A method for phase analysis, similar to the Rietveld method in X-ray diffraction, was not developed for electron diffraction (ED) in the transmission electron microscope (TEM), mainly due to the dynamic nature of ED. Nowadays, TEM laboratories encounter many thin samples with grain size in the 1–30 nm range, not too far from the kinematic ED conditions. This article describes a method that performs (semi)quantitative phase analysis for nanocrystalline samples from selected area electron diffraction (SAED) patterns. Fractions of the different nanocrystalline components are determined from rotationally symmetric ring patters. Both randomly oriented nanopowders and textured nanopowders, observed from the direction of the texture axis produce such SAED patterns. The textured fraction is determined as a separate component by fitting the spectral components, calculated for the previously identified phases with a priori known structures, to the measured distribution. The Blackman correction is applied to the set of kinematic diffraction lines to take into account dynamic effects for medium grain size. Parameters of the peak shapes and the other experimental parameters are refined by exploring the parameter space with the help of the Downhill-SIMPLEX. Part I presents the principles, while future publication of Parts II and III will elaborate on current implementation and will demonstrate its usage by examples, respectively.

The application of wide field-of-view detection systems to atom probe experiments emphasizes the importance of careful parameter selection in the tomographic reconstruction of the analyzed volume, as the sensitivity to errors rises steeply with increases in analysis dimensions. In this article, a self-consistent method is presented for the systematic determination of the main reconstruction parameters. In the proposed approach, the compression factor and the field factor are determined using geometrical projections from the desorption images. A three-dimensional Fourier transform is then applied to a series of reconstructions, and after comparing to the known material crystallography, the efficiency of the detector is estimated. The final results demonstrate a significant improvement in the accuracy of the reconstructed volumes.

A method for the experimental determination of the absolute efficiency of wavelength dispersive spectrometers was developed, based on the comparison of spectra measured with a wavelength dispersive system and with an energy dispersive spectrometer. The aim of studying this parameter arises because its knowledge is necessary to perform standardless analysis. A simple analytical expression was obtained for the efficiency curve for three crystals (TAP, PET, and LiF) of the spectrometer used, within an energy range from 0.77 to 10.83 keV. Although this expression is particular for the system used in this work, the method may be extended to other spectrometers and crystals for electron probe microanalysis and X-ray fluorescence.

Molecular dynamics simulations are performed to model milling via a focused ion beam (FIB). The goal of this investigation is to examine the fundamental dynamics associated with the use of FIBs, as well as the phenomena that govern the early stages of trench formation during the milling process. Using a gallium beam to bombard a silicon surface, the extent of lateral damage (atomic displacement) caused by the beam at incident energies of both 2 and 30 keV is examined. These simulations indicate that the lateral damage is several times larger than the beam itself and that the mechanism responsible for the formation of a V-shaped trench is due to both the removal of surface material, and the lateral and horizontal migration of subsurface silicon atoms toward the vacuum/crater interface. The results presented here provide complementary information to experimental images of trenches created during milling with FIBs.

A radioactive particle embedded in a sediment collected from the Irish Sea was examined with spectrometric methods to understand the potential bioavailability of its constituents. Images of the particle surface were acquired in the backscattering mode by scanning electron microscopy. The elemental composition of the particle surface layer was measured using energy dispersive (SEM-EDX) and wavelength dispersive (SEM-WDX) X-ray spectrometers. The investigation showed that the sample consists of a calcite matrix in which uranium is present in the form of separate inclusions. The diameter of U inclusions was less than 10 μm. Synchrotron radiation based X-ray fluorescence in confocal geometry (confocal μ-XRF) was used to determine the spatial distribution of elements in the particle. Three-dimensional reconstructions of the Ca, Cr, Mn, Fe, Zn, Sr, Ba, Pb, and U distributions were performed. The oxidation state of uranium in the different inclusions was determined by synchrotron radiation based X-ray absorption in confocal geometry (confocal μ-XANES). The isotopic composition of uranium was measured by secondary ion mass spectrometry. The results revealed that uranium was depleted in 235U. Pu and other actinides were not detected.

Layer- and tunnel-structured manganese oxide nanomaterials are important because of their potential applications in industrial catalysis. A novel soft chemistry method was developed for the synthesis of inorganic cryptomelane nanomaterials with high surface area. Bright field transmission electron microscopy (BF-TEM) and high-resolution transmission electron microscopy (HRTEM) techniques were employed to characterize this nanomaterial. A nanosized material with fibrous texture comprised of 140–160 nm striations was identified by BF-TEM imaging. HRTEM images show multiple atomic morphologies such as “helix-type,” “doughnut-like,” and tunnel structures lying on different crystallographic planes. The crystallographic parameters of this material were analyzed and measured by X-ray powder diffraction (XRD) showing that the synthesized nanomaterial is single phased and corresponds to cryptomelane with major diffraction peaks (for 10° < 2θ < 60°) at d-spacing values of 6.99, 4.94, 3.13, 2.40, 2.16, 1.84, 1.65, and 1.54 Å. A “doughnut-like” crystal structure was confirmed based on the crystallographic data. Structure and lattice parameters refinement was performed by XRD/Rietveld analysis. Simple simulation of HRTEM images and selected area diffraction patterns were applied to interpret the HRTEM images as observed.

Polyphosphates are used in drinking water to prevent the precipitation of cations such as calcium and iron. The possible negative impact of using polyphosphates is the undesirable complexation of lead that could result in elevated lead levels in consumers' tap water. Although the water industry has focused on complexation, lead polyphosphate solids such as lead pyrophosphate, Pb2P2O7, have been considered in other fields and not been shown to form in water. The ability to form lead pyrophosphate in water could have a potential impact on the strategies used to reduce lead levels in drinking water distribution systems. The objective of this work was to determine whether lead pyrophosphate could form under simulated potable drinking water conditions. Lead pyrophosphate was synthesized in water (pH 8.2, 10 mg C/L, 2.7 mg Cl2/L) after 13 days of aging. The formation of lead pyrophosphate was confirmed by X-ray diffraction and microscopy analysis. Synthesis did not require elevated temperatures or microwave assisted approaches used by past researchers. The findings suggest that lead (and possibly other metal) pyrophosphates could conceivably form in real drinking water systems, although much more work is necessary to determine the chemistry and kinetic boundaries.

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.

Spindle movement, including spindle migration during first meiosis and spindle rotation during second meiosis, is essential for asymmetric divisions in mouse oocytes. Previous studies by others and us have shown that microfilaments are required for both spindle migration and rotation. In the present study, we aimed to further investigate the mechanism controlling spindle movement during mouse oocyte meiosis. By employing drug treatment and immunofluorescence microscopy, we showed that dynamic microtubule assembly was involved in both spindle migration and rotation. Furthermore, we found that the calcium/CaM/CaMKII pathway was important for regulating spindle rotation.

Observation of the internal ultrastructure of human chromosomes by transmission electron microscopy (TEM) has frequently been attempted in spite of the difficulties in detaching metaphase chromosome spreads from the glass slide for further processing. In this study we have used a method in which metaphase chromosome spreads were prepared on a flexible thermoplastic membrane (ACLAR) film. To assess chromosome identity, a diamidino-phenylindole staining and karyotying was first done using a conventional cytogenetic system. The chromosome spreads were then fixed with 1% osmium tetroxide, stained with freshly prepared 2% tannic acid, dehydrated, and flat-embedded in epoxy resin. The resin sheet was easily detachable and carried whole chromosome spreads. By this method, TEM observation of chromosomes from normal human lymphocytes allowed a thorough examination of the ultrastructure of centromeres, telomeres, fragile sites, and other chromosomal regions. Various ultrastructural patterns including thick electron dense boundaries, less dense internal regions, and extended chromatin loops at the periphery of the chromosomes were discernible. Application of the present method to chromosome research is expected to provide comprehensive information on the internal ultrastructure of different chromosomal regions in relation to function.

Digital imaging has been applied to structure analysis of biological macromolecules in combination with electron energy filtering. Energy filtering can improve the image contrast of frozen-hydrated specimens, but needs a high-sensitivity imaging device instead of photographic film, because of a decrease in electrons after filtration. Here, a lens-coupled slow-scan charge-coupled device (SSCCD) camera with a post-column-type energy filter were examined to image bacterial flagellar filaments embedded in ice. We first measured the modulation transfer function of this camera and showed the remarkable improvement, compared to other fiber-coupled SSCCD cameras. The 3D structure calculated at ∼7-Å resolution clearly resolves α-helices. Furthermore, filtered datasets recorded on the SSCCD camera with liquid-nitrogen and liquid-helium cooling were compared with the previous unfiltered one on film with liquid-helium cooling. This report describes the suitability of digital imaging with energy filtering for higher-resolution structure studies from its practical application.