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DOE OSTI2025

Extracellular filaments revealed by affinity capture cryogenic-electron tomography

Cryogenic-electron tomography (cryo-ET) has provided an unprecedented glimpse into the nanoscale architecture of cells by combining cryogenic preservation of biological structures with electron tomography. Micropatterning of extracellular matrix proteins is increasingly used as a method to prepare adherent cell types for cryo-ET as it promotes optimal positioning of cells and subcellular regions of interest for vitrification, cryo-focused ion beam (cryo-FIB) milling, and data acquisition. Here we demonstrate a micropatterning workflow for capturing minimally adherent cell types, human T cells and Jurkat cells, for cryo-FIB and cryo-ET. Our affinity capture system facilitated the nanoscale imaging of Jurkat cells, revealing extracellular filamentous structures. It improved workflow efficiency by consistently producing grids with a sufficient number of well-positioned cells for an entire cryo-FIB session. Affinity capture can be extended to facilitate high-resolution imaging of other adherent and non-adherent cell types with cryo-ET.

Biochemistry↗

DOE OSTI2025

Progress in the development of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography

Cryo-electron tomography (cryo-ET) is a powerful modality for resolving cellular structures in their native state. While single-particle cryo-electron microscopy excels in determining protein structures purified from recombinant or endogenous sources due to an abundance of particles, weak contrast issues are accentuated in cryo-ET by low copy numbers in crowded cellular milieux. Continuous laser phase plates offer improved contrast in cryo-ET; however, their implementation demands exceptionally high-peak optical intensities. Instead, a novel experimental approach to enhance contrast in cryo-ET is to manipulate the phase of scattered pulsed electrons using ultrafast pulsed photons. Here, we outline the experimental design of a proof-of-concept electron microscope and demonstrate synchronization between electron packets and laser pulses. Furthermore, we show ultrabright photoemission of electrons from an alloy field emission tip using femtosecond ultraviolet pulses. These experiments pave the way toward exploring the utility of the ponderomotive effect using pulsed radiation to increase phase contrast in cryo-ET of subcellular protein complexes in situ, thus advancing the field of cell biology.

Du, Daniel X. [Columbia Univ., New York, NY (Unite↗

DOE OSTI2025

Model-based iterative reconstruction with adaptive regularization for artifact reduction in electron tomography

Obtaining high-quality 3D reconstructions from electron tomography of crystalline particles embedded in lighter support elements is crucial for various material systems such as catalysts for fuel cell applications. However, significant challenges arise due to the limited tilt range, sparse and low signal-to-noise ratio of the measurements. In addition, small metal particles can cause strong streaking and shading artifacts in the 3D reconstructions when using conventional reconstruction algorithms due to the presence of Bragg diffraction and the large scattering cross-section difference between the materials of the particles and the background support regions. These artifacts lead to errors in the downstream characterization affecting extraction of critical features such as the size of the metal particles, their distribution and the volume of the lighter support regions. In this paper, we present a two-stage algorithm based on metal artifact reduction, utilizing model-based iterative reconstruction methods with adaptive adjustment of regularization parameters. Our approach yields high-quality 3D reconstructions compared to traditional algorithms, accurately capturing both the metal particles as well as the background support. We demonstrate the effectiveness of our algorithm through simulated and experimental bright-field electron tomography data, showing significant improvements in reconstruction quality compared to traditional methods.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Optimal 3D chemical imaging with multimodal electron tomography

Accurate mapping of nanoscale chemistry in three dimensions (3D) has been a longstanding challenge. Modern electron microscopy provides chemical images by electron energy loss spectroscopy (EELS) and energy dispersive x-ray spectrometry (EDX) but requires high fluences that damage specimens. In 3D, the requirements are worse; electron tomography demands many high-fluence chemical maps for reconstruction, creating a tradeoff between resolution, accuracy, and sample survival. Fused multimodal electron tomography (MM-ET) alleviates this requirement by leveraging lower-fluence high-angle annular dark-field (HAADF) images alongside a few chemical maps to dramatically improve chemical resolution. Here, experimental and computational parameter space is systematically explored to determine when MM-ET performs best. Ideal imaging conditions balance sample survival with resolution and chemical specificity; we recommend a tilt range of at least ± 70°, acquiring 40 equally spaced HAADF projections (signal-to-noise > 10), and 7 EELS/EDX maps of each chemistry (signal-to-noise > 4).

36 MATERIALS SCIENCE↗

DOE OSTI2026

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021)View full citation, Nat. Methods, 18, 186–193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, subtomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L1/L2 losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.

contrast enhancement↗

DOE OSTI2024

Atomic Electron Tomography of Thin Films

In the past decade, the development of atomic electron tomography (AET) [1] has allowed for the 3D characterization of atomic positions in nanoparticle [2], monolayer [3], and needle [4] geometries. Furthermore, many technologically important systems are synthesized and utilized as thin films. Several challenges in sample preparation and data analysis have been overcome to expand the scope of AET to these systems. Polycrystalline yttrium-doped hafnium dioxide (HfO 2 ) was chosen as a model system, because it is technologically relevant as a high capacitance dielectric and ferroelectric.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Cryogenic electron tomography by the numbers: Charting underexplored lineages in structural cell biology

Imaging cells and their interactions across the whole biosphere with molecular-scale resolution is key for understanding structure–function relations. Cryogenic electron tomography (cryo-ET) is a powerful method for obtaining this critical information. However, cryo-ET studies are challenging and often limited to a small number of cell types per study. Here, we collate cryo-ET data from hundreds of cells and tissues across the biosphere to i) identify emerging methodological trends, ii) pinpoint strategies to reduce imaging time and costs, iii) quantitatively compare methods for cell freezing and sectioning, and iv) census cryo-ET species coverage across all domains of life. Comparing the fraction of cellular material within a single lamella across all domains of life reveals an order of magnitude difference between eukaryotes (1%) compared to bacteria (9%) and archaea (14%). We calculate the fraction of cellular material which can be imaged using distinct sectioning methods on multicellular communities and tissues—identifying serial lift-out as a powerful approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2 to 3 orders of magnitude lower than in sequence libraries and 4 to 5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and highlight where future cryo-ET research would be most impactful.

HPF↗

DOE OSTI2024

Quantitative Analysis of Rhodobacter sphaeroides Storage Organelles via Cryo-Electron Tomography and Light Microscopy

Bacterial cytoplasmic organelles are diverse and serve many varied purposes. Here, we employed Rhodobacter sphaeroides to investigate the accumulation of carbon and inorganic phosphate in the storage organelles, polyhydroxybutyrate (PHB) and polyphosphate (PP), respectively. Using cryo-electron tomography (cryo-ET), these organelles were observed to increase in size and abundance when growth was arrested by chloramphenicol treatment. The accumulation of PHB and PP was quantified from three-dimensional (3D) segmentations in cryo-tomograms and the analysis of these 3D models. The quantification of PHB using both segmentation analysis and liquid chromatography and mass spectrometry (LCMS) each demonstrated an over 10- to 20-fold accumulation of PHB. The cytoplasmic location of PHB in cells was assessed with fluorescence light microscopy using a PhaP-mNeonGreen fusion-protein construct. The subcellular location and enumeration of these organelles were correlated by comparing the cryo-ET and fluorescence microscopy data. A potential link between PHB and PP localization and possible explanations for co-localization are discussed. Finally, the study of PHB and PP granules, and their accumulation, is discussed in the context of advancing fundamental knowledge about bacterial stress response, the study of renewable sources of bioplastics, and highly energetic compounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Continuity of Mitochondrial Budding: Insights from BS-C-1 Cells by In Situ Cryo-electron Tomography

Mitochondrial division is a fundamental biological process essensial for cellular functionality and vitality. The prevailing hypothesis that dynamin related protein 1 (Drp1) provides principal control in mitochondrial division, in which it also involves the endoplasmic reticulum (ER) and the cytoskeleton, does not account for all the observations. Therefore. the hypothesis may be incomplete. Our previous study in HeLa cells led to a new hypothesis of mitochondrial division by budding. To follow-up our previous study, we employed in situ cryo-electron tomography to visualize mitochondrial budding in the intact healthy monkey kidney cells (BS-C-1 cells). Our findings reaffirm single and multiple mitochondrial budding, consistent with our observations in HeLa cells. Notably, the budding regions vary significantly in diameter and length, which may represent different stages of budding. More interestingly, neither rings nor ring-like structures, nor the wrapping of ER tubes was observed in the budding regions, suggesting mitochondrial budding is independent from Drp1 and ER. Meanwhile, we uncovered direct interactions between mitochondria and large vesicles that are distinct from small mitochondrial-derived vesicles and extracellular mitovesicles. In conclusion, we propose that these interacting vesicles may have mitochondrial origins.

(Cryo-EM)↗

DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Machine Learning Enabled Advanced Electron Tomography for Resolving Chemical Inhomogeneity and Materials Dynamics in Lithium-Ion Battery Electrodes

The objective of this project is to develop machine learning-assisted electron microscopy, together with three-dimensional, cryogenic, and in-situ imaging techniques, for resolving chemical inhomogeneity and materials dynamics in lithium battery electrodes and interfaces. The project aims to expand the spatial, temporal, and dimensional resolution of transmission electron microscopy and to enable quantitative analysis of beam-sensitive battery materials.

25 ENERGY STORAGE↗

DOE OSTI2024

Understanding Formation of Irradiation-Induced Defects through 4D-STEM, Electron Tomography, and WBDF-STEM

A major challenge in advancing nuclear materials for next-generation fission and proposed fusion reactors is to comprehensively understand the formation of irradiation-induced defects. Here it is essential to correlate the evolution of irradiation-induced defects and the degradation of mechanical properties, as they collectively dictate the material's lifespan and ensure nuclear safety. Scanning transmission electron microscopy (STEM) based techniques have emerged as indispensable tools for irradiation-induced defect characterization, offering high spatial resolution imaging and chemical analysis, such as electron energy loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDXS). These techniques have been effectively used to obtain an atomic-scale view of the defect structure. Recent advances in electron microscopy, particularly in 4D-STEM, offer detailed insight into microstructural evolution by capturing full 2D diffraction patterns at every pixel position. Using high-speed direct electron detectors, this technology generates a four-dimensional dataset, overcoming the limitations of traditional STEM imaging.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of focus limits

Electron ptychography is a powerful computational method for atomic-resolution imaging with high contrast for weakly and strongly scattering elements. Modern algorithms coupled with fast and efficient detectors allow imaging specimens with tens of nanometers thicknesses with sub-0.5 Ångstrom lateral resolution. However, the axial resolution in these approaches is currently limited to a few nanometers, limiting their ability to solve novel atomic structures ab initio. Here, we experimentally demonstrate multi-slice ptychographic electron tomography, which allows atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits. We reconstruct tilt-series 4D-STEM measurements of a $\mathrm{Co_3O_4}$ nanocube, yielding 2 Å axial and 0.7 Å transverse resolution in a reconstructed volume of $\mathrm{(18.2\,nm)^3}$. Our results demonstrate a 13.5-fold improvement in axial resolution compared to multi-slice ptychography while retaining the atomic lateral resolution and the capability to image volumes beyond the depth of field limit. Multi-slice ptychographic electron tomography significantly expands the volume of materials accessible using high-resolution electron microscopy. We discuss further experimental and algorithmic improvements necessary to also resolve single weakly scattering atoms in 3D.

36 MATERIALS SCIENCE↗

DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

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↗

DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗

DOE OSTI2024

A Three–Dimensional Nanoscale View of Electrocatalyst Degradation in Hydrogen Fuel Cells

The loss of platinum (Pt) electrochemically active surface area (ECSA) is a critical degradation mode that often becomes a limiting factor for heavy-duty proton exchange membrane fuel cell vehicles. High surface area carbon supports have been shown to improve Pt dispersion and limit detrimental ionomer-electrocatalyst interactions due to their large interior pore volume. Here, in this work, using automated scanning transmission electron tomography, the degradation of nanoparticles located on the interior versus exterior surfaces of the carbon support is compared following a catalyst-specific accelerated stress test (AST) of 90,000 voltage cycles between 0.6 V to 0.95 V. The results reveal a notable increase in median particle size for both interior and exterior Pt catalyst particles, with a slightly higher increase in particle size distribution and loss of specific surface area for the particles located on the exterior carbon surface. The fraction of Pt nanoparticles that reside within the interior of the carbon support also increased following the AST test, accompanied by evidence of an increase in average carbon mesopore size. Here, the results shed light on the degradation mechanisms affecting electrochemical properties and the enhanced particle accessibility at lower relative humidity.

08 HYDROGEN↗

DOE OSTI2026

Optical interference for the guidance of cryogenic focused ion beam milling beyond the axial diffraction limit

Cryogenic focused ion beam (Cryo-FIB) milling has become a standard step in the cryogenic electron tomography (Cryo-ET) workflow and is required to thin cells to electron-semitransparency. However, this destructive process removes the vast majority of the cellular material and raises a critical question: what thin section should be preserved for Cryo-ET analysis? Using a tri-coincident cryogenic FIB-SEM-LM system, we identify an interferometric optical response that can be used for targeting lamella production to fluorescently labeled structures with accuracy beyond the diffraction limit. Here we demonstrate this approach using synthetic samples of fluorescent beads embedded in micron-scale droplets of amorphous ice. We then apply the approach to capture virions inside host cells. Successful targeting is confirmed by Cryo-ET revealing clusters of virions in intracellular vesicles. The method does not require any fluorescent fiducials or axial registration and can be performed on any fluorescently labeled structure that is visible in widefield fluorescence microscopy.

Cryoelectron microscopy↗