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Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging

NanoPSD: A software for automatic detection of Nano-Particle Shape Distribution in electron microscopy images

Accurate quantification of the size and morphology of nanoparticles from electron microscopy (EM) images is essential to understand growth mechanisms, surface reactivity, and functional behavior in nanoscale materials. Manual analysis remains slow, subjective, and difficult to reproduce in large datasets. We introduce NanoPSD (Nano-Particle Shape Distribution), an open-source and fully automated framework for quantitative particle detection and morphology analysis from EM images. NanoPSD integrates adaptive contrast enhancement, polarity-agnostic scale-bar detection, Optical Character Recognition (OCR)-based calibration, and classical segmentation via Otsu thresholding with morphological refinement. Particle contours are used to extract geometric descriptors, including equivalent circular diameter, aspect ratio, circularity, and solidity, enabling automated classification into spherical, rod-like, and aggregate morphologies. The framework supports both single-image and batch processing, generating publication-quality visualizations, LaTeX-ready tables, and structured comma-separated values (CSV) datasets. As a demonstration, we applied NanoPSD to plasma-synthesized nanoparticle samples diagnosed via transmission electron microscopy (TEM). The code produced statistically robust size and morphology distributions spanning a few to tens of nanometers with minimal user supervision. The pipeline demonstrates high reproducibility and scalability, processing large image collections with consistent calibration and output formatting. Its modular design enables seamless integration of future deep-learning-based segmentation models, providing a pathway toward intelligent, data-driven electron microscopy analysis.

36 MATERIALS SCIENCE

Surface deposition of nanometer scale carbon structures on Bi 2 Sr 2 CaCu 2 O 8+δ using a low-cost scanning electron microscope

In this work, we investigate optically active nanostructures on Bi 2 Sr 2 CaCu 2 O 8+δ (BSCCO). The nanostructures are constructed from carbon nanocrystals formed using the electron beam of a scanning electron microscope to locally decompose residual hydrocarbons at the BSCCO surface. Atomic force microscopy is used to characterize the dimensions of these structures as a function of beam exposure time. This technique has been used to induce localized intercalation to form carbon nanoparticles up to tens of nanometers into a variety of 2D materials. Cross-sectional scanning transmission electron microscopy in BSCCO shows the presence of these carbon deposits on the surface, but there is no evidence they penetrate into the BSCCO substrate. Therefore, this technique is not suitable for localized intercalation in BSCCO, and it does have promise as a cost-effective approach to pattern nanometer scale etch stops.

2D materials

Fullerenes, PAH, Carbon Nanostructures, and Soot in Low Pressure Diffusion Flames

The formation of fullerenes C 60 and C 7O is known to occur in premixed laminar benzene/oxygen/argon flames operated at reduced pressures. High resolution transmission electron microscopy (HRTEM) images of material collected from these flames has identified a variety of multishelled nanotubes and fullerene 'onions' as well as some trigonous structures. These fullerenes and nanostructures resemble the material that results from commercial fullerene production systems using graphite vaporization. As a result, combustion is an interesting method for fullerenes synthesis. If commercial scale operation is to be considered, the use of diffusion flames might be safer and less cumbersome than premixed flames. However, it is not known whether diffusion flames produce the types and yields of fullerenes obtained from premixed benzene/oxygen flames. Therefore, the formation of fullerenes and carbon nanostructures, as well as polycyclic aromatic hydrocarbons (PAH) and soot, in acetylene and benzene diffusion flames is being studied using high performance liquid chromatography (HPLC) and high resolution transmission electron microscopy (HRTEM).

William J Grieco

Ultrafast One-Dimensional Peierls-Distortion Dynamics in 1⁢T′−Re⁢S 2 Revealed by 4D Electron Microscopy

Rhenium disulfide (ReS 2 ), a prototypical 2D semiconductor with an anisotropic 1⁢T′ structure due to the pronounced Peierls distortion, has demonstrated great potential for polarization-dependent optoelectronics and photonics. Here, we report an ultrafast phase transition occurring within 1 ps, accompanied by a one-dimensional Peierls-distortion relaxation in 1⁢T′−ReS 2 revealed with combined 4D electron microscopy and time-dependent density functional theory calculations. Upon femtosecond laser pulse excitation, the Re-Re dimerization morphology rapidly transforms from a diamond cluster to zigzag chains and persists for several nanoseconds. Here, this ultrafast Peierls-distortion relaxation is further verified by transient changes in optical anisotropy via polarization-dependent transient absorption spectroscopy. Time-dependent density functional theory calculations attribute this novel phase transition to strong correlation between Peierls distortion and impulsive photoexcited carrier doping, predicting a transient band-gap collapse. This Letter opens up an exciting avenue for ultrafast control of Peierls-distortion-induced anisotropy and the metal-insulator transition in 1⁢T′−ReS 2 .

1T’-ReS2

Quantifying the dislocation content of atomically resolved grain boundary line defects using the Nye tensor

The Nye tensor, which quantifies the density of Burgers vector for a given dislocation line direction, can be effectively used to characterize dislocation content in bulk crystals from atomic-resolution transmission electron microscopy images. The Nye tensor can be calculated from these images, in part because the reference state is simply defined by the lattice of the perfect crystal. The application of the Nye tensor to interfacial line defects, for which the natural reference state is the dichromatic pattern of the two grains in their reference orientation, poses additional challenges. In this work, we present a method that employs the Nye tensor to characterize the edge dislocation content of line defects at grain boundaries from atomic-resolution images. This approach enables us to rapidly characterize all edge dislocation content along a grain boundary. Additionally, the Nye tensor provides information about line defect core structure. Finally, we demonstrate this method on two exemplar defects: a twin boundary disconnection and a facet junction in face-centered cubic Au.

Crystallographic defects

The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy

High-resolution scanning transmission electron microscopy (S/TEM) is an indispensable tool for characterizing the structure and properties of materials down to the atomic scale. Conventional S/TEM imaging, however, is limited by the phase problem, whereby the phase of the electron exit wave is lost upon detection. Recent advances in diffractive imaging and 4D-STEM have enabled a range of phase-retrieval techniques that computationally reconstruct the missing information encoded in the phase of the transmission function. These approaches offer improved dose efficiency and enhanced sensitivity to weakly scattering signals, extending quantitative imaging to beam-sensitive materials composed of light elements. In this work, we introduce the phase problem in electron microscopy and survey the diverse landscape of phase-retrieval techniques used in the field. Despite their many acronyms and algorithmic variations, these techniques share a common physical and mathematical foundation. We present a unified framework that connects these seemingly distinct methods, from parallax imaging and tilt-corrected bright-field (tcBF-STEM), to aberration-corrected bright-field (acBF-STEM), optimum bright-field (OBF-STEM) and single-sideband (SSB) ptychography, as well as first-moment integrated center of mass techniques (iCOM) and iterative ptychographic algorithms. Based on these insights, we discuss the opportunities and practical limitations of applying these methods across different materials systems, detector designs, and microscope configurations.Graphical abstractRepresentative electron microscopy configurations used for phase retrieval and diffractive imaging in S/TEM: (a) Zernike phase-contrast transmission electron microscopy (TEM), (b) small-convergence-angle four-dimensional scanning transmission electron microscopy (4D-STEM) for nanobeam-based phase reconstruction methods, and (c) large-convergence-angle 4D-STEM for ptychographic and related diffractive imaging techniques reviewed in this work.

36 MATERIALS SCIENCE

Realignment and suppression of charge density waves in the rare-earth tritellurides 𝑅⁢Te 3 (𝑅 = La, Gd, Er)

The rare-earth tritellurides have a rich phase diagram that includes charge density waves (CDWs), superconductivity, and magnetic order, offering a platform to study the interplay between these phases on a square-net system. Prior studies have shown that defects can affect the CDW characteristics in these materials, yet coupling between the CDW order and the underlying microstructure has not been studied at the nanoscale. Here we use scanning transmission electron microscopy at cryogenic temperatures to directly visualize the effects of defects on the CDW order and provide a spatially resolved microscopic correlation between the CDW transition and structural defects. Here, we show that in the presence of extended defects, such as dislocations and stacking faults, the weak orthorhombicity of the rare-earth tritellurides is lost and the material becomes pseudotetragonal. Since the orthorhombicity acts as a symmetry breaking field for the CDW transitions in rare-earth tritellurides, the presence of these extended defects modulates the energetics of the CDWs and suppresses the ground-state CDW phase at low temperature.

Charge density waves

Impact of the Annealing Temperature on the Local Se Distribution and Optical Properties in CdSexTe1-x Solar Cells by Multimodal X-ray Microscopy

The introduction of Se in CdTe solar-cell absorbers has led to multiple beneficial effects in the devices, including an increased short-circuit current and an extended charge-carrier lifetime. A critical manufacturing step of CdSexTe1-x solar cells is CdCl2 annealing at high temperatures, during which Se diffuses through the absorber layer. Understanding the local Se distribution in the absorber and its impact on optical properties of the material is key for the further development of this thin-film solar cell technology. In a multimodal x-ray scanning microscopy approach, we investigated the impact of the annealing temperature of CdSexTe1-x solar cells on the Se distribution and on optical characteristics of the material. For this purpose, we exploited an upgraded x-ray excited optical luminescence (XEOL) detection unit that enables simultaneous spectrally and temporally resolved XEOL mapping at synchrotron facilities that are ideal for studying thin-film solar-cell materials with hard x-rays featuring high penetration depth and lateral resolution.

14 SOLAR ENERGY

Machine learning pipeline for denoising low signal-to-noise ratio and out-of-distribution transmission electron microscopy datasets

High-resolution transmission electron microscopy (HRTEM) is crucial for observing material’s structural and morphological evolution at Angstrom scales, but the electron beam can alter these processes. Devices such as CMOS-based direct-electron detectors operating in electron-counting mode can be utilized to substantially reduce the electron dosage. However, the resulting images often lead to a low signal-to-noise ratio, which requires frame integration that sacrifices temporal resolution. Several machine learning (ML) models have been recently developed to successfully denoise HRTEM images. Yet, these models are often computationally expensive, and their inference speeds on GPUs are outpaced by the imaging speed of advanced detectors, precluding in situ analysis. Furthermore, the performance of these denoising models on datasets with imaging conditions that deviate from the training datasets has not been evaluated. To mitigate these gaps, we propose a new self-supervised ML denoising pipeline specifically designed for time-series HRTEM images. This pipeline integrates a blind-spot convolution neural network with pre-processing and post-processing steps, including drift correction and low-pass filtering. Results demonstrate that our model outperforms various other ML and non-ML denoising methods in noise reduction and contrast enhancement, leading to improved visual clarity of atomic features. Additionally, the model is drastically faster than U-Net-based ML models and demonstrates excellent out-of-distribution generalization. The model’s computational inference speed is in the order of milliseconds per image, rendering it suitable for application in in-situ HRTEM experiments.

36 MATERIALS SCIENCE

Developing affordable and efficient heating devices for enhanced live cell imaging in confocal microscopy

Temperature control is crucial for live cell imaging, particularly in studies involving plant responses to high ambient temperatures and thermal stress. This study presents the design, development, and testing of two cost-effective heating devices tailored for confocal microscopy applications: an aluminum heat plate and a wireless mini-heater. The aluminum heat plate, engineered to integrate seamlessly with the standard 160 mm × 110 mm microscope stage, supports temperatures up to 36°C, suitable for studies in the range of non-stressful warm temperatures (e.g., 25-27°C forArabidopsis thaliana) and moderate heat stress (e.g., 30-36°C forA. thaliana). We also developed a wireless mini-heater that offers rapid, precise heating directly at the sample slide, with a temperature increase rate over 30 times faster than the heat plate. The wireless heater effectively maintained target temperatures up to 50°C, ideal for investigating severe heat stress and heat shock responses in plants. Both devices performed well in controlled studies, including the real-time analysis of heat shock protein accumulation and stress granule formation inA. thaliana. Our designs are effective and affordable, with total construction costs lower than $300. This accessibility makes them particularly valuable for small laboratories with limited funding. Future improvements could include enhanced heat uniformity, humidity control to mitigate evaporation, and more robust thermal management to minimize focus drift during extended imaging sessions. These modifications would further solidify the utility of our heating devices in live cell imaging, offering researchers reliable, budget-friendly tools for exploring plant thermal biology.

Plant Sciences

CO Adsorption on a Single‐Atom Catalyst Stably Embedded in Graphene

Abstract Confined single metal atoms in graphene‐based materials have proven to be excellent catalysts for several reactions and promising gas sensing systems. However, whether the chemical activity arises from the specific type of metal atom or is a direct consequence of the confinement itself remains unclear.

Chemistry

Breaking the Energy Barrier of Heavy Metal Ion Diffusion in Micropores with Mesoporous 3D Graphene for Fast and Efficient Cu2+ Removal

Efficient removal of heavy metals from water critically depends not only on adsorption capacity but also on ion diffusion kinetics and the associated energy barriers. In conventional carbon adsorbents, severe diffusion confinement within micropores restricts ion transport, resulting in sluggish adsorption kinetics and large apparent activation energies despite high specific surface areas. Here, we demonstrate that this fundamental limitation is overcome by engineering meso/macroporous architectures in the 3D graphene materials synthesized via our discovered alkali-metal reactions with\\\\r\\\\n2\\\\r\\\\nCO. The unique 3D graphene materials possess defect-rich graphene frameworks with interconnected meso/macroporous networks, exhibiting simultaneously high surface area and greatly enhanced meso/macropore volume that enable efficient access to adsorption sites. As a result, the Cu2+ adsorption on 3D graphene proceeds with very low activation energies (4.98 kJ mol–1), which is almost 4 times smaller than on activated carbon (23.1 kJ mol–1). This finding offers a promising platform for efficient and sustainable water purification.

25 ENERGY STORAGE

Answering old questions with new techniques: Understanding performance-limiting factors in transition metal dichalcogenide photoelectrochemical solar cells

In the late 1970s and early 1980s, several research groups reported high-efficiency and stable photoelectrochemical solar cells based on transition metal dichalcogenides (TMDS; e.g., MoS 2 , WSe 2 , and MoSe 2 ) immersed in iodide/tri-iodide electrolytes. A consensus emerged that smooth crystals were necessary for high efficiency based on significant evidence that rough crystals with exposed edge sites produced lower photocurrents and fill factors. However, anecdotal observations in the literature hinted at significant performance variation among apparently smooth crystals with the possibility of highly active “hot” edge sites. Furthermore, this mini-review article is a case study on how spatially resolved photoelectrochemical techniques developed in the 2020s are answering old questions regarding the origin of performance variation in high efficiency n-type TMD|I – ,I 3 – |Pt photoelectrochemical solar cells.

14 SOLAR ENERGY

Lithium Nucleation of Anode-Free Solid-State Batteries with a Dry Compressible Interlayer

Anode-free lithium batteries offer promising advantages, including increased energy density and the ability to address common mechanistic failures within the cell, thus increasing safety. One way that can make this possible is to control lithium nucleation. This could be achieved by reducing the overpotential required and implanting lithophilic nucleation sites in an anodic interlayer to aid in lithium ion transport and plating. The concept has been utilized in solid-state battery systems where electrolytes are solids with further improved safety and structural longevity. In this presentation, we discuss the use of a silver-holey graphene-based anodic interlayer that can be fabricated via direct dry compression without the use of solvent or binder. The addition of silver to the holey graphene matrix creates a route to lithium plating via a lower-energy intermediate. This idea is supported by the presence of a lithium-silver alloy that forms during the activation step. It is understood that the embedded silver acts as a nucleation site for lithium ions, thereby assisting in even plating. This control, combined with the added cushion of the holey graphene itself, can help reduce dendrite formation, ultimately increasing the safety and lifetime of the solid-state batteries.

Solid state batteries