Dose measurement in the TEM and STEM

Two- and three-dimensional electron imaging of beam-sensitive specimens

Radiation damage is the main factor that determines the spatial resolution of TEM and STEM images of beam-sensitive specimens, its influence being well represented by a dose-limited resolution (DLR). In this review, DLR is defined and evaluated for both thin and thick samples, for all common imaging modes, and for electron-accelerating voltages up to 3 MV. Damage mechanisms are discussed (including beam heating and electrostatic charge accumulation) with an emphasis on recently published work. Experimental methods for reducing beam damage are identified and future lines of investigation are suggested.

Tracking Dynamics of Supported Indium Oxide Catalysts in CO2 Hydrogenation to Methanol by In Situ TEM

Supported reducible oxides, such as indium oxide on monoclinic zirconia (In2O3/m-ZrO2), are promising catalysts for green methanol synthesis via CO2 hydrogenation. Growing evidence suggests that dynamic restructuring under reaction conditions plays a crucial but poorly understood role in catalytic performance. To address this, the direct visualization of the state-of-the-art In2O3/m-ZrO2 catalyst under CO2 hydrogenation conditions (T  =  553 K, P  =  1.9 bar, CO2:H2  =  1:4) is pioneered using in situ scanning transmission electron microscopy (STEM), comparing its behavior to In2O3 on supports with similar (tetragonal, t-ZrO2 or anatase TiO2) or lower (LSm-ZrO2) surface areas. Complementary in situ infrared spectroscopy and catalytic tests confirm methanol formation under equivalent conditions. A machine-learning-based difference imaging approach differentiates and ranks restructuring patterns, revealing that partially reduced InOx species on m-ZrO2 undergo cyclic aggregation-redispersion via atomic surface migration, maintaining high active phase dispersion. High-resolution ex situ STEM analysis further shows the epitaxial formation of In2O3 mono- and bilayers on (100) m-ZrO2 facets, highlighting strong oxide-support interactions. In contrast, sintering prevails on t-ZrO2, a-TiO2, and low-surface m-ZrO2, correlating with lower methanol productivity. This work underscores the pivotal role of oxide-support interfacial interactions in the reaction-induced restructuring of InOx species and establishes a framework for tracking nanoscale catalyst dynamics.

Commonsense and common nonsense opinions: PROSPECTS for further reducing beam damage in electron microscopy of radiation-sensitive specimens

Biological molecules are easily damaged by high-energy electrons, thus limiting the exposures that can be used to image such specimens by electron microscopy. It is argued here that many-electron, volume-plasmon excitations, which promptly transition into multiple types of single-electron ionization and excitation events, seem to be the predominant cause of damage in such materials. Although reducing the rate at which primary radiolysis occurs would allow one to record images that were much less noisy, many novel proposals for achieving this are unlikely to be realized in the near future, while others are manifestly ill-founded. As a result, the most realistic option currently is to more effectively use the available "budget" of electron exposure, i.e. to further improve the "dose efficiency" by which images are recorded. While progress in that direction is currently under way for both "conventional" (i.e. fixed-beam) and scanning EM, the former is expected to set a high standard for the latter to surpass.

Three-dimensional atomic-scale characterization of titanium oxyhydroxide nanoparticles by data-driven lattice correlation analysis

Metal oxyhydroxides are essential nanomaterials for recent technologies because of their diverse applications, such as catalysis, adsorbents, and precursors of metal oxides. These applications rely on the controlled crystal structures of metal oxyhydroxides formed via hydrolyzed metal monomers' condensation. However, characterizing the atomic-scale structures of the metal oxyhydroxides has still been challenging due to their diverse structural types, nanometer-scale sizes, and beam sensitivity. Here, we developed a data-driven analysis approach for atom-resolved transmission electron microscopy images of titanium oxyhydroxide (metatitanic acid) nanoparticles. Lattice spacings and angles were measured for each of the 1300 nanoparticles with random crystal orientations, providing three-dimensional structural information. Our findings reveal their anatase-like structure with alternating layers of titanium dioxide (TiO2) and titanium hydroxide (Ti(OH)4) planes. The revealed structure is key to understanding their role as a precursor for metastable anatase TiO2. Our approach unveils the three-dimensional structure of metal oxyhydroxides with high statistical reliability and low electron dose, paving the way for property understanding and application design.

Imaging of Hydrated and Living Cells in Transmission Electron Microscope: Summary, Challenges, and Perspectives

Transmission electron microscopy (TEM) is well-known for performing in situ studies in the nanoscale. Hence, scientists took this opportunity to explore the subtle processes occurring in living organisms. Nevertheless, such observations are complex─they require delicate samples kept in the liquid phase, low electron dose, and proper cell viability verification methods. Despite being highly demanding, so-called "live-cell" experiments have seen some degree of success. The presented review consists of an exhaustive literature review on reported "live-cell" studies and associated subjects, including liquid phase imaging, electron radiation interactions with liquids, and methods for cell viability testing. The challenges of modern, reliable research on living organisms are widely explained and discussed, and future perspectives for developing these techniques are presented.

Radiation Chemistry in Environmental Transmission Electron Microscopy

Environmental transmission electron microscopy (E-TEM) enables direct observation of nanoscale chemical processes crucial for catalysis and materials design. However, the high-energy electron probe can dramatically alter reaction pathways through radiolysis, the dissociation of molecules under electron beam irradiation. While extensively studied in liquid-cell TEM, the impact of radiolysis in gas phase reactions remains unexplored. Here, we present a numerical model elucidating radiation chemistry in both gas and liquid E-TEM environments. Our findings reveal that while gas phase E-TEM generates radiolytic species with lower reactivity than liquid phase systems, these species can accumulate to reaction-altering concentrations, particularly at elevated pressures. We validate our model through two case studies: the radiation-promoted oxidation of aluminum nanocubes and disproportionation of carbon monoxide. In both cases, increasing the electron beam dose rate directly accelerates their reaction kinetics, as demonstrated by enhanced AlOx growth and carbon deposition. Based on these insights, we establish practical guidelines for controlling radiolysis in closed-cell nanoreactors. This work not only resolves a fundamental challenge in electron microscopy but also advances our ability to rationally design materials with sub-Ångstrom resolution.

In Situ Transmission Electron Microscopy of Electrocatalyst Materials: Proposed Workflows, Technical Advances, Challenges, and Lessons Learned

In situ electrochemical liquid phase transmission electron microscopy (LP-TEM) measurements utilize micro-chip three-electrode cells with electron transparent silicon nitride windows that confine the liquid electrolyte. By imaging electrocatalysts deposited on micro-patterned electrodes, LP-TEM provides insight into morphological, phase structure, and compositional changes within electrocatalyst materials under electrochemical reaction conditions, which have practical implications on activity, selectivity, and durability. Despite LP-TEM capabilities becoming more accessible, in situ measurements under electrochemical reaction conditions remain non-trivial, with challenges including electron beam interactions with the electrolyte and electrode, the lack of well-defined experimental workflows, and difficulty interpreting particle behavior within a liquid. Herein a summary of the current state of LP-TEM technique capabilities alongside a discussion of the relevant experimental challenges researchers typically face, with a focus on in situ studies of electrochemical CO2 conversion catalysts is provided. A methodological approach for in situ LP-TEM measurements on CO2R catalysts prepared by electro-deposition, sputtering, or drop-casting is presented and include case studies where challenges and proposed workflows for each are highlighted. By providing a summary of LP-TEM technique capabilities and guidance for the measurements, the goal is for this paper to reduce barriers for researchers who are interested in utilizing LP-TEM characterization to answer their scientific questions.

Exploring Biomineralization Processes Using In Situ Liquid Transmission Electron Microscopy: A Review

Liquid transmission electron microscopy (TEM) is a newly established technique broadly used to study reactions in situ. Since its emergence, complex and multifaceted biomineralization processes have been revealed with real-time resolution, where classical and non-classical mineralization pathways have been dynamically observed primarily for Ca and Fe-based mineral systems in situ. For years, classical crystallization pathways have dominated theories on biomineralization progression despite observations of non-traditional routes involving precursor phases using traditional- and cryo-TEM. The new dynamic lens provided by liquid TEM is a key correlate to techniques limited to time-stamped, static observations - helping shift paradigms in biomineralization toward non-classical theories with dynamic mechanistic visualization. Liquid TEM provides new insights into fundamental biomineralization processes and essential physiological and pathological processes for a wide range of organisms. This review critically reviews a summary of recent in situ liquid TEM research related to the biomineralization field. Key liquid TEM preparation and imaging parameters are provided as a foundation for researchers while technical challenges are discussed. In future, the expansion of liquid TEM research in the biomineralization field will lead to transformative discoveries, providing complementary dynamic insights into biological systems.

Nano-scale characterization of iron-carbohydrate complexes by cryogenic scanning transmission electron microscopy: Building the bridge to biorelevant characterization

Iron deficiency and iron deficiency anemia pose significant health challenges worldwide. Iron carbohydrate nanoparticles administered intravenously are a mainstay of treatment to deliver elemental iron safely and effectively. However, despite decades of clinical use, a complete understanding of their physical structure and the significance for their behavior, particularly at the nano-bio interface, is still lacking, underscoring the need to employ more sophisticated characterization methods. Our study used cryogenic Scanning Transmission Electron Microscopy (cryo-STEM) to examine iron carbohydrate nanoparticle morphology. This method builds upon previous research, where direct visualization of the iron cores in these complexes was achieved using cryogenic Transmission Electron Microscopy (cryo-TEM). Our study confirms that the average size of the iron cores within these nanoparticles is approximately 2 nm across all iron-based products studied. Furthermore, our investigation revealed the existence of discernible cluster-like morphologies, not only for ferumoxytol, as previously reported, but also within all the examined iron-carbohydrate products. The application of cryo-STEM for the analyses of product morphologies provides high-contrast and high-resolution images of the nanoparticles, and facilitates the characterization at liquid nitrogen temperature, thereby preserving the structural integrity of these complex samples. The findings from this study offer valuable insights into the physical structure of iron-carbohydrate nanoparticles, a crucial step towards unraveling the intricate relationship between the structure and function of this widely used drug class in treating iron deficiency. Additionally, we developed and utilized the self-supervised machine learning workflow for the image analysis of iron-carbohydrate complexes, which might be further expanded into a useful characterization tool for comparability studies.

High-speed 4-dimensional scanning transmission electron microscopy using compressive sensing techniques

Here we show that compressive sensing allows 4-dimensional (4-D) STEM data to be obtained and accurately reconstructed with both high-speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4-D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide dataset shows that it is possible to recover over 25 dB peak signal-to-noise ratio in the recovered phase using 0.3% of the total data. Lay abstract: Four-dimensional scanning transmission electron microscopy (4-D STEM) is a powerful technique for characterizing complex nanoscale structures. In this method, a convergent beam electron diffraction pattern (CBED) is acquired at each probe location during the scan of the sample. This means that a 2-dimensional signal is acquired at each 2-D probe location, equating to a 4-D dataset. Despite the recent development of fast direct electron detectors, some capable of 100kHz frame rates, the limiting factor for 4-D STEM is acquisition times in the majority of cases, where cameras will typically operate on the order of 2kHz. This means that a raster scan containing 256^2 probe locations can take on the order of 30s, approximately 100-1000 times longer than a conventional STEM imaging technique using monolithic radial detectors. As a result, 4-D STEM acquisitions can be subject to adverse effects such as drift, beam damage, and sample contamination. Recent advances in computational imaging techniques for STEM have allowed for faster acquisition speeds by way of acquiring only a random subset of probe locations from the field of view. By doing this, the acquisition time is significantly reduced, in some cases by a factor of 10-100 times. The acquired data is then processed to fill-in or inpaint the missing data, taking advantage of the inherently low-complex signals which can be linearly combined to recover the information. In this work, similar methods are demonstrated for the acquisition of 4-D STEM data, where only a random subset of CBED patterns are acquired over the raster scan. We simulate the compressive sensing acquisition method for 4-D STEM and present our findings for a variety of analysis techniques such as ptychography and differential phase contrast. Our results show that acquisition times can be significantly reduced on the order of 100-300 times, therefore improving existing frame rates, as well as further reducing the electron fluence beyond just using a faster camera.

Doses for X-ray and electron diffraction: New features in RADDOSE-3D including intensity decay models

New features in the dose estimation program RADDOSE-3D are summarised. They include the facility to enter a diffraction intensity decay model which modifies the "Diffraction Weighted Dose" output from a "Fluence Weighted Dose" to a "Diffraction-Decay Weighted Dose", a description of RADDOSE-ED for use in electron diffraction experiments, where dose is historically quoted in electrons/Å2 rather than in gray (Gy), and finally the development of a RADDOSE-3D GUI, enabling easy access to all the options available in the program.

Voxel dose-limited resolution for thick beam-sensitive specimens imaged in a TEM or STEM

The resolution limit imposed by radiation damage is quantified in terms of a voxel dose-limited resolution (DLR), applicable to small features within a thick specimen. An analytical formula for this DLR is derived and applied to bright-field mass-thickness contrast from organic (polymer or biological) specimens of thickness between 400 nm and 20 µm. For a permissible dose of 330 MGy (typical of frozen-hydrated tissue), the TEM or STEM image resolution is determined by radiation damage rather than by lens aberrations or beam-broadening effects, which can be restricted by use of a small angle-limiting aperture. DLR is improved by a up to factor of 2 by increasing the primary-electron energy from 300 keV to 3 MeV, or by up to a factor of 3 by heavy-metal staining. For stained samples, a higher electron fluence allows better resolution but the improvement is modest because the voxel DLR is proportional to the 1/4 power of electron dose. The relevance of voxel and columnar DLR is discussed, for both thick and thin samples.

Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self-Assembling Peptides

A significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self-assembling peptides. Sheet-forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG400 - and PEG700 -peptide conjugates directly self-associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in-register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co-assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand-appended assemblies for cell targeting. This study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.

Radiation damage to biological macromolecules∗

In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.

Operando spectral imaging of the lithium ion battery's solid-electrolyte interphase

The lithium-ion battery is currently the preferred power source for applications ranging from smart phones to electric vehicles. Imaging the chemical reactions governing its function as they happen, with nanoscale spatial resolution and chemical specificity, is a long-standing open problem. Here, we demonstrate operando spectrum imaging of a Li-ion battery anode over multiple charge-discharge cycles using electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM). Using ultrathin Li-ion cells, we acquire reference EELS spectra for the various constituents of the solid-electrolyte interphase (SEI) layer and then apply these "chemical fingerprints" to high-resolution, real-space mapping of the corresponding physical structures. We observe the growth of Li and LiH dendrites in the SEI and fingerprint the SEI itself. High spatial- and spectral-resolution operando imaging of the air-sensitive liquid chemistries of the Li-ion cell opens a direct route to understanding the complex, dynamic mechanisms that affect battery safety, capacity, and lifetime.

Transmission electron microscopy of thick polymer and biological specimens

We explore the properties of elastic and inelastic scattering in a thick organic specimen, together with the mechanisms that provide contrast in a transmission electron microscope (TEM) and scanning-transmission electron microscope (STEM). Experimental data recorded from amorphous carbon are used to predict the bright-field image intensity, mass-thickness contrast and dose-limited resolution as a function of thickness, objective-aperture size, and primary-electron energy E₀. Combining this information with estimates of chromatic aberration, objective-aperture diffraction and beam broadening in the specimen, we calculate the achievable TEM and STEM resolution to be around 4 nm at E₀ = 300 keV (or below 3 nm at MeV energies) for a 10 µm-diameter objective aperture and 1 - 2 µm thickness of hydrated biological tissue. The 3 MeV resolution for a 10-μm tissue sample is probably closer to 10 nm. We also comment on the error involved in quadrature addition of resolution factors, when one or more of the point-spread functions are non-Gaussian.

Light-Induced In Situ Transmission Electron Microscopy─Development, Challenges, and Perspectives

Transmission electron microscopy is a basic technique used for examining matter at the highest magnification scale available. One of its most challenging branches is in situ microscopy, in which dynamic processes are observed in real time. Among the various stimuli, like strain, temperature, and magnetic or electric fields, the light-matter interaction is rarely observed. However, in recent years, a significant increase in the interest in this technique has been observed. Therefore, I present a summary and critical review of all the in situ experiments performed with light, various technical possibilities for bringing radiation inside the transmission electron microscope, and the most important differences between the effects of light and electrons on the studied matter. Finally, I summarize the most promising directions for further research using light excitation.

OUP accepted manuscript

We first review the significance of resolution and contrast in electron microscopy and the effect of the electron optics on these two quantities. We then outline the physics of the generation of secondary electrons (SEs) and their transport and emission from the surface of a specimen. Contrast and resolution are discussed for different kinds of SE imaging in scanning electron microscope (SEM) and scanning-transmission microscope instruments, with some emphasis on the observation of individual atoms and atomic columns in a thin specimen. The possibility of achieving atomic resolution from a bulk specimen at SEM energies is also considered.

Radiation damage to biological samples: still a pertinent issue

An understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques. For X-ray diffraction, an in-depth study of multi-crystal small-wedge data collection single-wavelength anomalous dispersion phasing protocols is presented, concluding that an absorbed dose of 5 MGy per crystal was optimal to allow reliable phasing. For small-angle X-ray scattering, experiments are reported that evaluate the efficacy of three radical scavengers using a protein designed to give a clear signature of damage in the form of a large conformational change upon the breakage of a disulfide bond. The use of X-rays to induce OH radicals from the radiolysis of water for X-ray footprinting are covered in two papers. In the first, new developments and the data collection pipeline at the NSLS-II high-throughput dedicated synchrotron beamline are described, and, in the second, the X-ray induced changes in three different proteins under aerobic and low-oxygen conditions are investigated and correlated with the absorbed dose. Studies in XFEL science are represented by a report on simulations of ultrafast dynamics in protic ionic liquids, and, lastly, a broad coverage of possible methods for dose efficiency improvement in modalities using electrons is presented. These papers, as well as a brief synopsis of some other relevant literature published since the last Journal of Synchrotron Radiation Special Issue on Radiation Damage in 2019, are summarized below.

Single-particle cryo-EM: alternative schemes to improve dose efficiency

Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.