Scanning transmission electron microscopy (STEM) is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric domain walls, extended defects, or second phase inclusions. Selecting regions to image for structural and chemical discovery via atomically resolved imaging has traditionally proceeded via human operators making semi-informed judgements on sampling locations and parameters. Recent efforts at automation for structural and physical discovery have pointed towards the use of "active learning" methods that utilize Bayesian optimization with surrogate models to quickly find relevant regions of interest. Yet despite the potential importance of this direction, there is a general lack of certainty in selecting relevant control algorithms and how to balance a priori knowledge of the material system with knowledge derived during experimentation. Here we address this gap by developing the automated experiment workflows with several combinations to both illustrate the effects of these choices and demonstrate the tradeoffs associated with each in terms of accuracy, robustness, and susceptibility to hyperparameters for structural discovery. We discuss possible methods to build descriptors using the raw image data and deep learning based semantic segmentation, as well as the implementation of variational autoencoder based representation. Furthermore, each workflow is applied to a range of feature sizes including NiO pillars within a La:SrMnO$_3$ matrix, ferroelectric domains in BiFeO$_3$, and topological defects in graphene. The code developed in this manuscript are open sourced and will be released at github.com/creangnc/AE_Workflows.
Sample thickness is an important parameter in transmission electron microscopy (TEM) imaging, for interpreting image contrast and understanding the relationship between properties and microstructure. In this study, we introduce a method for determining thickness in scanning transmission electron microscopy (STEM) mode based on scanning moiré fringe (SMF). Sample thickness can be determined in situ in the medium magnification using focal-series SMF imaging, with beam damage and contamination avoided to a large extent. This method provides a fast and convenient way for determining thickness in T…
Electronic conduction pathways in dielectric thin films are explored using automated experiments in scanning probe microscopy (SPM). Here, we use large field of view scanning to identify the position of localized conductive spots and develop a SPM workflow to probe their dynamic behavior at higher spatial resolution as a function of time, voltage, and scanning process in an automated fashion. Using this approach, we observe the variable behaviors of the conductive spots in a 20 nm thick ferroelectric Hf0.54Zr0.48O2 film, where conductive spots disappear and reappear during continuous scanning.…
Unwanted motion of the probe with respect to the sample is a ubiquitous problem in scanning probe microscopy, causing both linear and nonlinear artifacts in experimental images. We have designed a procedure to correct these artifacts by using orthogonal scan pairs to align each measurement line-by-line along the slow scan direction. We demonstrate the accuracy of our algorithm on both synthetic and experimental data and provide an implementation of our method.
We present numerical simulations of scattering-type Scanning Near-Field Optical Microscopy (s-SNOM) of 1D plasmonic graphene junctions. A comprehensive analysis of simulated s-SNOM spectra is performed for three types of junctions. We find conditions when the conventional interpretation of the plasmon reflection coefficients from s-SNOM measurements does not apply. Our results are applicable to other conducting 2D materials and provide a comprehensive understanding of the s-SNOM techniques for probing local transport properties of 2D materials.
Atomically resolved images of monolayer organic crystals have only been obtained with scanning probe methods so far. On the one hand, they are usually prepared on surfaces of bulk materials, which are not accessible by (scanning) transmission electron microscopy. On the other hand, the critical electron dose of a monolayer organic crystal is orders of magnitudes lower than the one for bulk crystals, making (scanning) transmission electron microscopy characterization very challenging. In this work we present an atomically resolved study on the dynamics of a monolayer CuPcCl\textsubscript{16} cr…
In this study, we have used a Zr-Nb alloy containing well-defined nano-precipitates as a model material in which to study imaging contrast inversions (atomic number or diffraction contrast) observed with the forescattered electron imaging system, ARGUSTM, in a scanning electron microscope (SEM) when imaging a thin foil in a transmission geometry. The study is based on Monte Carlo simulations and analysis of micrographs experimentally acquired under different imaging conditions. Based on the results, imaging conditions that enhance atomic number or diffraction contrast have been proposed. Data …
We present a theory and a simulation of thermal diffuse scattering due to the excitation of magnons in scanning transmission electron microscopy. The calculations indicate that magnons can present atomic contrast when detected by electron energy-loss spectroscopy using atomic-size electron beams. The results presented here indicate that the intensity of the magnon diffuse scattering in bcc iron at 300~K is 4 orders of magnitude weaker than the intensity of thermal diffuse scattering arising from atomic vibrations. In an energy range where the phonon and magnon dispersions do not overlap, a mon…
We predict the occurrence of metastable skyrmionic spin structures such as antiskyrmions and higher-order skyrmions in ultra-thin transition-metal films at surfaces using Monte Carlo simulations based on a spin Hamiltonian parametrized from density functional theory calculations. We show that such spin structures will appear with a similar contrast in spin-polarized scanning tunneling microscopy (SP-STM) images. Both skyrmions and antiskyrmions display a circular shape for out-of-plane magnetized tips and a two-lobe butterfly contrast for in-plane tips. An unambiguous distinction can be achiev…
Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor $f$ that has typical values of 4-20 for atomic resolution simulations. We show that in many cases PRISM can provide a speedup that scales with $f^4$ compared to multislice simulations, with a negligible loss of acc…
Ag atoms have been deposited on 3x3 silicene and R3xR3 silicene films by molecular beam epitaxy method in ultrahigh vacuum. Using scanning tunneling microscopy and Raman spectroscopy, we found that Ag atoms do not form chemical bonds with both 3x3 silicene and R3xR3 silicene films,which is due to chemically inert surface of silicene. On 3x3 silicene films, Ag atoms mostly form into stable flat top Ag islands. In contrast, Ag atoms form nanoclusters and glide on silicene films, suggesting more inert nature. Raman spectroscopy suggests that there is more sp2 hybridization in R3xR3 than in R7xR7/…
We show that a scanning capacitance microscope (SCM) can image buried delta-doped donor nanostructures fabricated in Si via a recently developed atomic-precision scanning tunneling microscopy (STM) lithography technique. A critical challenge in completing atomic-precision nanoelectronic devices is to accurately align mesoscopic metal contacts to the STM defined nanostructures. Utilizing the SCMs ability to image buried dopant nanostructures, we have developed a technique by which we are able to position metal electrodes on the surface to form contacts to underlying STM fabricated donor nanostr…
We propose a new analysis approach for scanning transmission electron microscopy (STEM) based on the Voronoi-cell integration method to determine the three-dimensional position of the InZn and VZn defect complex in ZnO. Using state of the art simulation software and hardware, we propose using a method of calculating Michelson Contrast on simulated images to determine the optimal acceptance angles to use in an experimental setting. The effect of defect position, DFT-relaxation and cooling the sample to liquid nitrogen temperatures is investigated. DFT-relaxation is shown to be of consequence to…
PICTS: A Novel Deep Reinforcement Learning Approach for Dynamic P-I Control in Scanning Probe Microscopy
National University of Singapore（新加坡国立大学）；Institute of Materials Research and Engineering, Agencies of Science, Technology and Research (A*STAR)（新加坡科技研究局材料研究与工程研究所）；NUS Research Institute (NUSRI)（新加坡国立大学研究院）
Complex oxide interfaces have been one of the central focuses in condensed matter physics and material science. Over the past decade, aberration corrected scanning transmission electron microscopy and spectroscopy has proven to be invaluable to visualize and understand the emerging quantum phenomena at an interface. In this paper, we briefly review some recent progress in the utilization of electron microscopy to probe interfaces. Specifically, we discuss several important challenges for electron microscopy to advance our understanding on interface phenomena, from the perspective of variable t…
Here a new microscopic method is proposed to image and characterize very thin samples like few-layer materials, organic molecules, and nanostructures with nanometer or sub-nanometer resolution using electron beams of energies lower than 20 eV. The microscopic technique achieves high resolution through the proximity (or near-field) effect, as in scanning tunneling microscopy (STM), while it also allows detection of transmitted electrons for imaging and spectroscopy, as in scanning transmission electron microscopy (STEM). This proximity transmission electron microscopy (PSTEM) does not require a…
We apply high resolution scanning tunneling microscopy to study intrinsic defect states of bulk FeSe. Four types of intrinsic defects including the type I dumbbell, type II dumbbell, top-layer Se vacancy and inner-layer Se-site defect are extensively analyzed by scanning tunneling spectroscopy. From characterized depression and enhancement of density of states measured in a large energy range, the type I dumbbell and type II dumbbell are determined to be the Fe vacancy and Se$_\mathrm{Fe}$ defect, respectively. The top-layer Se vacancy and possible inner-layer Se-site vacancy are also determin…
A sparse modeling approach is proposed for analyzing scanning tunneling microscopy topography data, which contains numerous peaks corresponding to surface atoms. The method, based on the relevance vector machine with $\mathrm{L}_1$ regularization and $k$-means clustering, enables separation of the peaks and atomic center positioning with accuracy beyond the resolution of the measurement grid. The validity and efficiency of the proposed method are demonstrated using synthetic data in comparison to the conventional least-square method. An application of the proposed method to experimental data o…
We show that scanning electron microscopy with polarization analysis (SEMPA) that is sensitive to both in-plane magnetization components can be used to image the out-of-plane magnetized multi-domain state in multilayered chiral spin textures. By depositing a thin layer of Fe on top of the multilayer we image the underlying out-of-plane domain state through the mapping of its stray fields in the Fe. We also demonstrate that SEMPA can be used to image the domain wall chirality in these systems after milling away the capping layer and imaging the topmost magnetic layer directly.
A universal challenge facing the development of electrochemical materials is our lack of understanding of physical and chemical processes at local length scales in 10-100 nm regime, and acquiring this understanding requires a new generation of imaging techniques. In this article, we introduce the scanning thermo-ionic microscopy (STIM) for probing local electrochemistry at the nanoscale, using for imaging the Vegard strain induced via thermal stress excitations. Since ionic oscillation is driven by the stress instead of voltage, the responses are insensitive to the electromechanical, electrost…
