A method for obtaining quantitative mean atomic number images in a scanning electron microscope for different kinds of samples has been developed. The backscattered electron signal is monotonically increasing with the mean atomic number Z, and accordingly Z can be given as a function of the image gray levels. From results obtained from Monte Carlo simulations, an exponential function is fitted to convert the backscattered registered gray levels into a Z image map. Once this fitting was performed, the reproducibility of the Z determination was checked through the acquisition of backscattered electron images from metal and mineral standards. The developed method can be applied to any unknown sample, always controlling the experimental conditions, as shown here for a thin section of a rock in which several unknown mineral phases are present; the results obtained herein are compared to quantitative assessments performed with X-ray spectra from each mineral phase.

Confocal fluorescence microscopy is a broadly used imaging technique that enhances the signal-to-noise ratio by removing out of focal plane fluorescence. Confocal microscopes come with a variety of modifications depending on the particular experimental goals. Microscopes, illumination pathways, and light collection were originally focused upon obtaining the highest resolution image possible, typically on fixed tissue. More recently, live-cell confocal imaging has gained importance. Since measured signals are often rapid or transient, thus requiring higher sampling rates, specializations are included to enhance spatial and temporal resolution while maintaining tissue viability. Thus, a balance between image quality, temporal resolution, and tissue viability is needed. A subtype of confocal imaging, termed swept field confocal (SFC) microscopy, can image live cells at high rates while maintaining confocality. SFC systems can use a pinhole array to obtain high spatial resolution, similar to spinning disc systems. In addition, SFC imaging can achieve faster rates by using a slit to sweep the light across the entire image plane, thus requiring a single scan to generate an image. Coupled to a high-speed charge-coupled device camera and a laser illumination source, images can be obtained at greater than 1,000 frames per second while maintaining confocality.

The use of plants as a source of medicine is an important component of the health care system in rural India. Carex baccans (Cyperaceae) and Potentilla fulgens (Rosaceae) have been known since ancient times in northeast India for their antitumor, antidiabetic, and antihelmintic properties. The present study was designed to determine the subacute toxicity profile of the root tuber extract of C. baccans and root-peel extract of P. fulgens in Wistar rats. The subacute oral toxicity was conducted using sublethal doses of 40, 50, 100, 150, 200, and 400 mgkg−1 body weights. Surface topographical and ultrastructural observations of liver and intestinal microvilli showed remarkable deformation and disruption, accompanied by quantitative changes in the liver enzymes, i.e., aspartate aminotransferase and alanine aminotransferase in comparison to those of the control group. Apoptotic cell death was observed in the liver cells of rats exposed to both of the plant extracts. A significant increase in splenic lymphocyte count was also observed in rats exposed to the highest concentration of both extracts. The results showed that consumption of the plant extracts at higher doses may cause toxicological effect if treatment continues for a long time.

Nanoscale resolution electron microscopy analysis combined with ion beam assisted techniques are presented here, to give answers to full characterization of morphology, growth mode, phase formation, and compositional distribution in nanocomposite TiAlSiN coatings deposited under different energetic conditions. Samples were prepared by magnetron sputtering, and the effects of substrate temperature and bias were investigated. The nanocomposite microstructure was demonstrated by the formation of a face-centered cubic (Ti,Al)N phase, obtained by substitution of Al in the cubic titanium nitride (c-TiN) phase, and an amorphous matrix at the column boundary regions mainly composed of Si, N (and O for the samples with higher oxygen contents). Oxygen impurities, predicted as the principal responsible for the degradation of properties, were identified, particularly in nonbiased samples and confirmed to occupy preferentially nitrogen positions at the column boundaries, being mainly associated to silicon forming oxynitride phases. It has been found that the columnar growth mode is not the most adequate to improve mechanical properties. Only the combination of moderate bias and additional substrate heating was able to reduce the oxygen content and eliminate the columnar microstructure leading to the nanocomposite structure with higher hardness (>30 GPa).

Specimen quality is vital to (scanning) transmission electron microscopy (TEM) investigations. In particular, thin specimens are required to obtain excellent high-resolution TEM images. Conventional focused ion beam (FIB) preparation methods cannot be employed to reliably create high quality specimens much thinner than 20 nm. We have developed a method for in situ target preparation of ultrathin TEM lamellae by FIB milling. With this method we are able to routinely obtain large area lamellae with coplanar faces, thinner than 10 nm. The resulting specimens are suitable for low kV TEM as well as scanning TEM. We have demonstrated atomic resolution by Cs-corrected high-resolution TEM at 20 kV on a FIB milled Si specimen only 4 nm thick; its amorphous layer measuring less than 1 nm in total.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Superoxide dismutases (SODs) are a class of antioxidant enzymes which catalyze the dismutation of superoxide into oxygen and hydrogen peroxide, therefore controlling cellular levels of Reactive Oxygen Species (ROS). In the mature pollen grains of the olive tree, the presence of several forms of CuZn-SOD and the cytosolic localization of the enzyme have been described. The present study was aimed to elucidate the adaptation of the oxidative metabolism to the changing conditions occurring during the course of olive pollen formation, hydration and pollen tube emergence and growth. We used a polyclonal antibody (raised against a KLH-linked synthetic peptide including a consensus sequence for CuZn-SODs in olive pollen) in immunocytochemical experiments carried out by Fluorescence (FM) and Transmission Electron Microcopy (TEM).

In this article, we demonstrate the application of a new compressed sensing three-dimensional reconstruction algorithm for electron tomography that increases the accuracy of morphological characterization of nanostructured materials such as nanocrystalline iron oxide particles. A powerful feature of the algorithm is an anisotropic total variation norm for the L1 minimization during algebraic reconstruction that effectively reduces the elongation artifacts caused by limited angle sampling during electron tomography. The algorithm provides faithful morphologies that have not been feasible with existing techniques.

Sedimentary carbonate rocks are one of the principal porous structures in natural reservoirs of hydrocarbons such as crude oil and natural gas. Efficient hydrocarbon recovery requires an understanding of the carbonate pore structure, but the nature of sedimentary carbonate rock formation and the toughness of the material make proper analysis difficult. In this study, a novel preparation method was used on a dolomitic carbonate sample, and selected regions were then serially sectioned and imaged by focused ion beam–scanning electron microscopy. The resulting series of images were used to construct detailed three-dimensional representations of the microscopic pore spaces and analyze them quantitatively. We show for the first time the presence of nanometer-scale pores (50–300 nm) inside the solid dolomite matrix. We also show the degree of connectivity of these pores with micron-scale pores (2–5 μm) that were observed to further link with bulk pores outside the matrix.

Metabolism and mitochondrial dysfunction are known to be involved in many different disease states. We have employed two-photon fluorescence imaging of intrinsic mitochondrial reduced nicotinamide adenine dinucleotide (NADH) to quantify the metabolic state of several cultured cell lines, multicell tumor spheroids, and the intact mouse organ of Corti. Historically, fluorescence intensity has commonly been used as an indicator of the NADH concentration in cells and tissues. More recently, fluorescence lifetime imaging has revealed that changes in metabolism produce not only changes in fluorescence intensity, but also significant changes in the lifetimes and concentrations of free and enzyme-bound pools of NADH. Since NADH binding changes with metabolic state, this approach presents a new opportunity to track the cellular metabolic state.

Optical and scanning electron microscopy (SEM) of red blood cells (RBCs) of common carp, Cyprinus carpio, inhabiting a polluted lake in Northeast India revealed a number of abnormalities. About 7% of the RBC showed the presence of a micronucleus, besides the presence of some bi-nucleated and abnormally shaped nuclei. RBCs, white blood cells, and hemoglobin content were found to be reduced significantly as compared to the control. SEM showed the presence of spherocytes, early stages of echinocytes, cytoplasmic blebbing, erythrocytes with contraction from one side, abnormal shape of erythrocytes (hexagonal/pentagonal/tetragonal), development of lobopodial projections, cell rupture, membrane internalization, and formation of ring-shaped RBC. Energy dispersive X-ray spectroscopy (EDS) showed the presence of a considerable percentage of silicon and lead in erythrocytes of the fish collected from the polluted lake, in contrast to a negligible concentration of the two elements in control fish. Significance of the study in relation to fish health in a polluted body of water and the importance of SEM, EDS, and light microscopy in utilizing hematological parameters as pollution indicators are discussed.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.

Recent technical advances have enabled the imaging of single fluorescent molecules. The application of single molecule visualization techniques has opened up new avenues of experimentation in biology at the molecular level. In this article, we review the application of single fluorescent molecule visualization and analysis to an important problem, that of subunit stoichiometry in membrane proteins, with particular emphasis on our approach. Single fluorescent molecules, coupled to fluorescent proteins, are localized in the membranes of cells. The molecules are then exposed to continuous low-level excitation until their fluorescent emissions reach background levels. The high sensitivity of modern instrumentation has enabled direct observations of discrete step decreases in the fluorescence of single molecules, which represent the bleaching of single fluorophores. By counting the number of steps over a large number of single molecules, an average step count is determined from which the stoichiometry is deduced using a binomial model. We examined the stoichiometry of a protein, prestin, that is central to mammalian hearing. We discuss how we prepared, identified, and imaged single molecules of prestin. The methodological considerations behind our approach are described and compared to similar procedures in other laboratories.

Nonwoven materials are found in a gamut of critical applications. This is partly due to the fact that these structures can be produced at high speed and engineered to deliver unique functionality at low cost. The behavior of these materials is highly dependent on alignment of fibers within the structure. The ability to characterize and also to control the structure is important, but very challenging due to the complex nature of the structures. Thus, to date, focus has been placed mainly on two-dimensional analysis techniques for describing the behavior of nonwovens. This article demonstrates the utility of three-dimensional (3D) digital volumetric imaging technique for visualizing and characterizing a complex 3D class of nonwoven structures produced by hydroentanglement.

The reproducibility of contrast in secondary electron (SE) imaging during continuous electron irradiation, which caused surface contamination, was investigated using SE high-pass energy filtering in low-voltage scanning electron microscopy (SEM). According to high-pass energy-filtered imaging, dopant contrast in an indium phosphide remained remarkably stable during continuous electron irradiation although the contrast in unfiltered SE images decreased rapidly as a contamination layer was formed. Charge neutralization and the SE energy distributions indicate that the contamination layer induces a positive charge. This results in a decrease of low-energy SE emissions and reduced dopant contrast in unfiltered SE images. The retention of contrast was also observed in high-pass energy-filtered images of a gold surface. These results suggest that this imaging method can be widely used when SE intensities decrease under continuous electron irradiation in unfiltered SE images. Thus, high-pass energy-filtered SE imaging will be of a great assistance for SEM users in the reproducibility of contrast such as a quantitative dopant mapping in semiconductors.

The epididymis is a long convoluted tubule that serves as a conduit for the transport of spermatozoa from the testis to the vas deferens and is the site where spermatozoa mature and acquire their functions of progressive motility and fertility. Unfortunately, very little is known about the human epididymis and its role in sperm maturation owing to the lack of studies conducted on normal human tissue. The role of epididymal luminal microenvironment and the mechanisms that epididymis uses to carry out its functions remain unsolved.

Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as a function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as a function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens.

Fossil embryos are paramount for our understanding of the development of extinct species. However, although thousands of fossil amniote eggs are known, very few embryos in ovo have been described. First reports of fossil embryos were based on broken eggs, where the embryonic remains were already exposed, because destructive methods on complete eggs were avoided. Investigations of complete eggs therefore required nondestructive approaches, such as X-ray microtomography (μCT). However, due to the general low density contrast between fossilized bones and infilling matrix, only a few specimens have been reported using these techniques. Using propagation phase contrast X-ray synchrotron microtomography (PPC-SR-μCT), we report here the discovery of three well-preserved embryos in Early Cretaceous eggs from Thailand. By scanning these eggs using different imaging techniques, we show that vastly different interpretations can be made regarding the preservation state and/or the developmental stage of these embryos. PPC-SR-μCT also revealed differential contrast between bone categories, presumably reflecting the ossification pattern of these embryos. Applying such an approach to large-scale studies of fossil eggs could lead to more discoveries and detailed studies of fossil embryos, providing important developmental and phylogenetic information on extinct and extant amniotes.

Atomic force microscopy (AFM) is one of the most sensitive tools for nanoscale imaging. As such, it is very sensitive to external noise sources that can affect the quality of collected data. The intensity of the disturbance depends on the noise source and the mode of operation. In some cases, the internal noise from commercial AFM controllers can be significant and difficult to remove. Thus, a new method based on spectrum analysis of the scanned images is proposed to reduce harmonic disturbances. The proposal is a post-processing method and can be applied at any time after measurements. This article includes a few methods of harmonic cancellation (e.g., median filtering, wavelet denoising, Savitzky-Golay smoothing) and compares their effectiveness. The proposed method, based on Fourier transform of the scanned images, was more productive than the other methods mentioned before. The presented data were achieved for images of conductive layers taken in a contact AFM mode.

Aspergillus fumigatus has become a leading cause of fungal morbidity and mortality, especially in immunocompromised patients. This fungus is able to grow as a multicellular community and produce a hydrophobic extracellular matrix (ECM), mainly composed of galactomannan and α-1,3 glucans, to protect itself from host defenses and antimicrobial drugs. This matrix envelops the fungus hyphae, binding them into a contiguous sheath on the colony surface, forming a biofilm and increasing the fungal resistance to adverse environmental factors. Adherence to host cells and resistance to physical removal play a key role in fungal colonization and invasion of the host and in a wide range of infections. Here we show that, by using atomic force spectroscopy, it is possible to exploit the peculiar hydrophobicity of the biofilm components (i.e., cell walls, ECM) to detect the biofilm spread, its growth, and lysis on rough surfaces. By means of this approach, we demonstrate that alginate lyase, an enzyme known to reduce negatively charged alginate levels in microbial biofilms, reduces the biofilm adhesion forces suggesting a loss of ECM from the biofilm, which could be used to enhance pharmacological treatments.