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.

Semicircular-aperture illumination scanning transmission electron microscopy

Scanning transmission electron microscopy (STEM) provides high-resolution visualization of atomic structures as well as various functional imaging modes utilizing phase contrasts. In this study we introduce a semicircular aperture in STEM bright field imaging, which gives a phase contrast transfer function that becomes complex and includes both lower and higher spatial frequency contrast transfer. This approach offers significant advantages over conventional phase plate methods, having no charge accumulation, degradation, or unwanted background noise, which are all problematic in the phase plate material. Also compared to the differential phase contrast or ptychography equipment, this semicircular aperture is far less costly. We apply this approach to visualization of polymer, biological and magnetic samples.

Retrieval of Phase Information from Low-Dose Electron Microscopy Experiments: Are We at the Limit Yet?

The challenge of imaging low-density objects in an electron microscope without causing beam damage is significant in modern transmission electron microscopy. This is especially true for life science imaging, where the sample, rather than the instrument, still determines the resolution limit. Here, we explore whether we have to accept this or can progress further in this area. To do this, we use numerical simulations to see how much information we can obtain from a weak phase object at different electron doses. Starting from a model with four phase values, we compare Zernike phase contrast with measuring diffracted intensity under multiple random phase illuminations to solve the inverse problem. Our simulations have shown that diffraction-based methods perform better than the Zernike method, as we have found and addressed a normalization issue that, in some other studies, led to an overly optimistic representation of the Zernike setup. We further validated this using more realistic 2D objects and found that random phase illuminated diffraction can be up to five times more efficient than an ideal Zernike implementation. These findings suggest that diffraction-based methods could be a promising approach for imaging beam-sensitive materials and that current low-dose imaging methods are not yet at the quantum limit.

Determination of the Critical Voltage for the Observation of Uncoated Wood Samples in Electron Microscopy

Electron microscopy (EM) is a key tool for studying the microstructure of wood; however, observing uncoated samples poses a challenge due to surface charging. This study aims to identify the critical voltage that allows for the effective observation of uncoated wood samples without significant loading. As part of the experiment, samples of different wood species were tested, including Acacia (Robinia pseudoacacia L.), Oak (Quercus robur L.), Maple (Acer pseudoplatanus spp.), Ash (Fraxinus excelsior L.), Spruce (Picea abies (L.) Karst.), Thermowood (Thermal modifed Spruce), Garapa (Apuleia leiocarpa), Ipé (Handroanthus spp.), Merbau (Intsia bijuga), and Massaranduba (Manilkara spp.). Several methods were tested for surface preparation for SEM analysis, including the use of a circular saw, a hand milling machine, and a microtome. The results show that the optimal voltage for observing uncoated wood samples varied depending on the wood species. Regarding the selection of wood species and the results obtained, it was found that uncoated samples could be effectively observed. This finding suggests that practical observations can be accelerated and more cost-effective, as all wood species exhibited the required voltage range of 1 kV to 1.6 kV. Additionally, it was determined that using a secondary electron detector was optimal for such observations, as it provided a sufficiently strong signal even at relatively low voltages. Conversely, when using a backscattered electron detector, it was more beneficial to use coated samples to achieve a sufficient signal at higher voltages. This study brings new knowledge that will facilitate further research and applications of electron microscopy in the study of other wood species or wood-based materials.

Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å

While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of small domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating anti-tumor toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.

Design of Electrostatic Aberration Correctors for Scanning Transmission Electron Microscopy

In a scanning transmission electron microscope (STEM), producing a high-resolution image generally requires an electron beam focused to the smallest point possible. However, the magnetic lenses used to focus the beam are unavoidably imperfect, introducing aberrations that limit resolution. Modern STEMs overcome this by using hardware aberration correctors comprised of many multipole elements, but these devices are complex, expensive, and can be difficult to tune. We demonstrate a design for an electrostatic phase plate that can act as an aberration corrector. The corrector is comprised of annular segments, each of which is an independent two-terminal device that can apply a constant or ramped phase shift to a portion of the electron beam. We show the improvement in image resolution using an electrostatic corrector. Engineering criteria impose that much of the beam within the probe-forming aperture be blocked by support bars, leading to large probe tails for the corrected probe that sample the specimen beyond the central lobe. We also show how this device can be used to create other STEM beam profiles such as vortex beams and probes with a high degree of phase diversity, which improve information transfer in ptychographic reconstructions.

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.

Defect Contrast with 4D-STEM: Understanding Crystalline Order with Virtual Detectors and Beam Modification

Material properties strongly depend on the nature and concentration of defects. Characterizing these features may require nano- to atomic-scale resolution to establish structure-property relationships. 4D-STEM, a technique where diffraction patterns are acquired at a grid of points on the sample, provides a versatile method for highlighting defects. Computational analysis of the diffraction patterns with virtual detectors produces images that can map material properties. Here, using multislice simulations, we explore different virtual detectors that can be applied to the diffraction patterns that go beyond the binary response functions that are possible using ordinary STEM detectors. Using graphene and lead titanate as model systems, we investigate the application of virtual detectors to study local order and in particular defects. We find that using a small convergence angle with a rotationally varying detector most efficiently highlights defect signals. With experimental graphene data, we demonstrate the effectiveness of these detectors in characterizing atomic features, including vacancies, as suggested in simulations. Phase and amplitude modification of the electron beam provides another process handle to change image contrast in a 4D-STEM experiment. We demonstrate how tailored electron beams can enhance signals from short-range order and how a vortex beam can be used to characterize local symmetry.

A strategy combining denoising and cryo-EM single particle analysis

In cryogenic electron microscopy (cryo-EM) single particle analysis (SPA), high-resolution three-dimensional structures of biological macromolecules are determined by iteratively aligning and averaging a large number of two-dimensional projections of molecules. Since the correlation measures are sensitive to the signal-to-noise ratio, various parameter estimation steps in SPA will be disturbed by the high-intensity noise in cryo-EM. However, denoising algorithms tend to damage high frequencies and suppress mid- and high-frequency contrast of micrographs, which exactly the precise parameter estimation relies on, therefore, limiting their application in SPA. In this study, we suggest combining a cryo-EM image processing pipeline with denoising and maximizing the signal's contribution in various parameter estimation steps. To solve the inherent flaws of denoising algorithms, we design an algorithm named MScale to correct the amplitude distortion caused by denoising and propose a new orientation determination strategy to compensate for the high-frequency loss. In the experiments on several real datasets, the denoised particles are successfully applied in the class assignment estimation and orientation determination tasks, ultimately enhancing the quality of biomacromolecule reconstruction. The case study on classification indicates that our strategy not only improves the resolution of difficult classes (up to 5 Å) but also resolves an additional class. In the case study on orientation determination, our strategy improves the resolution of the final reconstructed density map by 0.34 Å compared with conventional strategy. The code is available at https://github.com/zhanghui186/Mscale.

First step toward complex observations by 4D-STEM with phase plate

Quantitative measurements by electron microscopy are becoming increasingly important because we are often concerned with establishing quantitative relationships between the properties and structures of materials. This paper presents a method to derive the scattering and phase contrast components from scanning transmission electron microscope (STEM) images using a phase plate and two-dimensional electron detector and to quantitatively evaluate the amount of phase modulation. The phase-contrast transfer function (PCTF) modifies the phase contrast because it is not unity over all spatial frequency regions; therefore, the amount of phase modulation observed in the image becomes smaller than the actual value. We applied a filter function to the Fourier transform of image to perform PCTF correction and evaluated the phase modulation of the electron waves, which was quantitatively agreement with the values expected from the thickness estimated from the scattering contrast within 20% error. So far, few quantitative discussions on phase modulation have been conducted. Although the accuracy needs to be improved, this method is the first step toward quantitative complex observations.

Ultrafast Transverse Modulation of Free Electrons by Interaction with Shaped Optical Fields

Spatiotemporal electron-beam shaping is a bold frontier of electron microscopy. Over the past decade, shaping methods evolved from static phase plates to low-speed electrostatic and magnetostatic displays. Recently, a swift change of paradigm utilizing light to control free electrons has emerged. Here, we experimentally demonstrate arbitrary transverse modulation of electron beams without complicated electron-optics elements or material nanostructures, but rather using shaped light beams. On-demand spatial modulation of electron wavepackets is obtained via inelastic interaction with transversely shaped ultrafast light fields controlled by an external spatial light modulator. We illustrate this method for the cases of Hermite-Gaussian and Laguerre-Gaussian modulation and discuss their use in enhancing microscope sensitivity. Our approach dramatically widens the range of patterns that can be imprinted on the electron profile and greatly facilitates tailored electron-beam shaping.

Efficient manual annotation of cryogenic electron tomograms using IMOD

Annotation highlights and segmentation isolates features in cryogenic electron tomograms to improve visualization and quantification of features (for example, their size and abundance, and spatial relationships with other features), facilitating phenotypic structural analyses of cellular tomograms. Here, we present a manual annotation protocol using the open-source software IMOD and describe segmentation of three types of common cellular features: membranes, large globules, and filaments. IMOD's interpolation function can improve the speed of manual annotation up to an order of magnitude.

Origin of spurious intensity in vacuum near sample edge in bright field TEM images

Bright-field transmission electron microscope (BFTEM) images exhibit spurious image intensity in the vacuum near the sample edge. The spurious intensity gradually decreases with increasing distance from the sample edge. By taking into account angular and energy loss distribution of the scattered electrons and lens aberrations, the origin of the spurious intensity of BFTEM images can be explained. The spurious intensity extent and magnitude can be significantly reduced by using either electron energy filtering or a small collection semiangle.

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

Carbon-film-based Zernike phase plates with smooth thickness gradient for phase-contrast transmission electron microscopy with reduced fringing artifacts

Phase plates (PPs) in transmission electron microscopy (TEM) improve the contrast of weakly scattering objects under in-focus imaging conditions. A well-established PP type is the Zernike (Z)PP, which consists of a thin amorphous carbon (aC) film with a micro-scaled hole in the center. The mean inner potential of the aC film is exploited to shift the phase of the scattered electrons while the unscattered electrons in the zero-order beam propagate through the hole and remain unaffected. However, the abrupt thickness increase at the hole edge induces an abrupt change of the phase-shift distribution and leads to fringing, i.e., intensity oscillations around imaged objects, in TEM images. In this work, we have used focused-ion-beam milling to fabricate ZPPs with abrupt and graded thickness profiles around the center hole. Depending on the thickness gradient and inner hole radius, graded-ZPP-TEM images of an aC/vacuum interface and bundles of carbon nanotubes (CNTs) show strongly reduced fringing. Image simulations were performed with ZPP-phase-shift distributions derived from measured thickness profiles of graded ZPPs, which show good agreement with the experimental images. Fringing artifacts, i.e. intensity oscillations around imaged objects, are strongly reduced for Zernike phase plates with a graded thickness profile around the center hole. Focused-ion-beam milling is used to fabricate graded Zernike phase plates with specific inner hole radius and thickness gradients. The phase-shift distribution is obtained from measured thickness profiles around the center hole. Image simulations based on experimentally measured thickness/phase-shift distributions show good agreement with experimental Zernike phase-plate TEM images. This article is protected by copyright. All rights reserved.

High-Energy Electron Scattering in Thick Samples Evaluated by Bright-Field Transmission Electron Microscopy, Energy-Filtering Transmission Electron Microscopy, and Electron Tomography

Energy-filtering transmission electron microscopy (TEM) and bright-field TEM can be used to extract local sample thickness $t$ and to generate two-dimensional sample thickness maps. Electron tomography can be used to accurately verify the local $t$. The relations of log-ratio of zero-loss filtered energy-filtering TEM beam intensity ($I_{{\rm ZLP}}$) and unfiltered beam intensity ($I_{\rm u}$) versus sample thickness $t$ were measured for five values of collection angle in a microscope equipped with an energy filter. Furthermore, log-ratio of the incident (primary) beam intensity ($I_{\rm p}$) and the transmitted beam $I_{{\rm tr}}$ versus $t$ in bright-field TEM was measured utilizing a camera before the energy filter. The measurements were performed on a multilayer sample containing eight materials and thickness $t$ up to 800 nm. Local thickness $t$ was verified by electron tomography. The following results are reported:• The maximum thickness $t_{{\rm max}}$ yielding a linear relation of log-ratio, $\ln ( {I_{\rm u}}/{I_{{\rm ZLP}}})$ and $\ln ( {I_{\rm p}}/{I_{{\rm tr}}} )$, versus $t$.• Inelastic mean free path ($\lambda _{{\rm in}}$) for five values of collection angle.• Total mean free path ($\lambda _{{\rm total}}$) of electrons excluded by an angle-limiting aperture.• $\lambda _{{\rm in}}$ and $\lambda _{{\rm total}}$ are evaluated for the eight materials with atomic number from $\approx$10 to 79.The results can be utilized as a guide for upper limit of $t$ evaluation in energy-filtering TEM and bright-field TEM and for optimizing electron tomography experiments.

Making the Most of your Electrons: Challenges and Opportunities in Characterizing Hybrid Interfaces with STEM

Inspired by the unique architectures composed of hard and soft materials in natural and biological systems, synthetic hybrid structures and associated soft-hard interfaces have recently evoked significant interest. Soft matter is typically dominated by fluctuations even at room temperature, while hard matter (which often serves as the substrate or anchor for the soft component) is governed by rigid mechanical behavior. This dichotomy offers considerable opportunities to leverage the disparate properties offered by these components across a wide spectrum spanning from basic science to engineering insights with significant technological overtones. Such hybrid structures, which include polymer nanocomposites, DNA functionalized nanoparticle superlattices and metal organic frameworks to name a few, have delivered promising insights into the areas of catalysis, environmental remediation, optoelectronics, medicine, and beyond. The interfacial structure between these hard and soft phases exists across a variety of length scales and often strongly influence the functionality of hybrid systems. While scanning/transmission electron microscopy (S/TEM) has proven to be a valuable tool for acquiring intricate molecular and nanoscale details of these interfaces, the unusual nature of hybrid composites presents a suite of challenges that make assessing or establishing the classical structure-property relationships especially difficult. These include challenges associated with preparing electron-transparent samples and obtaining sufficient contrast to resolve the interface between dissimilar materials given the dose sensitivity of soft materials. We discuss each of these challenges and supplement a review of recent developments in the field with additional experimental investigations and simulations to present solutions for attaining a nano or atomic-level understanding of these interfaces. These solutions present a host of opportunities for investigating and understanding the role interfaces play in this unique class of functional materials.

Comparative image simulations for phase-plate transmission electron microscopy

Numerous physical phase plates (PP) for phase-contrast enhancement in transmission electron microscopy (TEM) have been proposed and studied with the hole-free or Volta PP having a high impact and interest in recent years. This study is concerned with comparative TEM image simulations considering realistic descriptions of various PP approaches and samples from three different fields of application covering a large range of object sizes. The simulated images provide an illustrative characterization of the typical image appearance and common artifacts of the different PPs and the influence of simulation parameters especially important for PP simulations. A quantitative contrast analysis shows the superior phase-shifting properties of the hole-free phase plate for biological applications and the benefits of adjustable phase plates. The application of PPs in high-resolution TEM imaging, especially of weak-phase objects such as (atomically thin) 2D materials, is shown to increase image interpretability. The software with graphical user interface written and used for the presented simulations is available for free usage.