Development of advanced electron tomography in materials science based on TEM and STEM

The recent developments of electron tomography（ET） based on transmission electron microscopy（TEM） and scanning transmission electron microscopy（STEM） in the field of materials science were introduced. The various types of ET based on TEM as well as STEM were described in detail, which included bright-field（BF）-TEM tomography, dark-field（DF）-TEM tomography, weak-beam dark-field（WBDF）-TEM tomography, annular dark-field（ADF）-TEM tomography, energy-filtered transmission electron microscopy（EFTEM） tomography, high-angle annular dark-field（HAADF）-STEM tomography, ADF-STEM tomography, incoherent bright field（IBF）-STEM tomography, electron energy loss spectroscopy（EELS）-STEM tomography and X-ray energy dispersive spectrometry（XEDS）-STEM tomography, and so on. The optimized tilt series such as dual-axis tilt tomography, on-axis tilt tomography, conical tilt tomography and equally-sloped tomography（EST） were reported. The advanced reconstruction algorithms, such as discrete algebraic reconstruction technique（DART）, compressed sensing（CS） algorithm and EST were overviewed. At last, the development tendency of ET in materials science was presented.

Heterogeneous Cu_(x)O Nano‑Skeletons from Waste Electronics for Enhanced Glucose Detection

Electronic waste(e-waste)and diabetes are global challenges to modern societies.However,solving these two challenges together has been challenging until now.Herein,we propose a laser-induced transfer method to fabricate portable glucose sensors by recycling copper from e-waste.We bring up a laser-induced full-automatic fabrication method for synthesizing continuous heterogeneous Cu_(x)O(h-Cu_(x)O)nano-skeletons electrode for glucose sensing,offering rapid(<1 min),clean,air-compatible,and continuous fabrication,applicable to a wide range of Cu-containing substrates.Leveraging this approach,h-Cu_(x)O nanoskeletons,with an inner core predominantly composed of Cu_(2)O with lower oxygen content,juxtaposed with an outer layer rich in amorphous Cu_(x)O(a-Cu_(x)O)with higher oxygen content,are derived from discarded printed circuit boards.When employed in glucose detection,the h-Cu_(x)O nano-skeletons undergo a structural evolution process,transitioning into rigid Cu_(2)O@CuO nano-skeletons prompted by electrochemical activation.This transformation yields exceptional glucose-sensing performance(sensitivity:9.893 mA mM^(-1) cm^(-2);detection limit:0.34μM),outperforming most previously reported glucose sensors.Density functional theory analysis elucidates that the heterogeneous structure facilitates gluconolactone desorption.This glucose detection device has also been downsized to optimize its scalability and portability for convenient integration into people’s everyday lives.

Electron tomography for sintered ceramic materials by a neural network algebraic reconstruction technique

The missing wedge effect in electron tomography introduces various types of artifacts in the tomograms and lowers the reconstruction resolution and quality.The artifacts produced in tomographic reconstruction of bulk materials can be very severe,particularly for sintered bulk ceramic materials in which there are often nano-pores or pore-like microstructure features.Here,we report a neural network algebraic reconstruction algorithm with no prior knowledge to perform electron tomography for a sintered SiC material with nano carbon zones.The results show that the proposed algorithm has a great suppressive effect on the missing wedge artifacts and a high tolerance for noise.The information in the missing wedge can be partly recovered by this technique.Thus,both the shape of the bulk SiC specimen and its irregular inner pore-like features are correctly retrieved in the obtained 3D image.Our study shows the effectiveness of the neural network algorithm for improving the reconstruction accuracy of electron tomography,in order to reveal sophisticated 3D microstructures generally existing in sintered ceramic materials.

AutoGDeterm： Automatic Geometry Determination for Electron Tomography

Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform （NUFFT） reconstruction （ICON） and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical ＂manual positioning＂ method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http：//ear.ict.ac.cn.

In Situ Transmission Electron Microscopy and Three-Dimensional Electron Tomography for Catalyst Studies

An in-depth understanding of the catalytic reaction mechanism is the key to designing efficient and stable catalysts. In situ transmission electron microscope(TEM) is the most powerful tool to visualize and analyze the microstructures of catalysts during catalysis. In situ TEM combined with three-dimensional(3D) electron tomography(ET) reconstruction technique enables interrogations of catalysts’ structural dynamics and chemical changes in high temporal and spatial dimensions. In this review, we discuss and summarize the recent advances in in situ TEM together with 3D ET for catalyst studies. Topics include the latest research progress of in situ TEM imaging as well as 3D visualization and quantitative analysis of catalysts. We also pay particular attention to artificial intelligence(AI)-enhanced smart 3D ET. These include deep learning(DL)-based data compression and storage for the analysis of large TEM data, recovery of wedge-shaped information lost in 3D ET reconstructions, and DL models for reducing residual artifacts in 3D reconstructed images. Finally, the challenges and development prospects of current in situ TEM and 3D ET research are discussed.

Quantitative Electron Tomography for Accurate Measurement of Precipitates Microstructure Parameters in Al–Cu–Li Alloys

Mechanical theories show that properties of alloys are strongly dependent on the morphological parameters oftheir strengthening precipitates.However,accurate measurement of precipitates microstructure parameters is still a challenging task.In this article,we develop a quantitative electron tomography method by combining computer vision technology to accurately characterize the three-dimensional microstructure parameters,such as volume fractions,sizes and distributions,of the T_(1) and δ’/θ’/δ’ precipitates in Al-Cu-Li(-Mg) alloys.Since they have extremely large aspect-ratios in shape and large numbers in density upon formation in the Al matrix,these thin plate-like precipitates are difficult to be characterized quantitatively without the assistance of computer vision technology.It is shown that the property difference between two peak-aged states of the alloy can be well explained with the quantitative precipitate parameters correctly measured.Using these correct precipitate data,we also tested the validity of current mechanical models for projecting the contribution of precipitates to the strengths of the alloy,demonstrating that quantitative relations between strength and micro structure parameters still need to be refined.

Electron Tomography in Plant Cell Biology

This review focuses on the contribution of electron tomography-based techniques to our understanding of cellular processes in plant cells. Electron microscopy techniques have evolved to provide better three-dimensional resolution and improved preservation of the subcellular components. In particular, the combination of cryofixation/freeze substitution and electron tomography have allowed plant cell biologists to image organelles and macromolecular complexes in their native cellular context with unprecedented three-dimensional resolution （4-7 nm）. Until now, electron tomography has been applied in plant cell biology for the study of cytokinesis, Golgi structure and trafficking, formation of plant endosome/prevacuolar compartments, and organization of photosynthetic membranes. We discuss in this review the new insights that these tomographic studies have brought to the plant biology field.

The Nanoscale Density Gradient as a Structural Stabilizer for Glass Formation

The rapid cooling of a metallic liquid(ML)results in short-range order(SRO)among the atomic arrangements and a disordered structure in the resulting metallic glass(MG).These phenomena cause various possible features in the microscopic structure of the MG,presenting a puzzle about the nature of the MGs’microscopic structure beyond SRO.In this study,the nanoscale density gradient(NDG)originating from a sequential arrangement of clusters with different atomic packing densities(APDs),representing the medium-range structural heterogeneity in Zr_(60)Cu_(30)Al_(10)MG,was characterized using electron tomography(ET)combined with image simulations based on structure modeling.The coarse polyhedrons with distinct facets identified in the three-dimensional images coincide with icosahedron-like clusters and represent the spatial positions of clusters with high APDs.Rearrangements of the different clusters according to descending APD order in the glass-forming process are responsible for the NDG that stabilizes both the supercooled ML and the amorphous states and acts as a hidden rule in the transition from ML to MG.

Severe/critical COVID-19 early warning system based on machine learning algorithms using novel imaging scores

BACKGROUND Early identification of severe/critical coronavirus disease 2019(COVID-19)is crucial for timely treatment and intervention.Chest computed tomography(CT)score has been shown to be a significant factor in the diagnosis and treatment of pneumonia,however,there is currently a lack of effective early warning systems for severe/critical COVID-19 based on dynamic CT evolution.AIM To develop a severe/critical COVID-19 prediction model using a combination of imaging scores,clinical features,and biomarker levels.METHODS This study used an improved scoring system to extract and describe the chest CT characteristics of COVID-19 patients.The study also took into consideration the general clinical indicators such as dyspnea,oxygen saturation,alternative lengthening of telomeres(ALT),and androgen suppression treatment(AST),which are commonly associated with severe/critical COVID-19 cases.The study employed lasso regression to evaluate and rank the significance of different disease characteristics.RESULTS The results showed that blood oxygen saturation,ALT,IL-6/IL-10,combined score,ground glass opacity score,age,crazy paving mode score,qsofa,AST,and overall lung involvement score were key factors in predicting severe/critical COVID-19 cases.The study established a COVID-19 severe/critical early warning system using various machine learning algorithms,including XGBClassifier,Logistic Regression,MLPClassifier,RandomForestClassifier,and AdaBoost Classifier.The study concluded that the prediction model based on the improved CT score and machine learning algorithms is a feasible method for early detection of severe/critical COVID-19 evolution.CONCLUSION The findings of this study suggest that a prediction model based on improved CT scores and machine learning algorithms is effective in detecting the early warning signals of severe/critical COVID-19.

CONTROLLING THE 3D NANOSCALE ORGANIZATION OF BULK HETEROJUNCTION POLYMER SOLAR CELLS

In this study,the three dimensional nanoscale organization in the photoactive layers of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) is revealed by transmission electron tomography.After annealing treatment,either at elevated temperature or during slow solvent evaporation,nanoscale interpenetrating networks are formed with high crystalline order and favorable concentration gradients of both components through the thickness of the photoactive layer.Such a tailored morphology account...

Bio-macromolecular dynamic structures and functions, illustrated with DNA, antibody, and lipoprotein

Bio-macromolecules, such as proteins and nucleic acids, are the basic materials that perform fundamental activities required for life. Their structural heterogeneities and dynamic personalities are vital to understand the underlying functional mechanisms of bio-macromolecules. With the rapid development of advanced technologies such as single-molecule tech- nologies and cryo-electron microscopy （cryo-EM）, an increasing number of their structural details and mechanics properties at molecular level have significantly raised awareness of basic life processes. In this review, firstly the basic principles of single-molecule method and cryo-EM are summarized, to shine a light on the development in these fields. Secondly, recent progress driven by the above two methods are underway to explore the dynamic structures and functions of DNA, antibody, and lipoprotein. Finally, an outlook is provided for the further research on both the dynamic structures and functions of bio-macromolecules, through single-molecule method and cryo-EM combining with molecular dynamics simulations.

Segmented tomographic evaluation of structural degradation of carbon support in proton exchange membrane fuel cells

The variation of the three-dimensional(3D)structure of the membrane electrode of a fuel cell during proton exchange cycling involves the corrosion/compaction of the carbon support.The increasing degradation of the carbon structure continuously reduces the electrocatalytic performance of proton exchange membrane fuel cells(PEM-FCs).This phenomenon can be explained by performing 3D tomographic analysis at the nanoscale.However,conventional tomographic approaches which present limited experimental feasibility,cannot perform such evaluation and have not provided sufficient structural information with statistical significance thus far.Therefore,a reliable methodology is required for the 3D geometrical evaluation of the carbon structure.Here,we propose a segmented tomographic approach which employs pore network analysis that enables the visualization of the geometrical parameters corresponding to the porous carbon structure at a high resolution.This approach can be utilized to evaluate the 3D structural degradation of the porous carbon structure after cycling in terms of local surface area,pore size distribution,and their 3D networking.These geometrical parameters of the carbon body were demonstrated to be substantially reduced owing to the cycling-induced degradation.This information enables a deeper understanding of the degradation phenomenon of carbon supports and can contribute to the development of stable PEM-FC electrodes.

Evaluation of coronary artery bypass graft patency using three-dimensional reconstruction and flow study of electron beam tomography

Objective To establish and evaluate two protocols for the noninvasive visualization and assessment of coronary artery bypass graft (CABG) patency on electron beam tomography (EBT).Methods Two hundred and fourteen consecutive patients who underwent coronary artery bypass graft surgery were scanned using both EBT angiography with 3-dimensional reconstruction and EBT flow study with time-density-curve analysis.Results There were 589 CABGs evaluated in this study (10 grafts were excluded because of artifacts). Among them, 133 (98.5％) of 135 arterial grafts were patent, and 345 (77.7％) of 444 saphenous-vein grafts were patent. Within 5 years or between 5 and 10 years after operation, arterial graft patency exceeded venous graft patency (P ＜ 0.001 ). Three-dimensional EBT angiography achieved higher sensitivity, specificity and accuracy (97.7％, 94.1％ and 96.7％, respectively) than did EBT flow study (88.4％, 82.4％ and 85.2％, respectively) for evaluating occlusion or patency of CABG. The intra-graft flow of patent arterial and venous grafts were 4.9 ± 2.2 mi · min-1 · g-1 and 6.9 ± 2.8 mi · min-1 · g-1,respectively (P＜0.001).Conclusion The combination of EBT three-dimensional reconstruction and flow study can be more effective in the assessment of CABG anatomy and quantification of patent CABG blood flow.

A compact design of four-degree-of-freedom transmission electron microscope holder for quasi-four-dimensional characterization

Electron tomography(ET) has been demonstrated to be a powerful tool in addressing challenging problems, such as understanding 3 D interactions among various microstructures. Advancing ET to broader applications requires novel instrumentation design to break the bottlenecks both in theory and in practice. In this work, we built a compact four-degree-of-freedom(threedirectional positionings plus self-rotation) nano-manipulator dedicated to ET applications, which is called X-Nano transmission electron microscope(TEM) holder. All the movements of the four degrees of freedom are precisely driven by built-in piezoelectric actuators, minimizing the artefacts due to vibration and drifting of the TEM stage. Full 360° rotation is realized with an accuracy of 0.05° in the whole range, which solves the missing wedge problem. Meanwhile, the specimen can move to the rotation axis with an integrated 3D nano-manipulator, greatly reducing the effort in tracking sample locations during tilting.Meanwhile, in-situ stimulation function can be seamlessly integrated into the X-Nano TEM holder so that dynamic information can be uncovered. We expect that more delicate researches, such as those about 3D microstructural evolution, can be carried out extensively by means of this holder in the near future.

Towards quantitative determination of atomic structures of amorphous materials in three dimensions

Amorphous materials such as glass,polymer and amorphous alloy have broad applications ranging from daily life to extreme conditions due to their unique properties in elasticity,strength and electrical resistivity.A better understanding of atomic structure of amorphous materials will provide invaluable information for their further engineering and applications.However,experimentally determining the three-dimensional(3D)atomic structure of amorphous materials has been a long-standing problem.Due to the disordered atomic arrangement,amorphous materials do not have any translational and rotational symmetry at long-range scale.Conventional characterization methods,such as the scattering and the microscopy imaging,can only provide the statistic structural information which is averaged over the macroscopic region.The knowledge of the 3D atomic structure of amorphous materials is limited.Recently atomic resolution electron tomography(AET)has proven an increasingly powerful tool for atomic scale structural characterization without any crystalline assumptions,which opens a door to determine the 3D structure of various amorphous materials.In this review,we summarize the state-of-art characterization methods for the exploration of atomic structures of amorphous materials in the past few decades,including X-ray/neutron diffraction,nano-beam and angstrom-beam electron diffraction,fluctuation electron microscopy,high-resolution scanning/transmission electron microscopy,and atom probe tomography.From experimental data and theoretical descriptions,3D structures of various amorphous materials have been built up.Particularly,we introduce the principles and recent progress of AET,and highlight the most recent groundbreaking feat accomplished by AET,i.e.,the first experimental determination of all 3D atomic positions in a multi-component glass-forming alloy and the 3D atomic packing in amorphous solids.We also discuss the new opportunities and challenges for characterizing the chemical and structural defects in amorphous materials.

Three-dimensional reconstruction and comparison of vacuolar membranes in response to viral infection

The vacuole is a unique plant organelle that plays an important role in maintaining cellular homeostasis under various environmental stress conditions. However, the effects of biotic stress on vacuole structure has not been examined using three-dimensional(3D) visualization. Here, we performed 3D electron tomography to compare the ultrastructural changes in the vacuole during infection with different viruses. The 3D models revealed that vacuoles are remodeled in cells infected with cucumber mosaic virus(CMV) or tobacco necrosis virus A Chinese isolate(TNV-AC), resulting in the formation of spherules at the periphery of the vacuole. These spherules contain neck-like channels that connect their interior with the cytosol. Confocal microscopy of CMV replication proteins 1 a and 2 a and TNV-AC auxiliary replication protein p23 showed that all of these proteins localize to the tonoplast.Electron microscopy revealed that the expression of these replication proteins alone is sufficient to induce spherule formation on the tonoplast, suggesting that these proteins play prominent roles in inducing vacuolar membrane remodeling. This is the first report of the 3D structures of viral replication factories built on the tonoplasts. These findings contribute to our understanding of vacuole biogenesis under normal conditions and during assembly of plant(+) RNA virus replication complexes.

Revisiting the Hierarchical Microstructures of an Al-Zn-Mg Alloy Fabricated by Pre-deformation and Aging

Pre-deformation before aging has been demonstrated to have a positive effect on the mechanical strength of the 7N01 alloy in our previous study,which is rather different from the general negative effects of pre-deformation on high-strength 7XXX aluminum alloys.In order to explain the strengthening mechanism relating to the positive effect,in the present study,the microstructure of the aged 7N01 alloy with different degrees of pre-deformation was investigated in detail using advanced electron microscopy techniques.Our results show that,without pre-deformation,the aged alloy is strengthened mainly by the η′type of hardening precipitates.In contrast,with pre-deformation,the aged alloy is strengthened by the hierarchical microstructure consisting of the GP-η′type of precipitates formed inside sub-grains,the ηp type of precipitates formed at small-angle boundaries,and the dislocation introduced by pre-deformation(residual work-hardening effect).By visualizing the distribution of theηp precipitates through three-dimensional electron tomography,the 3 D microstructures of dislocation cells are clearly revealed.Proper combinations of ηp precipitates,GP-η′precipitates and residual dislocations in the alloy are responsible for the positive effect of pre-deformation on its mechanical properties.

3-D Characterization of CdSe Nanoparticles Attached to Carbon Nanotubes

The crystallographic structure of CdSe nanoparticles attached to carbon nanotubes has been elucidated by means of high resolution transmission electron microscopy and high angle annular dark field scanning transmission electron microscopy tomography.CdSe rod-like nanoparticles,grown in solution together with carbon nanotubes,undergo a morphological transformation and become attached to the carbon surface.Electron tomography reveals that the nanoparticles are hexagonal-based with the(001)planes epitaxially matched to the outer graphene layer.