We have developed two integrated thermocouple (TC) crucible systems that allow precise measurement of sample temperature when using a furnace associated with an environmental scanning electron microscope (ESEM). Sample temperatures measured with these systems are precise (±5°C) and reliable. The TC crucible systems allow working with solids and liquids (silicate melts or ionic liquids), independent of the gas composition and pressure. These sample holder designs will allow end users to perform experiments at high temperature in the ESEM chamber with high precision control of the sample temperature.

In this paper, three-dimensional (3D) image data of ore particle systems is investigated. By combining X-ray microtomography with scanning electron microscope (SEM)-based image analysis, additional information about the mineralogical composition from certain planar sections can be gained. For the analysis of tomographic images of particle systems the extraction of single particles is essential. This is performed with a marker-based watershed algorithm and a post-processing step utilizing a neural network to reduce oversegmentation. The results are validated by comparing the 3D particle-wise segmentation empirically with 2D SEM images, which have been obtained with a different imaging process and segmentation algorithm. Finally, a stereological application is shown, in which planar SEM images are embedded into the tomographic 3D image. This allows the estimation of local X-ray attenuation coefficients, which are material-specific quantities, in the entire tomographic image.

For over a decade fluorescence microscopy has demonstrated the capacity to achieve single-molecule localization accuracies of a few nanometers, well below the ∼200 nm lateral and ∼500 nm axial resolution limit of conventional microscopy. Yet, only the recent development of new fluorescence labeling modalities, the increase in sensitivity of imaging hardware, and the creation of novel image analysis tools allow for the emergence of single-molecule-based super-resolution imaging techniques. Novel methods such as photoactivated localization microscopy and stochastic optical reconstruction microscopy can typically reach a tenfold increase in resolution compared to standard microscopy methods. Their implementation is relatively easy only requiring minimal changes to a conventional wide-field or total internal reflection fluorescence microscope. The recent translation of these two methods into commercial imaging systems has made them further accessible to researchers in biology. However, these methods are still evolving rapidly toward imaging live samples with high temporal resolution and depth. In this review, we recall the roots of single-molecule localization microscopy, summarize major recent developments, and offer perspective on potential applications.

Cation exchange capacity (CEC) characterizes the number of fixed negative charges of plant cell walls and is an important parameter in studies dealing with the uptake of ions into plant tissues, especially in roots. Conventional methods of CEC determination use bulk tissue, the results are the mean of many cells, and differences in the CEC of different tissue types are masked. Energy-dispersive microanalysis (EDX) in the transmission electron microscope allows CEC determinations on much finer scales. Shoot and fine root tissue of Picea abies was acid washed to remove exchangeable cations. Tissue blocks or semithin tissue sections were loaded with 0.2 mM CaCl2, AlCl3, or Pb(NO3)2 at pH 4.0. The amount of Ca, Al, or Pb adsorbed to the exchange sites of cell walls was determined by EDX. The CEC of cell walls of different tissue types was highly different, ranging in shoot tissues from 0 to 856 mM Ca and 5.8 to 1463 mM Al (block loading) or 4.3 to 1116 mM Ca and 0 to 2830 mM Al (section loading). In root tissue, Pb adsorption to semithin sections yielded CEC values between 29.1 and 954 mM Pb. In most P. abies shoot tissues, the binding capacity was clearly higher for Al than for Ca.

Sintering of a palladium catalyst supported on alumina (Al2O3) in an oxidizing environment was studied by in situ transmission electron microscopy (TEM). In the case of a fresh catalyst, sintering of Pd particles on an alumina surface in a 500 mTorr steam environment happened via traditional ripening or migration and coalescence mechanisms and was not significant unless heating above 500°C. After the catalyst was used for the hydrogenation of alkynes, TEM coupled with convergent beam electron diffraction and electron energy loss spectroscopy analysis revealed that most of the Pd particles were lifted from the alumina surface by hydrocarbon buildup. This dramatically different morphology totally changed the sintering mechanism of Pd particles during the regeneration process. Catalytic gasification of hydrocarbon around these particles in an oxidizing environment allowed the Pd particles to move around and coalesce with each other at temperatures as low as 350°C. For catalysts heating under 500 mTorr steam at 350°C, steam stripped hydrocarbon catalytically at the beginning, but the reaction stopped after 4 h. Heating in air resulted in both catalytic and noncatalytic stripping of hydrocarbon.

Contemporary research aims to understand biological processes not only by identifying participating proteins, but also by characterizing the dynamics of their interactions. Because Förster's Resonance Energy Transfer (FRET) is invaluable for the latter undertaking, its usage is steadily increasing. However, FRET measurements are notoriously error-prone, especially when its inherent efficiency is low, a not uncommon situation. Furthermore, many FRET methods are either difficult to implement, are not appropriate for observation of cellular dynamics, or report instrument-specific indices that hamper communication of results within the scientific community. We present here a novel comprehensive spectral methodology, SpRET, which substantially increases both the reliability and sensitivity of FRET microscopy, even under unfavorable conditions such as weak fluorescence or the presence of noise. While SpRET overcomes common pitfalls such as interchannel crosstalk and direct excitation of the acceptor, it also excels in removal of autofluorescence or background contaminations and in correcting chromatic aberrations, often overlooked factors that severely undermine FRET experiments. Finally, SpRET quantitatively reports absolute rather than relative FRET efficiency values, as well as the acceptor-to-donor molar ratio, which is critical for full and proper interpretation of FRET experiments. Thus, SpRET serves as an advanced, improved, and powerful tool in the cell biologist's toolbox.

Short illumination wavelength allows an extension of the diffraction limit toward nanometer scale; thus, improving spatial resolution in optical systems. Soft X-ray (SXR) radiation, from “water window” spectral range, λ=2.3–4.4 nm wavelength, which is particularly suitable for biological imaging due to natural optical contrast provides better spatial resolution than one obtained with visible light microscopes. The high contrast in the “water window” is obtained because of selective radiation absorption by carbon and water, which are constituents of the biological samples. The development of SXR microscopes permits the visualization of features on the nanometer scale, but often with a tradeoff, which can be seen between the exposure time and the size and complexity of the microscopes. Thus, herein, we present a desk-top system, which overcomes the already mentioned limitations and is capable of resolving 60 nm features with very short exposure time. Even though the system is in its initial stage of development, we present different applications of the system for biology and nanotechnology. Construction of the microscope with recently acquired images of various samples will be presented and discussed. Such a high resolution imaging system represents an interesting solution for biomedical, material science, and nanotechnology applications.

Genetic manipulation allows simultaneous expression of green fluorescent protein (GFP) and its derivatives with a wide variety of cellular proteins in a variety of living systems. Epifluorescent and confocal laser scanning microscopy (confocal) localization of GFP constructs within living tissue and cell cultures has become routine, but correlation of light microscopy and high resolution transmission electron microscopy (TEM) on components within identical cells has been problematic. In this study, we describe an approach that specifically localizes the position of GFP/yellow fluorescent protein (YFP) constructs within the same cultured cell imaged in the confocal and transmission electron microscopes. We present a simplified method for delivering cell cultures expressing fluorescent fusion proteins into LR White embedding media, which allows excellent GFP/YFP detection and also high-resolution imaging in the TEM. Confocal images from 0.5-μm-thick sections are overlaid atop TEM images of the same cells collected from the next serial ultrathin section. The overlay is achieved in Adobe Photoshop by making the confocal image somewhat transparent, then carefully aligning features within the confocal image over the same features visible in the TEM image. The method requires no specialized specimen preparation equipment; specimens are taken from live cultures to embedding within 8 h, and confocal transmission overlay microscopy can be completed within a few hours.

We summarize the findings from an interlaboratory study conducted between ten international research groups and investigate the use of the commonly used maximum separation distance and local concentration thresholding methods for solute clustering quantification. The study objectives are: to bring clarity to the range of applicability of the methods; identify existing and/or needed modifications; and interpretation of past published data. Participants collected experimental data from a proton-irradiated 304 stainless steel and analyzed Cu-rich and Ni–Si rich clusters. The datasets were also analyzed by one researcher to clarify variability originating from different operators. The Cu distribution fulfills the ideal requirements of the maximum separation method (MSM), namely a dilute matrix Cu concentration and concentrated Cu clusters. This enabled a relatively tight distribution of the cluster number density among the participants. By contrast, the group analysis of the Ni–Si rich clusters by the MSM was complicated by a high Ni matrix concentration and by the presence of Si-decorated dislocations, leading to larger variability among researchers. While local concentration filtering could, in principle, tighten the results, the cluster identification step inevitably maintained a high scatter. Recommendations regarding reporting, selection of analysis method, and expected variability when interpreting published data are discussed.

The details of ice interface dynamics in complex systems are critical to a variety of natural and commercial processes. A platform for low temperature environmental transmission electron microscopy is developed and applied to characterization of ice crystallization in colloidal solutions. The platform is utilized for studying the phase evolution in ice during crystallization and the dynamic interactions of Au nanoparticles at the crystallization front. The results indicate that models developed to treat ice–particle interactions at the micron scale extend well to the nanoscale.

Here, we report reproducible and accurate measurement of crystallographic parameters using scanning transmission electron microscopy. This is made possible by removing drift and residual scan distortion. We demonstrate real-space lattice parameter measurements with <0.1% error for complex-layered chalcogenides Bi2Te3, Bi2Se3, and a Bi2Te2.7Se0.3 nanostructured alloy. Pairing the technique with atomic resolution spectroscopy, we connect local structure with chemistry and bonding. Combining these results with density functional theory, we show that the incorporation of Se into Bi2Te3 causes charge redistribution that anomalously increases the van der Waals gap between building blocks of the layered structure. The results show that atomic resolution imaging with electrons can accurately and robustly quantify crystallography at the nanoscale.

Toxoplasma gondii, the causative agent of toxoplasmosis, is capable of actively penetrating and multiplying in any nucleated cell of warm-blooded animals. Its survival strategies include escape from fusion of the parasitophorous vacuole with host cell lysosomes and rearrangement of host cell organelles in relation to the parasitophorous vacuole. In this article we report the rearrangement of host cell organelles and elements of the cytoskeleton of LLCMK2 cells, a lineage derived from green monkey kidney epithelial cells, in response to infection by T. gondii tachyzoites. Transmission electron microscopy made on flat embedded monolayers cut horizontally to the apical side of the cells or field emission scanning electron microscopy of monolayers scraped with scotch tape before sputtering showed that association of mitochondria to the vacuole is much less frequent than previously described. On the other hand, all parasitophorous vacuoles were surrounded by elements of the endoplasmic reticulum. These data were complemented by observations by laser scanning microscopy using fluorescent probes from mitochondria and endoplasmic reticulum and reinforced by three-dimensional reconstruction from serial sections observed by transmission electron microscopy and labeling of mitochondria and endoplasmic reticulum by fluorescent probes.

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

The gap junction (GJ) is an aggregate of intercellular channels that facilitates cytoplasmic interchange of ions, second messengers, and other molecules of less than 1000 Da between cells. In excitable organs such as heart and brain, GJs configure extended intercellular pathways for stable and long-term propagation of action potential. In a previous study in adult rat heart, we have shown that the Drosophila disks-large related protein ZO-1 shows low to moderate colocalization at myocyte borders with the GJ protein Cx43. In the present study, we detail a protocol for characterizing the pattern and level of colocalization of ZO-1 with Cx43 in cultures of neonatal myocytes at the level of individual GJ plaques. The data indicate that ZO-1 shows on average a partial 26.6% overlap (SD = 11.3%) with Cx43 GJ plaques. There is a strong positive correlation between GJ plaque size and area of ZO-1 colocalization, indicating that the level of associated ZO-1 scales with the area of the GJ plaque. Qualitatively, the most prominent colocalization occurs at the plaque perimeter. These studies may provide insight into the presently unknown biological function of ZO-1 interaction with Cx43.

This study describes the use of transmission electron holography to determine the mean inner potential of polystyrene. Spherical nanoparticles of amorphous polystyrene are studied so that the effect of specimen thickness on the phase shift of an incident electron wave can be separated from the intrinsic refractive properties of the specimen. A recursive four-parameter χ-squared minimization routine is developed to determine the sphere center, radius, and mean inner potential (Φ0) at each pixel in the phase image. Because of the large number of pixels involved, the statistics associated with determining a single Φ0 value characteristic of a given sphere are quite good. Simulated holograms show that the holographic reconstruction procedure and the χ-squared analysis method are robust. Averaging the Φ0 data derived from ten phase images from ten different polystyrene spheres gives a value of Φ0PS = 8.5 V (σ) = 0.7 V). Specimen charging and electron-beam damage, if present, affect the measurement at a level below the current precision of the experiment.

Scanning transmission electron microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In recent years, attention has focused on the potential of STEM to explore beam induced chemical processes and especially manipulating atomic motion, enabling atom-by-atom fabrication. These applications, as well as traditional imaging of beam sensitive materials, necessitate increasing the dynamic range of STEM in imaging and manipulation modes, and increasing the absolute scanning speed which can be achieved by combining sparse sensing methods with nonrectangular scanning trajectories. Here we have developed a general method for real-time reconstruction of sparsely sampled images from high-speed, noninvasive and diverse scanning pathways, including spiral scan and Lissajous scan. This approach is demonstrated on both the synthetic data and experimental STEM data on the beam sensitive material graphene. This work opens the door for comprehensive investigation and optimal design of dose efficient scanning strategies and real-time adaptive inference and control of e-beam induced atomic fabrication.

Strained layer heterostructures provide ideal systems with which to study the dynamics of dislocation motion via in situ transmission electron microscopy, as the geometry, strain state, and kinetics can be characterized and directly controlled. We discuss how these structures are used to study dislocation-point defect interactions, emphasizing the experimental requirements necessary for quantification of dislocation motion. Following ion implantation, different concentrations and types of point defects are introduced within the SiGe epilayer depending on the implantation species, energy, and current density. By annealing samples in situ in the transmission electron microscope (TEM) following implantation, we can directly observe dislocation motion and quantify the effect of dislocation-point defect interactions on dislocation velocities. We find that dislocation motion is impeded if the implantation dose peak lies within the epilayer, as dislocations pin at point defect atmospheres. Shallow BF2 implantation into the sample capping layer results in more complicated behavior. For low current density implants, dislocation velocities may be dramatically increased; at higher current densities the magnitude of this increase is significantly smaller. Implantation of different ions separately implicates fluorine as the species responsible for the observed increases in dislocation velocities, presumably due to an electrical effect on the rate of dislocation kink nucleation.

Electron beam X-ray microanalysis with semiconductor energy-dispersive spectrometry (EDS) performed with standards and calculated matrix corrections can yield quantitative results with a distribution such that 95% of analyses fall within ±5% relative for major and minor constituents. Standardless methods substitute calculations for the standard intensities, based either on physical models of X-ray generation and propagation (first principles) or on mathematical fits to remotely measured standards (fitted standards). Error distributions have been measured for three different standardless analysis procedures with a suite of microanalysis standards including metal alloys, glasses, minerals, ceramics, and stoichiometric compounds. For the first-principles standardless procedure, the error distribution placed 95% of analyses within ±50% relative, whereas for two commercial fitted standards procedures, the error distributions placed 95% of analyses within ±25% relative. The implication of these error distributions for the accuracy of analytical results is considered, and recommendations for the use of standardless analysis are given.