA) Program, has provided an opportunity to study material collected from the light mantle formation during Apollo 17. The light mantle is thought to have been deposited via a landslide originating from the neighboring South Massif [4]. Spectral profiles and ferromagnetic resonance measurements of bulk soils sampled at cm-intervals from 73002 indicate the existence of mature regolith extending ~8 cm below the surface, suggesting the presence of an in-situ reworking zone in the core[5,6].Here we present the distribution of SEP track densities, solar wind damaged rim widths, and the corresponding surface exposure ages of grains residing in the proposed in-situ reworking zone of core 73002. Methods: Bulk samples of regolith from the first eight intervals and every following fourth interval down the core (dissection Pass 2) were delivered to Purdue University as <45 μm size fractions. The first eight0.5 cm intervals, representing the top 4cmof regolith, were individually dry sieved to a<20 μm size fraction, and grains were prepared by ultramicrotomy for analysis in the scanning transmission electron microscope (STEM). Bright field (BF) and dark field (DF) STEM images of solar flare tracks and solar wind damaged rims were acquired on a JEOL 2500SE TEM, equipped with a 60 mm2ultra-thin window silicon drift energy dispersive X-ray (EDX) spectrometer at NASA John-son Space Center. Grain compositions were determined by EDX compositional spectrum imaging. SEP track densities and amorphous rim thicknesses were measured on BF and DF images. Results: The fraction of grains with discernable space weathering features decreased with depth, with 100% in the first interval exhibiting space weathering features as opposed to ~60% in Interval 8.BF and DF STEM images show splash-melt and vapor deposited rims on outermost grain margins with embedded Fe-bearing nanoparticles ranging in size up to ~10 nm in diameter. Images also show solar-wind damaged rims below the vapor deposits, and SEP tracks present in grain interiors. The rim thicknesses and SEP track densities were determined using the methods of [3] for 54grains spanning the top 4 cm. ~80% of the grains analyzed were anorthite and ~20% were olivine. The track production rate from[3] was used to estimate the surface exposure times of the grains in this study. The majority of exposure times are in the 1 -5 MY range for all intervals. The lowest value was 3.8x 10¬5years in Interval 8and the highest value was1.1x 107years in Interval 6. Grains with the highest solar wind damage rim thicknesses and SEP track densities are found in Interval 6.The highest rim thickness and track density observed for anorthiteis126.5 nm and4.7 x 1011tracks/cm2, while for olivine they are 98.6 nm and 1.83 x 1011tracks/cm2, respectively. Discussion: Intervals from the top 4 cm of 73002 show similar SEP track density and solar wind damaged rim thickness distributions. Spectral and ferromagnetic resonance measurements of 73002 indicate an in-situ reworking zone up to~8 cm below the surface[5,6].The depth analyzed in this work is within the core’s uppermost in-situ reworking zone and may serve as an explanation to the homogenous distribution of exposure ages. The decreasing abundance of space weathered features with depth is consistent with regolith mixing models showing an exponential decay in regolith maturity with depth over time[7].A maximum surface exposure age determined via SEP track density is approximately 10million years. This timescale is consistent with the lower estimate of surface exposure ages of the light mantle determined in previous studies, which can range from 10s to over 100 Ma [4].It also falls within the core regolith reworking development timescale of ~17 Ma [5,6]. Additional analysis will be performed for a further seven intervals in 73002.

J A McFadden↗
DOE OSTI2023

Towards On-Chip Learning for Low Latency Reasoning with End-to-End Synthesis

The Software Defined Architectures (SODA) Synthesizer is an open-source compiler-based tool able to automatically generate domain-specialized systems targeting Application-Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) starting from high-level programming. SODA is composed of a frontend, SODA-OPT, which leverages the multilevel intermediate representation (MLIR) framework to interface with productive programming tools (e.g., machine learning frame-works), identify kernels suitable for acceleration, and perform high-level optimizations, and of a state-of-the-art high-level synthesis backend, Bambu from the PandA framework, to generate custom accelerators. One specific application of the SODA Synthesizer is the generation of accelerators to enable ultra-low latency inference and control on autonomous systems for scientific discovery (e.g., electron microscopes, sensors in particle accelerators, etc.). This paper provides an overview of the flow in the context of the generation of accelerators for edge processing to be integrated in transmission electron microscopy (TEM) devices, focusing on use cases from precision material synthesis. We show the tool in action with an example of design space exploration for inference on reconfigurable devices with a conventional deep neural network model (LeNet). Finally, we discuss the research directions and opportunities enabled by SODA in the area of autonomous control for scientific experimental workflows.

Castellana, Vito G.↗
DOE OSTI2020

An Open-Cell Environmental Transmission Electron Microscopy Technique for In Situ Characterization of Samples in Aqueous Liquid Solutions

The desire to image specimens in liquids has led to the development of open-cell and closed-cell techniques in transmission electron microscopy (TEM). The closed-cell approach is currently more common in TEM and has yielded new insights into a number of biological and materials processes in liquid environments. The open-cell approach, which requires an environmental TEM (ETEM), is technically challenging but may be advantageous in certain circumstances due to fewer restrictions on specimen and detector geometry. Here, we demonstrate a novel approach to open-cell liquid TEM, in which we use salt particles to facilitate the in situ formation of droplets of aqueous solution that envelope specimen particles coloaded with the salt. This is achieved by controlling sample temperature between 1 and 10°C and introducing water vapor to the ETEM chamber above the critical pressure for the formation of liquid water on the salt particles. Our use of in situ hydration enables specimens to be loaded into a microscope in a dry state using standard 3 mm TEM grids, allowing specimens to be prepared using trivial sample preparation techniques. Furthermore, our future aim will be to combine this technique with an in situ light source to study photocorrosion in aqueous environments.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

TEM-based phase characterization of $\mathrm{U–19Pu–10Zr}$ irradiated in ATR

We report the results of the microstructural examination of the irradiated U–19Pu–10Zr fuel. New insights gained using selective area electron diffraction analysis in a transmission electron microscope provide crystallographic information on the phases previously identified based primarily on the chemical compositions. After irradiation, the microstructure of the fuel separates into γ-(U, Pu, Zr) in the central region with a secondary nanocrystalline UO 2 phase, γ-(U, Pu, Zr) with a secondary ZrO 2 phase in the intermediate, and ζ-(U, Pu) in the outer regions. While the surface microstructural features and porosity indicate separation into three concentric zones consistent with the existing constituent redistribution model, crystallographically the fuel consists of two zones: inner (with γ-(U, Pu, Zr) as a matrix phase) and outer (with ζ-(U, Pu) as a matrix phase). Our results highlight the importance of crystal structure in phase identification and can be used to supplement the existing constituent redistribution model.

extreme environment↗