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.

We present a quantitative comparison between experimental position-averaged core-loss scattering from K-, L-, and M-shells of various elements and simulations based on a single-particle description of the core-loss process. To facilitate a direct comparison free of adjustable or compensating parameters, we compare absolute scattering cross-sections for zone-axis-aligned crystals whose thicknesses have been measured independently. The results show that the single-particle model accurately predicts the absolute scattering intensity from K-shells, and L-shells in some cases, but achieves only semi-quantitative agreement for M-shells.

The drying effect associated with utilizing transmission electron microscopy to study deoxyribonucleic acid (DNA)-coated gold nanoparticles (AuNPs) remains largely uninvestigated, though this technique is frequently utilized to characterize nanoparticle–DNA interactions. Investigation of the drying effect is essential to the progress of the many fields that utilize AuNPs, including cancer research. In this study, we compare DNA hybridization-directed nanoparticle assemblies with control samples omitting the necessary complementary DNA, effectively blocking directed assembly, in both the liquid state and the dry state, within a scanning transmission electron microscope. We show that the dry samples contain AuNPs spaced at significantly smaller intervals than identical samples measured in situ, with no dependence on the DNA bound to the AuNPs in the dry samples. A partially wet sample, with distances measured along the drying edge, provided an intermediate binding distance, strengthening the conclusion that drastic differences observed between the dry and in situ samples are due to a pronounced drying effect. This drying effect will falsely indicate certain grouping arrangements and will change the impression of the size of the groups formed, providing misinformation for the development of these controlled assemblies that could impact applications such as targeted drug vehicles for cancer treatment.

Ultrathin ferroelectric heterostructures (SrTiO3/BaTiO3/BaRuO3/SrRuO3) were studied by scanning transmission electron microscopy (STEM) in terms of structural distortions and atomic displacements. The TiO2-termination at the top interface of the BaTiO3 layer was changed into a BaO-termination by adding an additional BaRuO3 layer. High-angle annular dark-field (HAADF) imaging by aberration-corrected STEM revealed that an artificially introduced BaO-termination can be achieved by this interface engineering. By using fast sequential imaging and frame-by-frame drift correction, the effect of the specimen drift was significantly reduced and the signal-to-noise ratio of the HAADF images was improved. Thus, a quantitative analysis of the HAADF images was feasible, and an in-plane and out-of-plane lattice spacing of the BaTiO3 layer of 3.90 and 4.22 Å were determined. A 25 pm shift of the Ti columns from the center of the unit cell of BaTiO3 along the c-axis was observed. By spatially resolved electron energy-loss spectroscopy studies, a reduction of the crystal field splitting (CFS, ΔL3=1.93 eV) and an asymmetric broadening of the eg peak were observed in the BaTiO3 film. These results verify the presence of a ferroelectric polarization in the ultrathin BaTiO3 film.

A method to remove the effects of elastic and thermal diffuse scattering (TDS) of the incident electron probe from electron energy-loss and energy-dispersive X-ray spectroscopy data for atomically resolved spectrum images of single crystals of known thickness is presented. By calculating the distribution of the probe within a specimen of known structure, it is possible to deconvolve the channeling of the probe and TDS from experimental data by reformulating the inelastic cross-section as an inverse problem. In electron energy-loss spectroscopy this allows valid comparisons with first principles fine-structure calculations to be made. In energy-dispersive X-ray spectroscopy, direct compositional analyses such as ζ-factor and Cliff–Lorimer k-factor analysis can be performed without the complications of channeling and TDS. We explore in detail how this method can be incorporated into existing multislice programs, and demonstrate practical considerations in implementing this method using a simulated test specimen. We show the importance of taking into account the scattering of the probe in k-factor analysis in a zone axis orientation. The applicability and limitations of the method are discussed.

In an earlier publication Rosenauer et al. introduced a method for determination of composition in AlGaN/GaN heterostructures from high-angle annular dark field (HAADF) images. Static atomic displacements (SADs) were neglected during simulation of reference data because of the similar covalent radii of Al and Ga. However, SADs have been shown (Grillo et al.) to influence the intensity in HAADF images and therefore could be the reason for an observed slight discrepancy between measured and nominal concentrations. In the present study parameters of the Stillinger–Weber potential were varied in order to fit computed elastic constants, lattice parameters and bonding energies to experimental ones. A reference data set of HAADF images was simulated, in which the new parameterization was used to account for SADs. Two reference samples containing AlGaN layers with different Al concentrations were investigated and Al concentrations in the layers determined based on the new data set. We found that these concentrations were in good agreement with nominal concentrations as well as concentrations determined using alternative techniques such as strain state analysis and energy dispersive X-ray spectroscopy.

In this study we combine scanning transmission electron microscopy, electron energy loss spectroscopy and electron magnetic circular dichroism to get new insights into the electronic and magnetic structure of LaSr-2×4 manganese oxide molecular sieve nanowires integrated on a silicon substrate. These nanowires exhibit ferromagnetism with strongly enhanced Curie temperature (Tc>500 K), and we show that the new crystallographic structure of these LaSr-2×4 nanowires involves spin orbital coupling and a mixed-valence Mn3+/Mn4+, which is a must for ferromagnetic ordering to appear, in line with the standard double exchange explanation.

A connection between microscopic structure and macroscopic properties is expected for almost all material systems. High-resolution transmission electron microscopy is a technique offering insight into the atomic structure, but the analysis of large image series can be time consuming. The present work describes a method to automatically estimate the atomic structure in two-dimensional materials. As an example graphene is chosen, in which the positions of the carbon atoms are reconstructed. Lattice parameters are extracted in the frequency domain and an initial atom positioning is estimated. Next, a plausible neighborhood structure is estimated. Finally, atom positions are adjusted by simulation of a Markov random field model, integrating image evidence and the strong geometric prior. A pristine sample with high regularity and a sample with an induced hole are analyzed. False discovery rate-controlled large-scale simultaneous hypothesis testing is used as a statistical framework for interpretation of results. The first sample yields, as expected, a homogeneous distribution of carbon–carbon (C–C) bond lengths. The second sample exhibits regions of shorter C–C bond lengths with a preferred orientation, suggesting either strain in the structure or a buckling of the graphene sheet. The precision of the method is demonstrated on simulated model structures and by its application to multiple exposures of the two graphene samples.

Sample thickness is a decisive parameter for any quantification of image information and composition in transmission electron microscopy. In this context, we present a method to determine the local sample thickness by scanning transmission electron microscopy at primary energies below 30 keV. The image intensity is measured with respect to the intensity of the incident electron beam and can be directly compared with Monte Carlo simulations. Screened Rutherford and Mott scattering cross-sections are evaluated with respect to fitting experimental data with simulated image intensities as a function of the atomic number of the sample material and primary electron energy. The presented method is tested for sample materials covering a wide range of atomic numbers Z, that is, fluorenyl hexa-peri-hexabenzocoronene (Z = 3.5), carbon (Z = 6), silicon (Z = 14), gallium nitride (Z = 19), and tungsten (Z = 74). Investigations were conducted for two primary energies (15 and 30 keV) and a sample thickness range between 50 and 400 nm.

Electron microscopy of enclosed liquid samples requires the thinnest possible membranes as enclosing windows as well as nanoscale liquid sample thickness to achieve the best possible resolution. Today liquid sample systems for transmission electron microscopy (TEM) are typically made from two sandwiched microchips with thin membranes. We report on a new microfabricated chip system based on a monolithic design that enables membrane geometry on the scale of a few micrometers. The design is intended to reduce membrane deflection when the system is under pressure, a microfluidic channel for improved flow geometry, and a better space angle for auxiliary detectors such as energy-dispersive X-ray spectroscopy. We explain the system design and fabrication and show the first successful TEM images of liquid samples in the chips.

We report our effort to quantify atomic-scale chemical maps obtained by collecting energy-dispersive X-ray spectra (EDS) using scanning transmission electron microscopy (STEM) (STEM-EDS). With thin specimen conditions and localized EDS scattering potential, the X-ray counts from atomic columns can be properly counted by fitting Gaussian peaks at the atomic columns, and can then be used for site-by-site chemical quantification. The effects of specimen thickness and X-ray energy on the Gaussian peak width are investigated using SrTiO3 (STO) as a model specimen. The relationship between the peak width and spatial resolution of an EDS map is also studied. Furthermore, the method developed by this work is applied to study cation occupancy in a Sm-doped STO thin film and antiphase boundaries (APBs) present within the STO film. We find that Sm atoms occupy both Sr and Ti sites but preferably the Sr sites, and Sm atoms are relatively depleted at the APBs likely owing to the effect of strain.

Insight into dynamic electrochemical processes can be obtained with in situ electrochemical-scanning/transmission electron microscopy (ec-S/TEM), a technique that utilizes microfluidic electrochemical cells to characterize electrochemical processes with S/TEM imaging, diffraction, or spectroscopy. The microfluidic electrochemical cell is composed of microfabricated devices with glassy carbon and platinum microband electrodes in a three-electrode cell configuration. To establish the validity of this method for quantitative in situ electrochemistry research, cyclic voltammetry (CV), choronoamperometry (CA), and electrochemical impedance spectroscopy (EIS) were performed using a standard one electron transfer redox couple [Fe(CN)6]3−/4−-based electrolyte. Established relationships of the electrode geometry and microfluidic conditions were fitted with CV and chronoamperometic measurements of analyte diffusion coefficients and were found to agree with well-accepted values that are on the order of 10−5 cm2/s. Influence of the electron beam on electrochemical measurements was found to be negligible during CV scans where the current profile varied only within a few nA with the electron beam on and off, which is well within the hysteresis between multiple CV scans. The combination of experimental results provides a validation that quantitative electrochemistry experiments can be performed with these small-scale microfluidic electrochemical cells provided that accurate geometrical electrode configurations, diffusion boundary layers, and microfluidic conditions are accounted for.

Monochromated electron energy-loss spectroscopy (EELS) is employed to determine the optical properties of carbonaceous aerosols from the infrared to the ultraviolet region of the spectrum. It is essential to determine their optical properties to understand their accurate contribution to radiative forcing for climate change. The influence of surface and interface plasmon effects on the accuracy of dielectric data determined from EELS is discussed. Our measurements show that the standard thin film formulation of Kramers−Kronig analysis can be employed to make accurate determination of the dielectric function for carbonaceous particles down to about 40 nm in size. The complex refractive indices of graphitic and amorphous carbon spherules found in the atmosphere were determined over the wavelength range 200–1,200 nm. The graphitic carbon was strongly absorbing black carbon, whereas the amorphous carbon shows a more weakly absorbing brown carbon profile. The EELS approach provides an important tool for exploring the variation in optical properties of atmospheric carbon.

We present a deterministic approach to the ptychographic retrieval of the wave at the exit surface of a specimen of condensed matter illuminated by X-rays. The method is based on the solution of an overdetermined set of linear equations, and is robust to measurement noise. The set of linear equations is efficiently solved using the conjugate gradient least-squares method implemented using fast Fourier transforms. The method is demonstrated using a data set obtained from a gold–chromium nanostructured test object. It is shown that the transmission function retrieved by this linear method is quantitatively comparable with established methods of ptychography, with a large decrease in computational time, and is thus a good candidate for real-time reconstruction.

We discuss observations of InN nanowires (NWs) by plan-view high-resolution transmission electron microscopy (TEM). The main difficulties arise from suitable methods available for plan-view specimen preparation. We explore different approaches and find that the best results are obtained using a refined preparation method based on the conventional procedure for plan-view TEM of thin films, specifically modified for the NW morphology. The fundamental aspects of such a preparation are the initial mechanical stabilization of the NWs and the minimization of the ion-milling process after dimpling the samples until perforation. The combined analysis by plan-view and cross-sectional TEM of the NWs allows determination of the degree of strain relaxation and reveals the formation of an unintentional shell layer (2–3-nm thick) around the InN NWs. The shell layer is composed of bcc In2O3 nanocrystals with a preferred orientation with respect to the wurtzite InN: In2O3 [111] || InN [0001] and In2O3 <110> || InN< $$ 11\bar 20 $$ >.

Scanning transmission electron microscopy in scanning electron microscopy (STEM-in-SEM) is a convenient technique for soft materials characterization. Various specimen-holder geometries and detector arrangements have been used for bright-field (BF) STEM-in-SEM imaging. In this study, to further the characterization potential of STEM-IN-SEM, a new specimen holder has been developed to facilitate direct detection of BF signals and indirect detection of dark-field (DF) signals without the need for substantial instrument modification. DF imaging is conducted with the use of a gold (Au)-coated copper (Cu) plate attached to the specimen holder which directs highly scattered transmitted electrons to an off-axis yttrium-aluminum-garnet (YAG) detector. A hole in the copper plate allows for BF imaging with a transmission electron (TE) detector. The inclusion of an Au-coated Cu plate enhanced DF signal intensity. Experiments validating the acquisition of true DF signals revealed that atomic number (Z) contrast may be achieved for materials with large lattice spacing. However, materials with small lattice spacing still exhibit diffraction contrast effects in this approach. The calculated theoretical fine probe size is 1.8 nm. At 30 kV, in this indirect approach, DF spatial resolution is limited to 3.2 nm as confirmed experimentally.