A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors. The physics of the method is based on the well-known Diffraction Tomography formalism, but with the phase-retrieval step modified to include a conjugation of the phase (i.e., multiplication of the phase by a negative constant). At each illumination direction, numerically backpropagating the beam with the conjugated phase produces maximum contrast at the location of individual atoms in the molecule or nanoparticle. The resultant algorithm, Conjugated Holographic Reconstruction, can potentially be incorporated into established software tools for single-particle analysis, such as, for example, RELION or FREALIGN, in place of the conventional contrast transfer function correction procedure, in order to account for the Ewald sphere curvature and improve the spatial resolution of the three-dimensional reconstruction.

Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.

Although scanning transmission electron microscopy (STEM) images of individual heavy atoms were reported 50 years ago, the applications of atomic-resolution STEM imaging became wide spread only after the practical realization of aberration correctors on field-emission STEM/TEM instruments to form sub-Ångstrom electron probes. The innovative designs and advances of electron optical systems, the fundamental understanding of electron–specimen interaction processes, and the advances in detector technology all played a major role in achieving the goal of atomic-resolution STEM imaging of practical materials. It is clear that tremendous advances in computer technology and electronics, image acquisition and processing algorithms, image simulations, and precision machining synergistically made atomic-resolution STEM imaging routinely accessible. It is anticipated that further hardware/software development is needed to achieve three-dimensional atomic-resolution STEM imaging with single-atom chemical sensitivity, even for electron-beam-sensitive materials. Artificial intelligence, machine learning, and big-data science are expected to significantly enhance the impact of STEM and associated techniques on many research fields such as materials science and engineering, quantum and nanoscale science, physics and chemistry, and biology and medicine. This review focuses on advances of STEM imaging from the invention of the field-emission electron gun to the realization of aberration-corrected and monochromated atomic-resolution STEM and its broad applications.

Atom probe tomography (APT) helps elucidate the link between the nanoscale chemical variations and physical properties, but it has a limited structural resolution. Field ion microscopy (FIM), a predecessor technique to APT, is capable of attaining atomic resolution along certain sets of crystallographic planes albeit at the expense of elemental identification. We demonstrate how two commercially available atom probe instruments, one with a straight flight path and one fitted with a reflectron lens, can be used to acquire time-of-flight mass spectrometry data concomitant with a FIM experiment. We outline various experimental protocols making the use of temporal and spatial correlations to best discriminate field-evaporated signals from the large field-ionized background signal, demonstrating an unsophisticated yet efficient data mining strategy to provide this discrimination. We discuss the remaining experimental challenges that need to be addressed, notably concerned with accurate detection and identification of individual field-evaporated ions contained within the high field-ionized flux that contributes to a FIM image. Our hybrid experimental approach can, in principle, exhibit true atomic resolution with elemental discrimination capabilities, neither of which atom probe nor FIM can individually fully deliver—thereby making this new approach, here broadly termed analytical field ion microscopy (aFIM), unique.

With the wide application of ultra-microtome sectioning in the preparation of transmission electron microscopy (TEM) specimens with bio- and organic materials, here, we report an ultra-microtome-based method for the preparation of TEM specimens from cathodes of Li-ion batteries. The ultra-microtome sectioning reduces the sample thickness to tens of nanometers and yields atomic resolution from the core region of particles of hundreds of nanometers. Analysis indicates that the mechanical cross-sectioning introduces no observable microstructural artifacts or structural damage, such as microcracking and nanoporosity. These results demonstrate the high efficiency of the ultra-microtome approach in preparing well-thinned specimens of particulate materials that allow for atomic-scale TEM imaging of a large number of sectioned particles in one single TEM specimen, thereby providing statistically significant results of the TEM analysis.

The scanning tunneling microscope is essential to nanoscience and nanotechnology because it can provide images of surfaces at the atomic level with sub-nanometer resolution. Now a LabVIEW-based virtual instrument is available as a free-download at our company website (www.newpathresearch.com) for simulating the full operation of a scanning tunneling microscope. This is an executable version to be run on a Windows operating system without requiring other software.

An automated procedure has been developed for the reconstruction of field ion microscopy (FIM) data that maintains its atomistic nature. FIM characterizes individual atoms on the specimen’s surface, evolving subject to field evaporation, in a series of two-dimensional (2D) images. Its unique spatial resolution enables direct imaging of crystal defects as small as single vacancies. To fully exploit FIM’s potential, automated analysis tools are required. The reconstruction algorithm developed here relies on minimal assumptions and is sensitive to atomic coordinates of all imaged atoms. It tracks the atoms across a sequence of images, allocating each to its respective crystallographic plane. The result is a highly accurate 3D lattice-resolved reconstruction. The procedure is applied to over 2000 tungsten atoms, including ion-implanted planes. The approach is further adapted to analyze carbides in a steel matrix, demonstrating its applicability to a range of materials. A vast amount of information is collected during the experiment that can underpin advanced analyses such as automated detection of “out of sequence” events, subangstrom surface displacements and defects effects on neighboring atoms. These analyses have the potential to reveal new insights into the field evaporation process and contribute to improving accuracy and scope of 3D FIM and atom probe characterization.

Here, we report the development of an approach to map atomic resolution images into a convenient matrix representation. Through the combination of two-dimensional Gaussian fitting and the projective standard deviation, atom column locations are projected onto two noncollinear reference lattice vectors that are used to assign each a unique (i, j) matrix index. By doing so, straightforward atomic resolution image analysis becomes possible. Using practical examples, we demonstrate that the matrix representation greatly simplifies categorizing atom columns to different sublattices. This enables a myriad of direct analyses, such as mapping atom column properties and correlating long-range atom column pairs. MATLAB source code can be downloaded from https://github.com/subangstrom/aci.

A newly designed, 100 mm2, silicon drift detector has been installed on an aberration-corrected scanning transmission electron microscope equipped with an ultra-high resolution pole piece, without requiring column modifications. With its unique, windowless design, the detector’s active region is in close proximity to the sample, resulting in a dramatic increase in count rate, while demonstrating an increased sensitivity to low energy X-rays and a muted tilt dependence. Numerous examples of X-ray energy dispersive spectrometry are presented on relevant materials such as AlxGa1−xN nanowires, perovskite oxides, and polycrystalline CdTe thin films, across both varying length scales and accelerating voltages.

Observation of growth, synthesis, dynamics, and electrochemical reactions in the liquid state is an important yet largely unstudied aspect of nanotechnology. The only techniques that can potentially provide the insights necessary to advance our understanding of these mechanisms is simultaneous atomic-scale imaging and quantitative chemical analysis (through spectroscopy) under environmental conditions in the transmission electron microscope. In this study we describe the experimental and technical conditions necessary to obtain electron energy loss (EEL) spectra from a nanoparticle in colloidal suspension using aberration-corrected scanning transmission electron microscopy (STEM) combined with the environmental liquid stage. At a fluid path length below 400 nm, atomic resolution images can be obtained and simultaneous compositional analysis can be achieved. We show that EEL spectroscopy can be used to quantify the total fluid path length around the nanoparticle and demonstrate that characteristic core-loss signals from the suspended nanoparticles can be resolved and analyzed to provide information on the local interfacial chemistry with the surrounding environment. The combined approach using aberration-corrected STEM and EEL spectra with the in situ fluid stage demonstrates a plenary platform for detailed investigations of solution-based catalysis.

Electron holography has been shown to allow a posteriori aberration correction. Therefore, an aberration corrector in the transmission electron microscope does not seem to be needed with electron holography to achieve atomic lateral resolution. However, to reach a signal resolution sufficient for detecting single light atoms and very small interatomic fields, the aberration corrector has turned out to be very helpful. The basic reason is the optimized use of the limited number of “coherent” electrons that are provided by the electron source, as described by the brightness. Finally, quantitative interpretation of atomic structures benefits from the holographic facilities of fine-tuning of the aberration coefficients a posteriori and from evaluating both amplitude and phase.

Otto Scherzer was one of the pioneers of theoretical electron optics. He was coauthor of the first comprehensive book on electron optics and was the first to understand that round electron lenses could not be combined to correct aberrations, as is the case in light optics. He subsequently was the first to describe several alternative means to correct spherical and chromatic aberration of electron lenses. These ideas were put into practice by his laboratory and students at Darmstadt and their successors, leading to the fully corrected electron microscopes now in operation.

Ag on γ-alumina is a promising catalyst for hydrocarbon selective catalytic reduction in lean-burn gasoline and diesel engines for transportation applications. Although much is known about the mechanism of NOx reduction and the various intermediates, little agreement exists on the nature of the active silver species. In the present work, aberration-corrected STEM has provided new information about the nature of Ag on alumina both as impregnated and following treatments at various temperatures with exposure to simulated exhaust gas. Ex situ techniques have provided new insights into the evolution of Ag on alumina following exposure to temperature and simulated exhaust gas.

The resolution-limiting aberrations of round electromagnetic lenses can now be successfully overcome via the use of multipole element “aberration correctors.” The installation and performance of a hexapole-based corrector (CEOS GmbH) integrated on the probe-forming side of a JEOL 2200FS FEG STEM/TEM is described. For the resolution of the microscope not to be severely compromised by its environment, a new, specially designed building at Oak Ridge National Laboratory has been built. The Advanced Microscopy Laboratory was designed with the goal of providing a suitable location for aberration-corrected electron microscopes. Construction methods and performance of the building are discussed in the context of the performance of the microscope. Initial performance of the microscope on relevant specimens and modifications made to eliminate resolution-limiting conditions are also discussed.

It is shown that the ultimate resolution is not limited by the bandwidth of the microscope but by the bandwidth (i.e., the scattering power) of the object. In the case of a crystal oriented along a zone axis, the scattering is enhanced by the channeling of the electrons. However, if the object is aperiodic along the beam direction, the bandwidth is much more reduced. A particular challenge are the amorphous objects. For amorphous materials, the natural bandwidth is that of the single atom and of the order of 1 Å−1, which can be reached with the present generation of medium voltage microscopes without aberration correctors. A clear distinction is made between resolving a structure and refining, that is, between resolution and precision. In the case of an amorphous structure, the natural bandwidth also puts a limit on the number of atom coordinates that can be refined quantitatively. As a consequence, amorphous structures cannot be determined from one projection, but only by using atomic resolution tomography. Finally a theory of experiment design is presented that can be used to predict the optimal experimental setting or the best instrumental improvement. Using this approach it is suggested that the study of amorphous objects should be done at low accelerating voltage with correction of both spherical and chromatic aberration.

In situ real-time environmental high resolution electron microscopy (EHREM) under controlled reaction environments permits direct atomic resolution imaging of dynamic surface and sub-surface microstructures of reacting catalysts. Using the EHREM and complementary microscopy methods, we have investigated selective hydrogenation reaction mechanisms over novel xerogel catalysts of ruthenium and Ru with Co and Au promoters on titania supports, and report an alternative heterogeneous catalytic process for the hydrogenation of adiponitrile (ADN) in the manufacture of Nylon 6,6. The direct EHREM observations are supported by ultra-high resolution low voltage scanning electron microscope (SEM) of spatial distributions of the highly dispersed nanometer-size catalyst particles and parallel chemical studies. The results demonstrate the important role of in situ EHREM in the design of heterogeneous catalytic hydrogenation processes on the nanoscale.

We report the 0.75 Å crystal structure of a racemic mixture of the 12-residue designed peptide “Alpha-1” (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is described in the accompanying paper. Equivalent solutions of the centrosymmetric bilayers were determined by two direct phasing programs in space groups P1 and P1. The unit cell contains two l-alpha-helices and two d-alpha-helices. The columnar-sheet bilayer motif seen in l-Alpha-1 is maintained in the d,l-Alpha-1 structure except that each sheet of head-to-tail helices is composed of one enantiomer and is related to its neighboring sheets by inversion symmetry. Comparison to the l-Alpha-1 structure provides further insight into peptide design. The high resolution and small asymmetric unit allowed building an intricate model (R = 13.1%, Rfree = 14.5%) that incorporates much of the discrete disorder of peptide and solvent. Ethanolamine and 2-methyl-2,4-pentanediol (MPD) molecules bind near helix termini. Rigid body analysis identifies sites of restricted displacements and torsions. Side-chain discrete disorder propagates into the backbone of one helix but not the other. Although no side chain in Alpha-1 is rigid, the environments in the crystal restrict some of them to no or only one active torsion.

A 12-residue peptide designed to form an α-helix and self-associate into an antiparallel 4-α-helical bundle yields a 0.9 Å crystal structure revealing unanticipated features. The structure was determined by direct phasing with the “Shake-and-Bake” program, and contains four crystallographically distinct 12-mer peptide molecules plus solvent for a total of 479 atoms. The crystal is formed from nearly ideal α-helices hydrogen bonded head-to-tail into columns, which in turn pack side-by-side into sheets spanning the width of the crystal. Within each sheet, the α-helices run antiparallel and are closely spaced (9–10 Å center-to-center). The sheets are more loosely packed against each other (13–14 Å between helix centers). Each sheet is amphiphilic: apolar leucine side chains project from one face, charged lysine and glutamate side chains from the other face. The sheets are stacked with two polar faces opposing and two apolar faces opposing. The result is a periodic biomaterial composed of packed protein bilayers, with alternating polar and apolar interfaces. All of the 30 water molecules in the unit cell lie in the polar interface or between the stacked termini of helices. A section through the sheet reveals that the helices packed at the apolar interface resemble the four-α-helical bundle of the design, but the helices overhang parts of the adjacent bundles, and the helix crossing angles are less steep than intended (7–11° rather than 18°).