Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures

Exploring guest species in zeolites using transmission electron microscopy: a review and outlook

Zeolites, with their well-defined microporous frameworks, accommodate diverse guest species, including metal ions, atoms, clusters, complexes, and organic molecules. Direct imaging of these species and their interactions with the framework is crucial for understanding their structural and functional roles. Transmission electron microscopy (TEM), particularly aberration-corrected scanning TEM (STEM), has become an indispensable tool, offering atomic-resolution real-space insights. This review summarizes key (S)TEM techniques for probing guest species in zeolites, with a focus on low-dose strategies to minimize beam damage. We discuss the principles, applications, and limitations of various imaging modalities and highlight recent advances in visualizing metallic and organic species. Finally, we explore future directions for (S)TEM in zeolite research, emphasizing the opportunities and challenges of in situ, three-dimensional, and cryogenic imaging for resolving host-guest interactions with greater precision.

Enhanced Imaging in Scanning Transmission X-Ray Microscopy Assisted by Ptychography

Scanning transmission X-ray microscopy (STXM) is a direct imaging technique with nanoscale resolution. But its resolution is limited by the spot size on the sample, i.e., by the manufacturing technique of the focusing element. As an emerging high-resolution X-ray imaging technique, ptychography utilizes highly redundant data from overlapping scans as well as phase retrieval algorithms to simultaneously reconstruct a high-resolution sample image and a probe function. In this study, we designed an accurate reconstruction strategy to obtain the probe spot with the vibration effects being eliminated, and developed an image enhancement technique for STXM by combining the reconstructed probe with the deconvolution algorithm. This approach significantly improves the resolution of STXM imaging and can break the limitation of the focal spot on STXM resolution when the scanning step size is near or below the spot size, while the data processing time is much shorter than that of ptychography. Both simulations and experiments show that this approach can be applied to STXM data at different energies and different scan steps using the same focal spot retrieved via ptychography.

Improved Three-Dimensional Reconstructions in Electron Ptychography through Defocus Series Measurements

A detailed analysis of ptychography for three-dimensional (3D) phase reconstructions of thick specimens is performed. We introduce multi-focus ptychography, which incorporates a 4D-STEM defocus series to enhance the quality of 3D reconstructions along the beam direction through a higher overdetermination ratio. This method is compared with established multi-slice ptychography techniques, such as conventional ptychography, regularized ptychography, and multi-mode ptychography. Additionally, we contrast multi-focus ptychography with an alternative method that uses virtual optical sectioning through a reconstructed scattering matrix (S-matrix), which offers more precise 3D structure information compared to conventional ptychography. Our findings from multiple 3D reconstructions based on simulated and experimental data demonstrate that multi-focus ptychography surpasses other techniques, particularly in accurately reconstructing the surfaces and interface regions of thick specimens.

Simulation Study of Low-Dose 4D-STEM Phase Contrast Techniques at the Nanoscale in SEM

Phase contrast imaging is well-suited for studying weakly scattering samples. Its strength lies in its ability to measure how the phase of the electron beam is affected by the sample, even when other imaging techniques yield low contrast. In this study, we explore via simulations two phase contrast techniques: integrated center of mass (iCOM) and ptychography, specifically using the extended ptychographical iterative engine (ePIE). We simulate the four-dimensional scanning transmission electron microscopy (4D-STEM) datasets for specific parameters corresponding to a scanning electron microscope (SEM) with an immersive objective and a given pixelated detector. The performance of these phase contrast techniques is analyzed using a contrast transfer function. Simulated datasets from a sample consisting of graphene sheets and carbon nanotubes are used for iCOM and ePIE reconstructions for two aperture sizes and two electron doses. We highlight the influence of aperture size, showing that for a smaller aperture, the radiation dose is spent mostly on larger sample features, which may aid in imaging sensitive samples while minimizing radiation damage.

Liquid Phase Electron Microscopy of Bacterial Ultrastructure

Recent advances in liquid phase scanning transmission electron microscopy (LP-STEM) have enabled the study of dynamic biological processes at nanometer resolutions, paving the way for live-cell imaging using electron microscopy. However, this technique is often hampered by the inherent thickness of whole cell samples and damage from electron beam irradiation. These restrictions degrade image quality and resolution, impeding biological interpretation. Using graphene encapsulation, scanning transmission electron microscopy (STEM), and energy-dispersive X-ray (EDX) spectroscopy to mitigate these issues provides unprecedented levels of intracellular detail in aqueous specimens. This study demonstrates the potential of LP-STEM to examine and identify internal cellular structures in thick biological samples. Specifically, it highlights the use of LP-STEM to investigate the radiation resistant, gram-positive bacterium, Deinococcus radiodurans using various imaging techniques.

X-Ray Multibeam Ptychography at up to 20 keV: Nano-Lithography Enhances X-Ray Nano-Imaging

Hard X-rays are needed for non-destructive nano-imaging of solid matter. Synchrotron radiation facilities (SRF) provide the highest-quality images with single-digit nm resolution using advanced techniques such as X-ray ptychography. However, the resolution or field of view is ultimately constrained by the available coherent flux. To address this, the beam's incoherent fraction can be exploited using multiple parallel beams in an X-ray multibeam ptychography (MBP) approach. This expands the domain of X-ray ptychography to larger samples or more rapid measurements. Both qualities favor the study of complex composite or functional samples, such as catalysts, energy materials, or electronic devices. The challenge of performing ptychography at high energy and with many parallel beams must be overcome to extract the full advantages for extended samples while minimizing beam attenuation. Here, that challenge is overcome by creating a lens array using cutting-edge laser printing technology and applying it to perform scanning with MBP with up to 12 beams and at photon energies of 13 and 20 keV. This exceeds the measurement limits of conventional hard X-ray ptychography without compromising image quality for various samples: Siemens star test pattern, Ni/Al2O3 catalyst, microchip, and gold nano-crystal clusters.

Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy

Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.

Local-orbital ptychography for ultrahigh-resolution imaging

Technical advances paired with developments in methodology have enabled electron microscopy to reach atomic resolution. Further improving the information limit in microscopic imaging requires further improvements in methodology. Here we report a ptychographic method that describes the object as the sum of discrete atomic-orbital-like functions (for example, Gaussian functions) and the probe in terms of aberration functions. Using this method, we realize an improved information limit of microscopic imaging, reaching down to 14 pm. High-quality probes and objects contribute to superior signal-to-noise ratios at low electron doses, allowing for relaxation of the sample thickness restriction to 50 nm for dense materials. Additionally, our method has the capability to decompose the total phase into element components, revealing that the information limit is element dependent. With enhanced spatial resolution, signal-to-noise ratio and thickness threshold compared with conventional ptychography methods, our local-orbital ptychography may find applications in atomic-resolution imaging of metals, ceramics, electronic devices or beam-sensitive material.

Achieving sub-0.5-angstrom-resolution ptychography in an uncorrected electron microscope

Subangstrom resolution has long been limited to aberration-corrected electron microscopy, where it is a powerful tool for understanding the atomic structure and properties of matter. Here, we demonstrate electron ptychography in an uncorrected scanning transmission electron microscope (STEM) with deep subangstrom spatial resolution down to 0.44 angstroms, exceeding the conventional resolution of aberration-corrected tools and rivaling their highest ptychographic resolutions​. Our approach, which we demonstrate on twisted two-dimensional materials in a widely available commercial microscope, far surpasses prior ptychographic resolutions (1 to 5 angstroms) of uncorrected STEMs. We further show how geometric aberrations can create optimized, structured beams for dose-efficient electron ptychography. Our results demonstrate that expensive aberration correctors are no longer required for deep subangstrom resolution.

Cryo-electron ptychography: Applications and potential in biological characterisation

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions. Using this method with increased information content from multiple sampled regions of interest potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution in systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations, and potential areas for future development of this approach for both single particle analysis and applications to heterogeneous large objects.

Solving complex nanostructures with ptychographic atomic electron tomography

Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50 structure containing a previously unobserved ZrTe2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.

A general image misalignment correction method for tomography experiments

Tomography experiments generate three-dimensional (3D) reconstructed slices from a series of two-dimensional (2D) projection images. However, the mechanical system generates joint offsets that result in unaligned 2D projections. This misalignment affects the reconstructed images and reduces their actual spatial resolution. In this study, we present a novel method called outer contour-based misalignment correction (OCMC) for correcting image misalignments in tomography. We use the sample's outer contour structure as auxiliary information to estimate the extent of misalignment in each image. This method is generic and can be used with various tomography imaging techniques. We validated our method with five datasets collected from different samples and across various tomography techniques. The OCMC method demonstrated significant advantages in terms alignment accuracy and time efficiency. As an end-to-end correction method, OCMC can be easily integrated into an online tomography data processing pipeline and facilitate feedback control in future synchrotron tomography experiments.

Applications of Transmission Electron Microscopy in Phase Engineering of Nanomaterials

Phase engineering of nanomaterials (PEN) is an emerging field that aims to tailor the physicochemical properties of nanomaterials by precisely manipulating their crystal phases. To advance PEN effectively, it is vital to possess the capability of characterizing the structures and compositions of nanomaterials with precision. Transmission electron microscopy (TEM) is a versatile tool that combines reciprocal-space diffraction, real-space imaging, and spectroscopic techniques, allowing for comprehensive characterization with exceptional resolution in the domains of time, space, momentum, and, increasingly, even energy. In this Review, we first introduce the fundamental mechanisms behind various TEM-related techniques, along with their respective application scopes and limitations. Subsequently, we review notable applications of TEM in PEN research, including applications in fields such as metallic nanostructures, carbon allotropes, low-dimensional materials, and nanoporous materials. Specifically, we underscore its efficacy in phase identification, composition and chemical state analysis, in situ observations of phase evolution, as well as the challenges encountered when dealing with beam-sensitive materials. Furthermore, we discuss the potential generation of artifacts during TEM imaging, particularly in scanning modes, and propose methods to minimize their occurrence. Finally, we offer our insights into the present state and future trends of this field, discussing emerging technologies including four-dimensional scanning TEM, three-dimensional atomic-resolution imaging, and electron microscopy automation while highlighting the significance and feasibility of these advancements.

Three-dimensional inhomogeneity of zeolite structure and composition revealed by electron ptychography

Structural and compositional inhomogeneity is common in zeolites and considerably affects their properties. Thickness-limited lateral resolution, lack of depth resolution, and electron dose-constrained focusing limit local structural studies of zeolites in conventional transmission electron microscopy (TEM). We demonstrate that a multislice ptychography method based on four-dimensional scanning TEM (4D-STEM) data can overcome these limitations. Images obtained from a ~40-nanometer-thick MFI zeolite exhibited a lateral resolution of ~0.85 angstrom that enabled the identification of individual framework oxygen (O) atoms and the precise determination of the orientations of adsorbed molecules. Furthermore, a depth resolution of ~6.6 nanometers allowed probing of the three-dimensional distribution of O vacancies, as well as the phase boundaries in intergrown MFI and MEL zeolites. The 4D-STEM ptychography can be generally applied to other materials with similar high electron-beam sensitivity.

Initial probe function construction in ptychography based on zone-plate optics

X-ray ptychography is a popular variant of coherent diffraction imaging that offers ultrahigh resolution for extended samples. In x-ray ptychography instruments, the Fresnel zone-plate (FZP) is the most commonly used optical probe system for both soft x-ray and hard x-ray. In FZP-based ptychography with a highly curved defocus probe wavefront, the reconstructed image quality can be significantly impacted by the initial probe function form, necessitating the construction of a suitable initial probe for successful reconstruction. To investigate the effects of initial probe forms on FZP-based ptychography reconstruction, we constructed four single-mode initial probe models (IPMs) and three multi-mode IPMs in this study, and systematically compared their corresponding simulated and experimental reconstructions. The results show that the Fresnel IPM, spherical IPM, and Fresnel-based multi-mode IPMs can result in successful reconstructions for both near-focus and defocus cases, while random IPMs and constant IPMs work only for near-focus cases. Consequently, for FZP-based ptychography, the elaborately constructed IPMs that closely resemble real probes in wavefront phase form are more advantageous than natural IPMs such as the random or constant model. Furthermore, these IPMs with high phase similarity to the high-curvature large-sized probe adopted in experiments can help greatly improve ptychography experiment efficiency and decrease radiation damage to samples.

Ptychographic measurements of varying size and shape along zeolite channels

Sub-angstrom resolution imaging of porous materials like zeolites is important to reveal their structure-property relationships involved in ion exchange, molecule adsorption and separation, and catalysis. Using multislice electron ptychography, we successfully measured the atomic structure of zeolite at sub-angstrom lateral resolution for 100-nanometer-thick samples. Both lateral and depth deformations of the straight channels are mapped, showing the three-dimensional structural inhomogeneity and flexibility. Since most zeolites in industrial applications are usually tens to hundreds of nanometers thick, the sub-angstrom resolution imaging and accurate measurements of depth-dependent local structures with electron ptychography at low-dose condition will find wide applications in porous materials close to their industrially relevant conditions.