Transmission electron microscopy and associated methods, such as single particle analysis, two-dimensional crystallography, helical reconstruction, and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source.

In variable phase bright-field contrast, a bright-field image based on axial or concentric-peripheral light is optically superimposed with a phase-contrast image, so that typical details that are imminent in one or the other technique contribute to the resulting composite image. In particular, complex structured specimens consisting of high-density light absorbing details and additional low-density phase shifting components can be observed with improved clarity. As both partial images interfere with each other, fine details within thin specimens can be highlighted further by additional contrast effects based on interference. Haloing and shade-off are significantly reduced when compared with phase contrast carried out stand-alone. Our method is characterized by several technical means that are relevant for the high image quality that can be achieved: both illuminating light components associated with bright field and phase contrast are filtered at different colors and separated from each other so that they meet the specimen at different angles of incidence. The intensities of the phase-contrast- and bright-field-producing light can be selectively regulated so that the final image can be dominated by phase contrast or bright field, or be equalized. The condenser aperture diaphragm can be used for modulations of the image's appearance.

Here we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal subcellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm half-pitch spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 μm thick. Structures as small as 90 nm can be detected in tomographic reconstructions following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft X-ray microscopy, and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft X-ray microscope will enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.

Environmental scanning electron microscopy has been extensively used for studying the wetting properties of different materials. For some types of investigation, however, the traditional ways of conducting in situ dynamic wetting experiments do not offer sufficient control over the wetting process. Here, we present a novel method for controlled wetting of materials in the environmental scanning electron microscope (ESEM). It offers improved control of the point of interaction between the water and the specimen and renders it more accessible for imaging. It also enables the study of water transport through a material by direct imaging. The method is based on the use of a piezo-driven nanomanipulator to bring a specimen in contact with a water reservoir in the ESEM chamber. The water reservoir is established by local condensation on a Peltier-cooled surface. A fixture was designed to make the experimental setup compatible with the standard Peltier cooling stage of the microscope. The developed technique was successfully applied to individual cellulose fibers, and the absorption and transport of water by individual cellulose fibers were imaged.

Radiation damage is often an issue during high-resolution imaging, making low-dose focusing and stigmation essential, in particular when no part of the sample can be “sacrificed” for this. An example is serial block-face electron microscopy, where the imaging resolution must be kept optimal during automated acquisition that can last months. Here, we present an algorithm, which we call “Maximum-A-Posteriori Focusing and Stigmation (MAPFoSt),” that was designed to make optimal use of the available signal. We show that MAPFoSt outperforms the built-in focusing algorithm of a commercial scanning electron microscope even at a tenfold reduced total dose. MAPFoSt estimates multiple aberration modes (focus and the two astigmatism coefficients) using just two test images taken at different focus settings. Using an incident electron dose density of 2,500 electrons/pixel and a signal-to-noise ratio of about one, all three coefficients could be estimated to within <7% of the depth of focus, using 19 detected secondary electrons per pixel. A generalization to higher-order aberrations and to other forms of imaging in both two and three dimensions appears possible.

A Monte Carlo simulation was used to determine geometry correction factors that increase accuracy of quantitative X-ray microanalysis of laterally semithick biological materials. A model composed of cellulose with homogeneously distributed biological elements and lateral dimensions between 0.5–25 μm was chosen. The specimen was exposed to 5, 10, and 15 keV electrons, the net intensities of characteristic X-rays registered for the elements, and presented as a function of the lateral dimensions of the model. This showed the double decay exponential function fitted the distribution of X-ray intensities in relation to the model size. The applicability of the function as a correction method was successfully tested for 30 specimens with varying composition and dimensions. The value of relative error decreased from ±60% to ±5% when the correction was applied. Moreover, the minimal lateral size of the material was defined, below which the correction is not required. The simulation also revealed that the difference of the weighted sum of Z2/A between the unknown and the standard could reach 25% without significant influence on the quantitative results. The correction method could be helpful for accurate assessment of elemental composition in biological or organic matrices, when their lateral dimensions are smaller than the distribution range.

Given an unknown multicomponent alloy, and a set of standard compounds or alloys of known composition, can one improve upon popular standards-based methods for energy dispersive X-ray (EDX) spectrometry to quantify the elemental composition of the unknown specimen? A method is presented here for determining elemental composition of alloys using transmission electron microscopy–based EDX with appropriate standards. The method begins with a discrete set of related reference standards of known composition, applies multivariate statistical analysis to those spectra, and evaluates the compositions with a linear matrix algebra method to relate the spectra to elemental composition. By using associated standards, only limited assumptions about the physical origins of the EDX spectra are needed. Spectral absorption corrections can be performed by providing an estimate of the foil thickness of one or more reference standards. The technique was applied to III-V multicomponent alloy thin films: composition and foil thickness were determined for various III-V alloys. The results were then validated by comparing with X-ray diffraction and photoluminescence analysis, demonstrating accuracy of approximately 1% in atomic fraction.

A method that enables high precision extraction of transmission electron microscope (TEM) specimens in low contrast materials has been developed. The main idea behind this work is to produce high contrast markers on both sides of and close to the area of interest. The markers are filled during the depositing of the protective layer. The marker material can be of either Pt or C depending on which one gives the highest contrast. It is thereby possible to distinguish the location of the area of interest during focused ion beam (FIB) milling and ensure that the TEM sample is extracted precisely at the desired position. This method is generally applicable and enables FIB/scanning electron microscope users to make high quality TEM specimens from small features and low contrast materials without a need for special holders. We explain the details of this method and illustrate its potential by examples from three different types of materials.

A method for the fabrication of a wedge-shaped thin NiO lamella by focused ion beam is reported. The starting sample is an oxidized bulk single crystalline, ⟨100⟩ oriented, Ni commercial standard. The lamella is employed for the determination, by analytical electron microscopy at 200 kV of the experimental k(O-Ni) Cliff-Lorimer (G. Cliff & G.W. Lorimer, J Microsc103, 203–207, 1975) coefficient, according to the extrapolation method by Van Cappellen (E. Van Cappellen, Microsc Microstruct Microanal1, 1–22, 1990). The result thus obtained is compared to the theoretical k(O-Ni) values either implemented into the commercial software for X-ray microanalysis quantification of the scanning transmission electron microscopy/energy dispersive spectrometry equipment or calculated by the Monte Carlo method. Significant differences among the three values are found. This confirms that for a reliable quantification of binary alloys containing light elements, the choice of the Cliff-Lorimer coefficients is crucial and experimental values are recommended.

Three-dimensional focused ion beam/scanning electron microscopy (FIB/SEM tomography) is currently an important technique to characterize in 3D a complex semiconductor device or a specific failure. However, the industrial context demands low turnaround time making the technique less useful. To make it more attractive, the following study focuses on a specific methodology going from sample preparation to the final volume reconstruction to reduce the global time analysis while keeping reliable results. The FIB/SEM parameters available will be first analyzed to acquire a relevant dataset in a reasonable time (few hours). Then, a new alignment strategy based on specific alignment marks [using tetraethoxylisane (TEOS) and Pt deposition] is proposed to improve the volume reconstruction speed. These points combined represent a considerable improvement regarding the reliability of the results and the time consumption (gain of factor 3). This method is then applied to various case studies illustrating the benefits of the FIB/SEM tomography technique such as the precise identification of the origin of 3D defects, or the capability to perform a virtual top-down deprocessing on soft material not possible by any mechanical solution.

The lateral and axial resolution of three-dimensional (3D) focal series aberration-corrected scanning transmission electron microscopy was studied for samples of different thicknesses. The samples consisted of gold nanoparticles placed on the top and at the bottom of silicon nitride membranes of thickness between 50 and 500 nm. Atomic resolution was obtained for nanoparticles on top of 50-, 100-, and 200-nm-thick membranes with respect to the electron beam traveling downward. Atomic resolution was also achieved for nanoparticles placed below 50-, 100-, and 200-nm-thick membranes but with a lower contrast at the larger thicknesses. Beam broadening led to a reduced resolution for a 500-nm-thick membrane. The influence of the beam broadening on the axial resolution was also studied using Monte Carlo simulations with a 3D sample geometry.

The ordered structures in different doping levels (x = 0.1, 0.15, 0.2, 0.25, 0.3) of yttrium doped ceria (YDC, Ce(1−x)YxO2−δ) electrolytes were investigated by electron diffraction, high-resolution transmission electron microscopy (TEM), scanning TEM, and electron energy loss spectroscopy. Oxygen vacancy ordering was experimentally confirmed within the ordered structures. With increasing the doping level, the concentration of trivalent Ce cations was increased in YDC samples and such trivalent Ce cations were supposed to mainly exist in the ordered structures. Based on our electron microscopic observation and microanalysis, a crystal model for the ordered structures is proposed.

Stereological analysis has been coupled with transmission electron microscope (TEM) orientation mapping to investigate the grain boundary character distribution in nanocrystalline copper thin films. The use of the nanosized (<5 nm) beam in the TEM for collecting spot diffraction patterns renders an order of magnitude improvement in spatial resolution compared to the analysis of electron backscatter diffraction patterns in the scanning electron microscope. Electron beam precession is used to reduce dynamical effects and increase the reliability of orientation solutions. The misorientation distribution function shows a strong misorientation texture with a peak at 60°/[111], corresponding to the Σ3 misorientation. The grain boundary plane distribution shows {111} as the most frequently occurring plane, indicating a significant population of coherent twin boundaries. This study demonstrates the use of nanoscale orientation mapping in the TEM to quantify the five-parameter grain boundary distribution in nanocrystalline materials.

During laser deposition of Ni-Cr-B-Si-C alloys with high amounts of Cr and B, various microstructures and phases can be generated from the same chemical composition that results in heterogeneous properties in the clad layer. In this study, the microstructure and phase constitution of a high-alloy Ni-Cr-B-Si-C coating deposited by laser cladding were analyzed by a combination of several microscopy characterization techniques including scanning electron microscopy in secondary and backscatter imaging modes, energy dispersive spectroscopy (EDS), electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM). The combination of EDS and EBSD allowed unequivocal identification of micron-sized precipitates as polycrystalline orthorhombic CrB, single crystal tetragonal Cr5B3, and single crystal hexagonal Cr7C3. In addition, TEM characterization showed various equilibrium and metastable Ni-B, Ni-Si, and Ni-Si-B eutectic products in the alloy matrix. The findings of this study can be used to explain the phase formation reactions and to tune the microstructure of Ni-Cr-B-Si-C coatings to obtain the desired properties.

Organic matter (OM) entrapped in calcite is regularly used for environmental studies; however, insertion mechanisms and types of interaction remain poorly understood. The present study used a new methodology to investigate interactions between OM and the calcite matrix during crystallization processes with humic acid (HA) entrapment. A multimethod approach confirmed that HA is both adsorbed onto the calcite surface and incorporated into the calcite lattice during crystallization. Our results also confirm the log-linear correlation between fluorescence intensity and calcite matrix HA concentration. Fourier transform infrared spectroscopy showed that HA in colloidal conformation is adsorbed onto the calcite surface as a result of the structure of the OH stretching band. We also developed a new method based on synchrotron analysis that uses sulfur as a tracer element for entrapped HA and that localizes the OM electrostatically adsorbed onto the calcite surface. Changes in the sulfur environment, determined using X-ray absorption near-edge structure spectroscopy, indicated more complex insertion mechanisms than simple adsorption of HA during calcite crystallization. Desorption experiments revealed the stability of the OM atomic structure and its layered nature. These results allowed us to draw up a general model of OM insertion in calcite.

Elucidation of protein structure using X-ray crystallography relies on the quality of the crystal. Crystals suffer from many different types of disorder, some of which occur during crystal nucleation and early crystal growth. To date, there are few studies surrounding the quality and nucleation of protein crystals partly due to difficulties surrounding viewing biological samples at high resolution. Recent research has led our current understanding of nucleation to be a two-step mechanism involving the formation of nuclei from dense liquid clusters; it is still unclear whether nuclei first start as amorphous aggregate or as crystalline lattices. Our research examines this mechanism through the use of electron microscopy. Using scanning electron microscopy imaging of the protein crystal growth process, a stacking, spiraling manner of growth is observed. The tops of the pyramid-like tetragonal protein crystal structures measure ~0.2 μm across and contain ~125,000 lysozyme units. This noncrystalline area experiences strain due to growth of the protein crystal. Our work shows that it is possible to view detailed early stage protein crystal growth using a wet scanning electron microscopy technique, thereby overcoming the problem of viewing liquids in a vacuum.

We report the development of a method to analyze receptor and β-arrestin2 mobilization between Class A and B GPCRs via time-resolved fluorescent microscopy coupled with semiautomated high-content multiparametric analysis. Using transiently expressed, tagged β2-adrenergic receptor (β2-AR) or parathyroid hormone receptor type 1 (PTH1R), we quantified trafficking of the receptors along with the mobilization and colocalization of coexpressed tagged β-arrestin2. This classification system allows for exclusion of cells with nonoptimal characteristics and calculation of multiple morphological and spatial parameters including receptor endosome formation, β-arrestin mobilization, colocalization, areas, and shape. Stimulated Class A and B receptors demonstrate dramatically different patterns with regard to β-arrestin interactions. The method provides high kinetic resolution measurement of receptor translocation, which allows for the identification of the fleeting β-arrestin interaction found with β2-AR agonist stimulation, in contrast to stronger mobilization and receptor colocalization with agonist stimulation of the PTH1R. Though especially appropriate for receptor kinetic studies, this method is generalizable to any dual fluorescence probe system in which quantification of object formation and movement is desired. These methodologies allow for quantitative, unbiased measurement of microscopy data and are further enhanced by providing real-time kinetics.

Fluorescence resonance energy transfer (FRET) measurement based on partial acceptor photobleaching (PbFRET) is easy to implement without external references. However, the current PbFRET methods are inapplicable to the construct with multiple acceptors, which largely increase the Förster distance. Here, we proposed a linear theory for the dependence of the acceptor photobleaching probability of construct with multiple acceptors on the photobleaching degree (x) and developed a multiple acceptors PbFRET method (Ma-PbFRET) to measure the FRET efficiency of construct with multiple acceptors (n) by measuring the fluorescence intensities of both donor and acceptor channels before and after acceptor photobleaching. The Ma-PbFRET method was validated by measuring the FRET efficiency of construct with two or three acceptors under different x in living cells. Our experimental results demonstrate that the Ma-PbFRET method is capable of exactly quantifying the FRET efficiency of construct with multiple acceptors, providing a simple and powerful tool to investigate the assembly/disassembly of biomolecular complexes with larger distance in living cells.

Podosomes are cellular adhesion structures involved in matrix degradation and invasion that comprise an actin core and a ring of cytoskeletal adaptor proteins. They are most often identified by staining with phalloidin, which binds F-actin and therefore visualizes the core. However, not only podosomes, but also many other cytoskeletal structures contain actin, which makes podosome segmentation by automated image processing difficult. Here, we have developed a quantitative image analysis algorithm that is optimized to identify podosome cores within a typical sample stained with phalloidin. By sequential local and global thresholding, our analysis identifies up to 76% of podosome cores excluding other F-actin-based structures. Based on the overlap in podosome identifications and quantification of podosome numbers, our algorithm performs equally well compared to three experts. Using our algorithm we show effects of actin polymerization and myosin II inhibition on the actin intensity in both podosome core and associated actin network. Furthermore, by expanding the core segmentations, we reveal a previously unappreciated differential distribution of cytoskeletal adaptor proteins within the podosome ring. These applications illustrate that our algorithm is a valuable tool for rapid and accurate large-scale analysis of podosomes to increase our understanding of these characteristic adhesion structures.

It is well known that extracellular signal-regulated kinase 8 (ERK8) plays pivotal roles in various mitotic events. But its physiological roles in oocyte meiotic maturation remain unclear. In this study, we found that although no specific ERK8 signal was detected in oocyte at the germinal vesicle stage, ERK8 began to migrate to the periphery of chromosomes shortly after germinal vesicle breakdown. At prometaphase I, metaphase I (MI), anaphase I, telophase I, and metaphase II (MII) stages, ERK8 was stably detected at the spindles. By taxol treatment, we clarified that the ERK8 signal was stained on the spindle fibers as well as microtubule asters in MI and MII oocytes. In fertilized eggs, the ERK8 signal was not observed in the two pronuclei stages. At prometaphase, metaphase, and anaphase of the first mitosis, ERK8 was detected on the mitotic spindle. ERK8 knock down by antibody microinjection and specific siRNA caused abnormal spindles, failed chromosome congression, and decreased first polar body extrusion. Taken together, our results suggest that ERK8 plays an important role in spindle organization during mouse oocyte meiotic maturation and early embryo cleavage.