Optimizing Contrast in Automated 4D STEM Cryotomography.

4D STEM is an emerging approach to electron microscopy. While it was developed principally for high-resolution studies in materials science, the possibility to collect the entire transmitted flux makes it attractive for cryomicroscopy in application to life science and radiation-sensitive materials where dose efficiency is of utmost importance. We present a workflow to acquire tomographic tilt series of 4D STEM data sets using a segmented diode and an ultrafast pixelated detector, demonstrating the methods using a specimen of a T4 bacteriophage. Full integration with the SerialEM platform conveniently provides all the tools for grid navigation and automation of the data collection. Scripts are provided to convert the raw data to mrc format files and further to generate a variety of modes representing both scattering and phase contrasts, including incoherent and annular bright field, integrated center of mass, and parallax decomposition of a simulated integrated differential phase contrast. Principal component analysis of virtual annular detectors proves particularly useful, and axial contrast is improved by 3D deconvolution with an optimized point spread function. Contrast optimization enables visualization of irregular features such as DNA strands and thin filaments of the phage tails, which would be lost upon averaging or imposition of an inappropriate symmetry.

DFT-Assisted Investigation of the Electric Field and Charge Density Distribution of Pristine and Defective 2D WSe2 by Differential Phase Contrast Imaging.

Most properties of solid materials are defined by their internal electric field and charge density distributions which so far are difficult to measure with high spatial resolution. Especially for 2D materials, the atomic electric fields influence the optoelectronic properties. In this study, the atomic-scale electric field and charge density distribution of WSe2 bi- and trilayers are revealed using an emerging microscopy technique, differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). For pristine material, a higher positive charge density located at the selenium atomic columns compared to the tungsten atomic columns is obtained and tentatively explained by a coherent scattering effect. Furthermore, the change in the electric field distribution induced by a missing selenium atomic column is investigated. A characteristic electric field distribution in the vicinity of the defect with locally reduced magnitudes compared to the pristine lattice is observed. This effect is accompanied by a considerable inward relaxation of the surrounding lattice, which according to first principles DFT calculation is fully compatible with a missing column of Se atoms. This shows that DPC imaging, as an electric field sensitive technique, provides additional and remarkable information to the otherwise only structural analysis obtained with conventional STEM imaging.

Single-shot differential phase contrast microscopy using ring-shaped polarisation multiplexing illumination.

We propose a differential phase contrast microscopy that enables single-shot phase imaging for unstained biological samples. The proposed approach employs a ring-shaped LED array for polarisation multiplexing illumination and a polarisation camera for image acquisition. As such, multiple images of different polarisation angles can be simultaneously captured with a single shot. Through polarisation demultiplexing, the sample phase can therefore be recovered from the single-shot measurement. Both simulations and experiments demonstrate the effectiveness of the approach. We also demonstrate that ring-shaped illumination enables higher contrast and lower-distortion imaging results than disk-shaped illumination does. The proposed single-shot approach potentially enables phase contrast imaging for live cell samples in vitro. Lay Description: We propose a microscopy that enables imaging of transparent samples, unstained cells, etc. We demonstrate that the proposed method enables higher contrast and lower-distortion imaging results than conventional methods, and significantly improves imaging efficiency. The proposed method potentially enables dynamic imaging for live cell samples in vitro.

Measuring electrical properties in semiconductor devices by pixelated STEM and off-axis electron holography (or convergent beams vs. plane waves).

We demonstrate the use of both pixelated differential phase contrast (DPC) scanning transmission electron microscopy (STEM) and off-axis electron holography (EH) for the measurement of electric fields and assess the advantages and limitations of each technique when applied to technologically relevant samples. Three different types of samples are examined, firstly a simple highly-doped Si pn junction. Then a SiGe superlattice is examined to evaluate the effects of the mean inner potential on the measured signal. Finally, an InGaN/GaN microwire light-emitting diode (LED) device is examined which has a polarization field, variations of mean inner potential and a wurtzite crystal lattice. We discuss aspects such as spatial resolution and sensitivity, and the concept of pseudo-field is defined. However, the most important point is the need to limit the influence of diffraction contrast to obtain accurate measurements. In this respect, the use of a plane electron wave for EH is clearly beneficial when compared to the use of a convergent beam for pixelated DPC STEM.

Simulated Guidance in Interpreting Nano-Patterned Co70Fe30 Film Imaging with Differential Phase Contrast.

Our paper introduces a simulation-based framework designed to interpret differential phase contrast (DPC) magnetic imaging within the transmission electron microscope (TEM). We investigate patterned magnetic membranes, particularly focusing on nano-patterned Co70Fe30 thin-film membranes fabricated via focused ion beam (FIB) milling. Our direct magnetic imaging reveals regular magnetic domain patterns in these carefully prepared systems. Notably, the observed magnetic structure aligns precisely with micromagnetic simulations based on the dimensions of the underlying nanostructures. This agreement emphasizes the usefulness of micromagnetic simulations, not only for the interpretation of DPC data, but also for the prediction of possible microstructures in magnetic sensor systems with nano-patterns.

Improving Magnetic STEM-Differential Phase Contrast Imaging using Precession.

Differential phase contrast in scanning transmission electron microscopy (STEM-DPC) is a technique used to image electromagnetic fields in materials. STEM-DPC is based on tracking the minute changes in the position of the bright-field disk, so any effects which cause inhomogeneities in the intensity or geometry of the disk can lead to the contrast from the electromagnetic fields to be obscured. Structural changes, like grain boundaries, thickness variations, or local crystallographic orientation, are a major cause of these inhomogeneities. In this paper, we present how precession of the STEM probe with the objective lens turned off, providing a near field-free environment for magnetic imaging, can average out nonsystematic inhomogeneities in the electron beam. The methodology was tested on a polycrystalline Fe60Al40 thin film with embedded ferromagnetic structures. The effect of precession was assessed on magnetic induction maps created by three different processing algorithms. Results demonstrate that precessed STEM-DPC with the objective lens turned off shows an improvement in the form of smoothing of the variations found in the DPC signal arising from the underlying polycrystalline background.

Differential phase contrast for quantitative imaging and spectro-microscopy at a nanoprobe beamline.

The interaction of a focused X-ray beam with a sample in a scanning probe experiment can provide a variety of information about the interaction volume. In many scanning probe experiments X-ray fluorescence (XRF) is supplemented with measurements of the transmitted or scattered intensity using a pixelated detector. The automated extraction of different signals from an area pixelated detector is described, in particular the methodology for extracting differential phase contrast (DPC) is demonstrated and different processing methods are compared across a range of samples. The phase shift of the transmitted X-ray beam by the sample, extracted from DPC, is also compared with ptychography measurements to provide a qualitative and quantitative comparison. While ptychography produces a superior image, DPC can offer a simple, flexible method for phase contrast imaging which can provide fast results and feedback during an experiment; furthermore, for many science problems, such as registration of XRF in a lighter matrix, DPC can provide sufficient information to meet the experimental aims. As the DPC technique is a quantitative measurement, it can be expanded to spectroscopic studies and a demonstration of DPC for spectro-microscopy measurements is presented. Where ptychography can separate the absorption and phase shifts by the sample, quantitative interpretation of a DPC image or spectro-microscopy signal can only be performed directly when absorption is negligible or where the absorption contribution is known and the contributions can be fitted.

Retinex-qDPC: Automatic background-rectified quantitative differential phase contrast imaging.

BACKGROUND AND OBJECTIVE: The quality of quantitative differential phase contrast reconstruction (qDPC) can be severely degenerated by the mismatch of the background of two oblique illuminated images, yielding problematic phase recovery results. These background mismatches may result from illumination patterns, inhomogeneous media distribution, or other defocusing layers. In previous reports, the background is manually calibrated which is time-consuming, and unstable, since new calibrations are needed if any modification to the optical system was made. It is also impossible to calibrate the background from the defocusing layers, or for high dynamic observation as the background changes over time. The background mismatch reduces the experimental robustness of qDPC and largely limits its applications. To tackle the mismatch of background and increases the experimental robustness, we propose the Retinex-qDPC. METHODS: In Retinex-qDPC, we replace the data fidelity term of the previous cost function for qDPC inverse problem, by the images' edge features yielding L2-Retinex-qDPC and L1-Retinex-qDPC for high background-robustness qDPC reconstruction. The split Bregman method is used to solve the L1-Retinex DPC. We compare both Retinex-qDPC models against state-of-the-art DPC reconstruction algorithms including total-variation regularized qDPC, and isotropic-qDPC using both simulated and experimental data. RESULTS: Retinex qDPC can significantly improve the phase recovery quality by suppressing the impact of mismatch background. Within, the L1-Retinex-qDPC is better than L2-Retinex and other state-of-the-art qDPC algorithms. CONCLUSIONS: The Retinex-qDPC increases the experimental robustness against background illumination without any modification of the optical system, which will benefit all qDPC applications.

Diffracted beam interferometry - Differential phase contrast image of an amorphous thin film material.

Differential phase contrast based on diffracted beam interferometry is used to explain the good phase contrast found of an amorphous thin film material deposited on the surface of a gold (Au) crystal substrate. An electron biprism is used to interfere two symmetrically diffracted beams generated by the Au crystal substrate that carried the phase of the amorphous material specimen. Bragg diffraction from the Au crystal substrate is used to explain why the phase of the amorphous thin film material is so well phase imaged. The phase of the amorphous material that was deposited on the specimen's upper surface of the Au crystal substrate is canceled and thus not revealed in the phase image whereas the phase due to the amorphous material deposited on the bottom surface of the Au crystal substrate does not cancel due to having a lateral phase shift in the amorphous material specimen plane proportional to the substrate thickness and Bragg angle of the diffracted beams. The lateral phase shift enabled differential phase contrast of the amorphous material specimen.

Morphology analysis of unlabeled red blood cells based on quantitative differential phase contrast microscopy.

The current classical blood smear technique to observe the morphology of single red blood cells (RBCs) for classification is a laborious and error-prone process. To objectively evaluate the morphology of blood cells, we established a method of computational imaging based on a programmable light emitting diode array. By using quantitative differential phase contrast (qDPC), we characterized the morphology of unlabeled RBCs as well as blood smears. By focusing on comparing the difference of imaging between unlabeled RBCs and stained RBCs under multimode microscopic imaging technology, we demonstrated that qDPC could clearly differentiate discocytes and spherocytes in both unlabeled RBCs and blood smears. The phase map provided by quantitative phase imaging further enhanced the classification accuracy. According to statistical analysis from morphological indexes, the qDPC imaging has a significantly improvement in non-circularity, texture inhomogeneity and equivalent diameters of cells. Thus, this method has a significant superiority in the capability to analyze the morphology of RBCs and could be applied to clinical assays for determining morphological, functional, and structural deterioration of RBCs.

Integrated Differential Phase Contrast (IDPC)-STEM Utilizing a Multi-Sector Detector for Imaging Thick Samples.

The integrated differential phase contrast (IDPC) method is useful for generating the potential map of a thin sample. We evaluate theoretically the potential of IDPC imaging for thick samples by varying the focus at different sample thicknesses. Our calculations show that high defocus values result in enhanced anisotropy of the contrast transfer function (CTF) and uninterpretable images, if a quadrant detector is applied. We further show that applying a multi-sector detector can result in an almost isotropic CTF. By sector number-dependent calculations for both Cc/C3-corrected and C3-corrected scanning transmission electron microscopy (STEM), we show that the increase of detector sectors not only removes the anisotropy of the CTF, but also improves image contrast and resolution. For a proof-of-principle IDPC-STEM (uncorrected) experiment, we realize the functionality of a 12-sector detector from a physical quadrant detector and demonstrate the improvement in contrast and resolution on the example of InGaN/GaN quantum well structure.

Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique.

Scanning transmission electron microscopy (STEM) is a powerful imaging technique and has been widely used in current material science research. The attempts of applying STEM (annual dark field (ADF)-STEM or annular bright field (ABF)-STEM) into biological research have been going on for decades while applications have still been limited because of the existing bottlenecks in dose efficiency and non-linearity in contrast. Recently, integrated differential phase contrast (iDPC) STEM technique emerged and achieved a linear phase contrast imaging condition, while resolving signals of light elements next to heavy ones even at low electron dose. This enables successful investigation of beam sensitive materials. Here, we investigate iDPC-STEM advantages in biology, in particular, chemically fixed and resin embedded biological tissues. By comparing results to the conventional TEM, we have found that iDPC-STEM not only shows better contrast but also resolves more structural details at molecular level, including conditions of extremely low dose and minimal heavy-atom staining. We also compare iDPC-STEM with ABF-STEM and found that contrast of iDPC-STEM is even further improved, moderately in lower frequency domains while highly with preserving high frequency biological structural details. For thick sample sections, iDPC-STEM is particularly advantageous. It avoids contrast inversion canceling effects, and by adjusting the depth of focus, fully preserves the contrast of structural details along with the sample. In addition, using depth-sectioning, iDPC-STEM enables resolving in-depth structural variation. Our results suggest that iDPC-STEM have the place and advantages within the future biological research.

Robust Atomic-Resolution Imaging of Lithium in Battery Materials by Center-of-Mass Scanning Transmission Electron Microscopy.

The performance of energy storage materials is often governed by their structure at the atomic scale. Conventional electron microscopy can provide detailed information about materials at these length scales, but direct imaging of light elements such as lithium presents a challenge. While several recent techniques allow lithium columns to be distinguished, these typically either involve complex contrast mechanisms that make image interpretation difficult or require significant expertise to perform. Here, we demonstrate how center-of-mass scanning transmission electron microscopy (CoM-STEM) provides an enhanced ability for simultaneous imaging of lithium and heavier element columns in lithium ion conductors. Through a combination of experiments and multislice electron scattering calculations, we show that CoM-STEM is straightforward to perform and produces directly interpretable contrast for thin samples, while being more robust to variations in experimental parameters than previously demonstrated techniques. As a result, CoM-STEM is positioned to become a reliable and facile method for directly probing all elements within energy storage materials at the atomic scale.

Performance evaluation of dual-energy CT and differential phase contrast CT in quantitative imaging applications.

PURPOSE: The purpose of this study is to evaluate and compare the quantitative material decomposition performance of the dual-energy CT (DECT) and differential phase contrast CT (DPCT) via numerical observer studies. METHODS: The electron density ( ρ e $\rho _{{\rm e}}$ ) and the effective atomic number ( Z eff $Z_{{\rm eff}}$ ) are selected as the decomposition bases. The image domain based decomposition algorithms with certain noise suppression are used to extract the ρ e $\rho _{{\rm e}}$ and Z eff $\text{Z}_{{\rm eff}}$ information under three different spatial resolutions (0.3 mm, 0.1 mm, and 0.03 mm). The contrast-to-noise-ratio (CNR) and the numerical human observer model which is sensitive to the noise textures are investigated to compare the quantitative imaging performance of DECT and DPCT under varied radiation dose levels. RESULTS: The model observer results show that the DECT is superior to DPCT at 0.3 mm spatial resolution (300 mm object size); the DECT and DPCT show similar quantitative imaging performance at 0.1 mm spatial resolution (100 mm object size); and the DPCT outperforms the DECT by approximately 1.5 times for the 0.3 mm sized imaging target at 0.03 mm spatial resolution (30 mm object size). CONCLUSIONS: In conclusion, the DECT would be recommended to obtain ρ e $\rho _{{\rm e}}$ and Z eff $Z_{{\rm eff}}$ for the low spatial resolution quantitative imaging applications such as the diagnostic CT imaging. Whereas, the DPCT would be recommended for ultra high spatial resolution imaging tasks of small objects such as the micro-CT imaging. This study provides a reference to determine the most appropriate quantitative X-ray CT imaging method for a certain radiation dose level.

Atomic Electrostatic Maps of Point Defects in MoS2.

In this study, we use differential phase contrast images obtained by scanning transmission electron microscopy combined with computer simulations to map the atomic electrostatic fields of MoS2 monolayers and investigate the effect of sulfur monovacancies and divancancies on the atomic electric field and total charge distribution. A significant redistribution of the electric field in the regions containing defects is observed, with a progressive decrease in the strength of the projected electric field for each sulfur atom removed from its position. The electric field strength at the sulfur monovacancy sites is reduced by approximately 50% and nearly vanishes at the divacancy sites, where it drops to around 15% of the original value, demonstrating the tendency of these defects to attract positively charged ions or particles. In addition, the absence of the sulfur atoms leads to an inversion in the polarity of the total charge distribution in these regions.

Reprint of: Automated geometric aberration correction for large-angle illumination STEM.

Depth resolution in scanning transmission electron microscopy (STEM) is physically limited by the illumination angle. In recent notable progress on aberration correction technology, the illumination angle is significantly improved to be larger than 60 milliradians, which is 2 or 3 times larger than those in the previous generation. However, for three-dimensional depth sectioning with the large illumination angles, it is prerequisite to ultimately minimize lower orders of aberrations such as 2- and 3-fold astigmatisms and axial coma. Here, we demonstrate a live aberration correction using atomic-resolution STEM images rather than Ronchigram images. The present method could save the required time for aberration correction, and moreover, it is possible to build up a fully automated program. We demonstrate the method should be useful not only for axial depth sectioning but also phase imaging in STEM including differential phase-contrast imaging.

Signal Retrieval from Non-Sinusoidal Intensity Modulations in X-ray and Neutron Interferometry Using Piecewise-Defined Polynomial Function.

Grating-based phase-contrast and dark-field imaging systems create intensity modulations that are usually modeled with sinusoidal functions to extract transmission, differential-phase shift, and scatter information. Under certain system-related conditions, the modulations become non-sinusoidal and cause artifacts in conventional processing. To account for that, we introduce a piecewise-defined periodic polynomial function that resembles the physical signal formation process, modeling convolutions of binary periodic functions. Additionally, we extend the model with an iterative expectation-maximization algorithm that can account for imprecise grating positions during phase-stepping. We show that this approach can process a higher variety of simulated and experimentally acquired data, avoiding most artifacts.

Flexible STEM with Simultaneous Phase and Depth Contrast.

Recent advances in scanning transmission electron microscopy (STEM) have rekindled interest in multi-channel detectors and prompted the exploration of unconventional scan patterns. These emerging needs are not yet addressed by standard commercial hardware. The system described here incorporates a flexible scan generator that enables exploration of low-acceleration scan patterns, while data are recorded by a scalable eight-channel array of nonmultiplexed analog-to-digital converters. System integration with SerialEM provides a flexible route for automated acquisition protocols including tomography. Using a solid-state quadrant detector with additional annular rings, we explore the generation and detection of various STEM contrast modes. Through-focus bright-field scans relate to phase contrast, similarly to wide-field TEM. More strikingly, comparing images acquired from different off-axis detector elements reveals lateral shifts dependent on defocus. Compensation of this parallax effect leads to decomposition of integrated differential phase contrast (iDPC) to separable contributions relating to projected electric potential and to defocus. Thus, a single scan provides both a computationally refocused phase contrast image and a second image in which the signed intensity, bright or dark, represents the degree of defocus.

Two-dimensional characterization of three-dimensional magnetic bubbles in Fe3Sn2 nanostructures.

We report differential phase contrast scanning transmission electron microscopy (TEM) of nanoscale magnetic objects in Kagome ferromagnet Fe3Sn2 nanostructures. This technique can directly detect the deflection angle of a focused electron beam, thus allowing clear identification of the real magnetic structures of two magnetic objects including three-ring and complex arch-shaped vortices in Fe3Sn2 by Lorentz-TEM imaging. Numerical calculations based on real material-specific parameters well reproduced the experimental results, showing that the magnetic objects can be attributed to integral magnetizations of two types of complex three-dimensional (3D) magnetic bubbles with depth-modulated spin twisting. Magnetic configurations obtained using the high-resolution TEM are generally considered as two-dimensional (2D) magnetic objects previously. Our results imply the importance of the integral magnetizations of underestimated 3D magnetic structures in 2D TEM magnetic characterizations.

Spatial Mapping of Electrostatic Fields in 2D Heterostructures.

In situ electron microscopy is an effective tool for understanding the mechanisms driving novel phenomena in 2D structures. However, due to practical challenges, it is difficult to address these technologically relevant 2D heterostructures with electron microscopy. Here, we use the differential phase contrast (DPC) imaging technique to build a methodology for probing local electrostatic fields during electrical operation with nanoscale spatial resolution in such materials. We find that, by combining a traditional DPC setup with a high-pass filter, we can largely eliminate electric fluctuations emanating from short-range atomic potentials. Using a method based on this filtering algorithm, a priori electric field expectations can be directly compared with experimentally derived values to readily identify inhomogeneities and potentially problematic regions. We use this platform to analyze the electric field and charge density distribution across layers of hBN and MoS2.