Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Mineral borates, the primary industrial source of boron, are found in a large variety of compositions. One such source, kernite (Na2B4O6(OH)2·3H2O), offers an array of challenges for traditional electron-probe microanalysis (EPMA)—it is hygroscopic, an electrical insulator, composed entirely of light elements, and sensitive to both low pressures and the electron beam. However, the approximate stoichiometric composition of kernite can be analyzed with careful preparation, proper selection of reference materials, and attention to the details of quantification procedures, including correction for the time dependency of the sodium X-ray signal. Moreover, a reasonable estimation of the mineral's water content can also be made by comparing the measured oxygen to the calculated stoichiometric oxygen content. X-ray diffraction, variable-pressure electron imaging, and visual inspection elucidate the structural consequences of high vacuum treatment of kernite, while Auger electron spectroscopy and X-ray photoelectron spectroscopy confirm electron beam-driven migration of sodium and oxygen out of the near-surface region (sampling depth ≈ 2 nm). These surface effects are insufficiently large to significantly affect the EPMA results (sampling depth ≈ 400 nm at 5 keV).

In this study, we present a fully automated method to investigate and reconstruct the three-dimensional crack structure beneath an indent in a highly insulating material. This work concentrates on issues arising from a long automatic acquisition process, the insulating nature of the specimen, and the introduction of minimal damage to the original cracks resulting from indentation.

Extracellular matrix (ECM) plays essential signaling and structural roles required for the proper function of cardiac valves. Cardiac valves initially form as jelly-like cushions, which must adapt to withstand the increased circulation hemodynamics associated with fetal development and birth. This increased biomechanical stability of the developing valves is largely imparted by ECM proteins, which form a highly organized fibrous meshwork. Since heart valve defects contribute to most congenital heart diseases, understanding valve development will provide insight into the pathogenesis of various congenital valve anomalies. Thus, the goal of this study is to describe the spatiotemporal deposition of fibrous ECM proteins during cardiac valve development. Chick embryonic and fetal atrioventricular and semilunar valves were examined by light, confocal, and transmission electron microscopy (TEM). Our data demonstrate that fibrous ECM proteins are deposited when the leaflets are adopting an elongated and compacted phenotype. A general pattern of increased fibrotic ECM deposition was detected in valve tissues. Also, each ECM protein examined displayed a unique pattern of organization, suggesting that regulation of fibrous protein deposition is complex and likely involves both genetic and mechanical factors. In addition, the TEM study revealed the presence of membrane protrusions from valvular endocardium, indicating a potential mechanism for mechanical force transduction.

Eight FePt thin film specimens of various thicknesses, compositions, and order parameters have been analyzed to determine the robustness and fidelity of multislice simulations in determining the chemical order parameter via electron diffraction (ED). The shape of the simulated curves depends significantly on the orientation and thickness of the specimen. The ED results are compared to kinematical scattering order parameters, from the same films, acquired from synchrotron X-ray diffraction (XRD). For the specimens analyzed with convergent beam electron diffraction conditions, the order parameter closely matched the order parameter as determined by the XRD methodology. However, the specimens analyzed by selected area electron diffraction conditions did not show good agreement. This has been attributed to substrate effects that hindered the ability to accurately quantify the intensity values of the superlattice and fundamental reflections.

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Karyotype analysis and classification of buckwheat chromosomes were performed without chemical banding or staining using atomic force microscopy (AFM). Fagopyrum esculentum (common buckwheat) and Fagopyrum tartaricum (Tartarian buckwheat) chromosomes were isolated from root tissues using an enzymatic maceration technique and spread over a glass substrate. Air-dried chromosomes had a surface with ridges, and the height of common and tartary buckwheat were approximately 350 and 150 nm. Volumes of metaphase sets of buckwheat chromosomes were calculated using three-dimensional AFM measurements. Chromosomes were morphologically characterized by the size, volume, arm lengths, and ratios. The calculated volumes of the F. esculentum and F. tartaricum chromosomes were in the ranges of 1.08–2.09 μm3 and 0.49–0.78 μm3, respectively. The parameters such as the relative arm length, centromere position, and the chromosome volumes measured using AFM provide accurate karyomorphological classification by avoiding the subjective inconsistencies in banding patterns of conventional methods. The karyotype evolutionary trend indicates that F. esculentum is an ancient species compared to F. tartaricum. This is the first report of a cytological karyotype of buckwheat using AFM.

A culture's confluency is a fundamental measure in the field of biology, and routine quantification of confluence in cell culture protocols, biological assays and tissue engineering work is important. However, current techniques for obtaining confluency are either subjective, destructive, not simple enough, or time-consuming. We developed an image processing method for automated confluency measurement from a single microscope image without any chemical staining. To demonstrate utility we monitored the confluency of three cell types: NIH3T3 fibroblasts, C2C12 myoblasts, and 3T3L1 pre-adipocytes for 5 days, twice a day. The captured micrographs had different and uneven illumination, the cell types varied in cell-to-background contrast, and the confluency ranged between 10% and 100%. Despite these variable conditions, our method was shown to be practical, economic, and easy to implement, providing quantitative confluency measurements over time in each culture case. The method is hence suitable for routine automatic determination of confluency to standardize handling of cells, achieve reproducibility across trials, and improve accuracy in experimental outcome measures.

Lizard erythrocytic viruses (LEVs) have previously been described in Lacerta monticola from Serra da Estrela, Portugal. Like other known erythrocytic viruses of heterothermic vertebrates, these viruses have never been adapted to cell cultures and remain uncharacterized at the molecular level. In this study, we made attempts to adapt the virus to cell cultures that resulted instead in the isolation of a previously undetected Ranavirus closely related to FV3. The Ranavirus was subsequently detected by polymerase chain reaction (PCR) in the blood of infected lizards using primers for a conserved portion of the Ranavirus major capsid protein gene. Electron microscopic study of the new Ranavirus disclosed, among other features, the presence of intranuclear viruses that may be related to an unrecognized intranuclear morphogenetic process. Attempts to detect by PCR a portion of the DNA polymerase gene of the LEV in infected lizard blood were successful. The recovered sequence had 65.2/69.4% nt/aa% homology with a previously detected sequence from a snake erythrocytic virus from Florida, which is ultrastructurally different from the studied LEV. These results further support the hypothesis that erythrocytic viruses are related to one another and may represent a new group of nucleo-cytoplasmic large deoxyriboviruses.

The present work shows results on elemental distribution analyses in Cu(In,Ga)Se2 thin films for solar cells performed by use of wavelength-dispersive and energy-dispersive X-ray spectrometry (EDX) in a scanning electron microscope, EDX in a transmission electron microscope, X-ray photoelectron, angle-dependent soft X-ray emission, secondary ion-mass (SIMS), time-of-flight SIMS, sputtered neutral mass, glow-discharge optical emission and glow-discharge mass, Auger electron, and Rutherford backscattering spectrometry, by use of scanning Auger electron microscopy, Raman depth profiling, and Raman mapping, as well as by use of elastic recoil detection analysis, grazing-incidence X-ray and electron backscatter diffraction, and grazing-incidence X-ray fluorescence analysis. The Cu(In,Ga)Se2 thin films used for the present comparison were produced during the same identical deposition run and exhibit thicknesses of about 2 μm. The analysis techniques were compared with respect to their spatial and depth resolutions, measuring speeds, availabilities, and detection limits.

We show in this article that it is possible to obtain elemental compositional maps and profiles with atomic-column resolution across an InxGa1−xAs multilayer structure from 5th-order aberration-corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) images. The compositional profiles obtained from the analysis of HAADF-STEM images describe accurately the distribution of In in the studied multilayer in good agreement with Muraki's segregation model [Muraki, K., Fukatsu, S., Shiraki, Y. & Ito, R. (1992). Surface segregation of In atoms during molecular beam epitaxy and its influence on the energy levels in InGaAs/GaAs quantums wells. Appl Phys Lett61, 557–559].

X-ray elemental mapping and X-ray spectrum imaging are powerful microanalytical tools. However, their scope is often limited spatially by the raster area of a scanning electron microscope or microprobe. Limited sampling size becomes a significant issue when large area (>10 cm2), heterogeneous materials such as concrete samples or others must be examined. In such specimens, macro-scale structures, inclusions, and concentration gradients are often of interest, yet microbeam methods are insufficient or at least inefficient for analyzing them. Such requirements largely exclude the samples of interest presented in this article from electron probe microanalysis. Micro X-ray fluorescence–X-ray spectrum imaging (μXRF-XSI) provides a solution to the problem of macro-scale X-ray imaging through an X-ray excitation source, which can be used to analyze a variety of large specimens without many of the limitations found in electron-excitation sources. Using a mid-sized beam coupled with an X-ray excitation source has a number of advantages, such as the ability to work at atmospheric pressure and lower limits of detection owing to the absence of electron-induced bremsstrahlung. μXRF-XSI also acts as a complement, where applicable, to electron microbeam X-ray output, highlighting areas of interest for follow-up microanalysis at a finer length scale.

The elemental composition and microscopic-level shape of inclusions inside industrial materials are considered important factors in fracture analytical studies. In this work, a three-dimensional (3D) microscopic elemental analysis system based on a serial sectioning technique was developed to observe the internal structure of such materials. This 3D elemental mapping system included an X-ray fluorescence analyzer and a high-precision milling machine. Control signals for the X-ray observation process were automatically sent from a data I/O system synchronized with the precision positioning on the milling machine. Composite specimens were used to confirm the resolution and the accuracy of 3D models generated from this system. Each of the two specimens was composed of three metal wires of 0.5 mm diameter braided into a single twisted wire that was placed inside a metal pipe; the pipe was then filled with either epoxy resin or Sn. The milling machine was used to create a mirror-finish cross-sectional surface on these specimens, and elemental analyses were performed. The twisted wire structure was clearly observed in the resulting 3D models. This system enables automated investigation of the 3D internal structure of materials as well as the identification of their elemental components.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Microscopy & Microanalysis 2011, the premier conference of the field, is this year being hosted by the Microscopy Society of America, the Microanalysis Society, and the International Metallographic Society. On behalf of our respective societies, we welcome you to Nashville, Tennessee, the Music City, truly one of the most entertaining cities in America. We are confident that Nashville will serve as a wonderful location for our meeting, and that the conference will prove to be stimulating and worthwhile for all both on a professional and personal level.

When biological specimens are cut into physical sections for three-dimensional (3D) imaging by confocal laser scanning microscopy, the slices may get distorted or ruptured. For subsequent 3D reconstruction, images from different physical sections need to be spatially aligned by optimization of a function composed of a data fidelity term evaluating similarity between the reference and target images, and a regularization term enforcing transformation smoothness. A regularization term evaluating the total variation (TV), which enables the registration algorithm to account for discontinuities in slice deformation (ruptures), while enforcing smoothness on continuously deformed regions, was proposed previously. The function with TV regularization was optimized using a graph-cut (GC) based iterative solution. However, GC may generate visible registration artifacts, which impair the 3D reconstruction. We present an alternative, multilabel TV optimization algorithm, which in the examined samples prevents the artifacts produced by GC. The algorithm is slower than GC but can be sped up several times when implemented in a multiprocessor computing environment. For image pairs with uneven brightness distribution, we introduce a reformulation of the TV-based registration, in which intensity-based data terms are replaced by comparison of salient features in the reference and target images quantified by local image entropies.

Procedures to study the molecular and morphological characteristics of microscopic organisms are often incompatible with each other. Therein, the realization of alternatives that make the characterization of these features compatible and simultaneously permit the deposition of the original material as a voucher sample into a reference collection is one of the foremost goals of biodiversity studies. In this study, we show that genomic extraction does not necessarily compromise the detailed study of the external morphology of microscopic organisms, and to do so, we used a group of aquatic mites (Acari, Hydrachnidia) as a test group. Hydrachnidia morphology is difficult to study when specimens have been stored in pure ethanol; however, proteinase K extraction leaves them flexible and easy to dissect, while, at the same time, maintaining all of their diagnostic features intact. Furthermore, autofluorescence is significantly enhanced after proteinase extraction. Our study was conducted with aquatic mites that were stored in absolute ethanol in the field and processed for DNA extraction using a Qiagen QIAamp minikit. Before and after molecular extraction, a laser scanning confocal microscopy morphological examination was carried out.

We demonstrate for the first time that multivariate statistical analysis techniques can be applied to atom probe tomography data to estimate the chemical composition of a sample at the full spatial resolution of the atom probe in three dimensions. Whereas the raw atom probe data provide the specific identity of an atom at a precise location, the multivariate results can be interpreted in terms of the probabilities that an atom representing a particular chemical phase is situated there. When aggregated to the size scale of a single atom (∼0.2 nm), atom probe spectral-image datasets are huge and extremely sparse. In fact, the average spectrum will have somewhat less than one total count per spectrum due to imperfect detection efficiency. These conditions, under which the variance in the data is completely dominated by counting noise, test the limits of multivariate analysis, and an extensive discussion of how to extract the chemical information is presented. Efficient numerical approaches to performing principal component analysis (PCA) on these datasets, which may number hundreds of millions of individual spectra, are put forward, and it is shown that PCA can be computed in a few seconds on a typical laptop computer.

Fellow Microscopists and Microanalysts, Colleagues and most importantly Students, welcome to Microscopy & Microanalysis 2011 here in Nashville, Tennessee, our seventeenth conference under that appellation.

The twin interface structure in twinning superlattice InP nanowires with zincblende structure has been investigated using electron exit wavefunction restoration from focal series images recorded on an aberration-corrected transmission electron microscope. By comparing the exit wavefunction phase with simulations from model structures, it was possible to determine the twin structure to be the ortho type with preserved In-P bonding order across the interface. The bending of the thin nanowires away from the intended ⟨110⟩ axis could be estimated locally from the calculated diffraction pattern, and this parameter was successfully taken into account in the simulations.