Despite the many demonstrated applications of factor analysis (FA) in analyzing hyperspectral materials images, FA does have inherent mathematical limitations, preventing it from solving certain materials characterization problems. A notable limitation of FA is its parsimony restriction, referring to the fact that in FA the number of components cannot exceed the chemical rank of a dataset. Clustering is a promising alternative to FA for the phase classification of hyperspectral materials images. In contrast with FA, the phases extracted by clustering do not have to be parsimonious. Clustering has an added advantage in its insensitivity to spectral collinearity that can result in phase mixing using FA. For representative energy dispersive X-ray spectroscopy materials images, namely a solder bump dataset and a braze interface dataset, clustering generates phase classification results that are superior to those obtained using representative FA-based methods. For the solder bump dataset, clustering identifies a Cu-Sn intermetallic phase that cannot be isolated using FA alone due to the parsimony restriction. For the braze interface sample that has collinearity among the phase spectra, the clustering results do not exhibit the physically unrealistic phase mixing obtained by multivariate curve resolution, a commonly utilized FA algorithm.

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

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.

The process of autophagy has been detected in the midgut epithelium of four millipede species: Julus scandinavius, Polyxenus lagurus, Archispirostreptus gigas, and Telodeinopus aoutii. It has been examined using transmission electron microscopy (TEM), which enabled differentiation of cells in the midgut epithelium, and some histochemical methods (light microscope and fluorescence microscope). While autophagy appeared in the cytoplasm of digestive, secretory, and regenerative cells in J. scandinavius and A. gigas, in the two other species, T. aoutii and P. lagurus, it was only detected in the digestive cells. Both types of macroautophagy, the selective and nonselective processes, are described using TEM. Phagophore formation appeared as the first step of autophagy. After its blind ends fusion, the autophagosomes were formed. The autophagosomes fused with lysosomes and were transformed into autolysosomes. As the final step of autophagy, the residual bodies were detected. Autophagic structures can be removed from the midgut epithelium via, e.g., atypical exocytosis. Additionally, in P. lagurus and J. scandinavius, it was observed as the neutralization of pathogens such as Rickettsia-like microorganisms. Autophagy and apoptosis ca be analyzed using TEM, while specific histochemical methods may confirm it.

Laser capture microdissection uses a microscope to identify specific cells for microdissection and then a laser-sensitive plastic to capture and remove the cells from their substrate. This efficient capture method was originally developed to capture cells for genetic analysis. However, it has also been used to capture cells for proteonomic analysis. In this article, we extend the uses of laser-capture microdissection by reporting a method for preparing captured cells for ultrastructural analysis by transmission electron microscopy. Cells prepared by our methodology show good fine structure preservation and are easily sectioned by standard ultramicrotomy.

High-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images of electron-transparent samples show dominant atomic number (Z-) contrast with a high lateral resolution. HAADF STEM at low electron energies <30 keV is applied in this work for quantitative composition analyses of InGaAs quantum wells. To determine the local composition, normalized experimental image intensities are compared with results of Monte Carlo simulations. For verification of the technique, InGaAs/GaAs quantum-well structures with known In concentration are used. Transmission electron microscopy samples with known thickness are prepared by the focused-ion-beam technique. The method can be extended to other material systems and is particularly promising for the analysis of materials that are sensitive toward knock-on damage.

Scanning electron microscopy (SEM) is widely used in surface studies and continuous efforts are carried out in the search of estimators of different surface characteristics. By using the variogram, we developed two of these estimators that were used to characterize the surface roughness from the SEM image texture. One of the estimators is related to the crossover between fractal region at low scale and the periodic region at high scale, whereas the other estimator characterizes the periodic region. In this work, a full study of these estimators and the fractal dimension in two dimensions (2D) and three dimensions (3D) was carried out for emery papers. We show that the obtained fractal dimension with only one image is good enough to characterize the roughness surface because its behavior is similar to those obtained with 3D height data. We show also that the estimator that indicates the crossover is related to the minimum cell size in 2D and to the average particle size in 3D. The other estimator has different values for the three studied emery papers in 2D but it does not have a clear meaning, and these values are similar for those studied samples in 3D. Nevertheless, it indicates the formation tendency of compound cells. The fractal dimension values from the variogram and from an area versus step log–log graph were studied with 3D data. Both methods yield different values corresponding to different information from the samples.

This article reviews recent advances utilizing field-ion microscopy (FIM) to extract atomic-scale three-dimensional images of materials. This capability is not new, as the first atomic-scale reconstructions of features utilizing FIM were demonstrated decades ago. The rise of atom probe tomography, and the application of this latter technique in place of FIM has unfortunately severely limited further FIM development. Currently, the ubiquitous availability of extensive computing power makes it possible to treat and reconstruct FIM data digitally and this development allows the image sequences obtained utilizing FIM to be extremely valuable for many material science and engineering applications. This article demonstrates different applications of these capabilities, focusing on its use in physical metallurgy and semiconductor science and technology.

For a few years, the biological effects on ecosystems and the public of the bioaccumulation of radionuclides in situations of chronic exposures have been studied. This work, in keeping with the ENVIRHOM French research program, presents the uranium microdistribution by secondary ion mass spectrometry (SIMS) technique in the renal cortex of rats following chronic exposure to this low level element in the drinking water (40 mg/L) as a function to exposure duration (6, 9, 12, and 18 months). The SIMS mass spectra and 238U+ ion images produced with a SIMS CAMECA 4F-E7 show the kinetic of uranium accumulation in the different structures of the kidney. For the rats contaminated up to 12 months, the radioelement is mainly fixed in the proximal tubules; then after 18 exposure months, uranium is detected in all the segments of the nephron. This work has also shown that ion microscopy is an analytical method to detect trace elements and give elemental cartography at the micrometer scale.

It has long been the bane of analytical electron microscopy (AEM) that the use of focused probes during microanalysis of specimens increases the local rate of hydrocarbon contamination. This is most succinctly observed by the formation of contamination deposits (fig.l) during focused probe work typical of AEM studies. While serving to indicate the location of the electron probe, the contamination obliterates the area of the specimen being analyzed and adversely affects all quantitative microanalysis methodologies. A variety of methods including: UV, electron beam flooding, heating and/or cooling can decrease the rate of contamination, however, none of these methods directly attack the source of specimen borne contamination . Research has shown that reactive gas plasmas may be used to clean both the specimen and stage for AEM, in this study we report on quantitative measurements of the reduction in contamination rates in an AEM as a function of operating conditions and plasma gases.

This article presents my reminiscences of the work in Chicago on the correction or reduction of lens aberrations. Studies began in the early 1960s and extended over a period of almost 40 years, although it was never the primary focus of the work of the laboratory. The account is almost entirely based on my own memory, which is not a very reliable instrument. It is not intended to be a review and is more accurately describable as a personal recollection.

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

The taxonomy of fungal species, similar to that of many other microorganisms, suffers frequent revisions due to the discovery of new species and to the development and gathering of characterization data and morphological information. Morpho-taxonomy helps in the identification of many species. This work presents the macro, micro-morphological, and spectral mass analyses for phenotypic characterization of 13 species of Aspergillus section Nigri, showing that the characterization of spores (conidia) by scanning electron microscopy can be used as a tool to discriminate key morphological characteristics and separate closely related fungi. These results were corroborated by colony plates, stereomicroscopy, light microscopy, and spectral mass data.

Cathodoluminescence (CL) spectra from silicon doped and undoped wurtzite n-type GaN have been measured in a SEM under a wide range of electron beam excitation conditions, which include accelerating voltage, beam current, magnification, beam diameter, and specimen temperature. The CL intensity dependence on excitation density was analyzed using a power-law model (ICL ∝ Jm) for each of the observed CL bands in this material. The yellow luminescence band present in both silicon and undoped GaN exhibits a close to cube root (m = 0.33) dependence on electron beam excitation at both 77 K and 300 K. However, the blue (at 300 K) and donor-acceptor pair (at 77 K) emission peaks observed in undoped GaN follow power laws with exponents of m = 1 and m = 0.5, respectively. As expected from its excitonic character, the near band edge emission intensity depends linearly (m = 1) in silicon doped GaN and superlinearly (m = 1.2) in undoped GaN on the electron beam current. Results show that the intensities of the CL bands are highly dependent not only on the defect concentration but also on the electron-hole pair density and injection rate. Furthermore, the size of the focussed electron beam was found to have a considerable effect on the relative intensities of the CL emission peaks. Hence SEM parameters such as the objective lens aperture size, astigmatism, and the condenser lens setting must also be considered when assessing CL data based on intensity measurements from this material.

We report the ultrastructure and 3D transmission electron tomography of collagen fibrils (CFs), proteoglycans (PGs), and microfibrils within the CF of corneas of patients with macular corneal dystrophy (MCD). Three normal corneas and three MCD corneas from three Saudi patients (aged 25, 31, and 49 years, respectively) were used for this study. The corneas were processed for light and electron microscopy studies. 3D images were composed from a set of 120 ultrastructural images using the program “Composer” and visualized using the program “Visuliser Kai”. 3D image analysis of MCD cornea showed a clear organization of PGs around the CF at very high magnification and degeneration of the microfibrils within the CF. Within the MCD cornea, the PG area in the anterior stroma was significantly larger than in the middle and posterior stroma. The PG area in the MCD cornea was significantly larger compared with the PG area in the normal cornea. The CF diameter and inter-fibrillar spacing of the MCD cornea were significantly smaller compared with those of the normal cornea. Ultrastructural 3D imaging showed that the production of unsulfated keratin sulfate (KS) may lead to the degeneration of micro-CFs within the CFs. The effect of the unsulfated KS was higher in the anterior stroma compared with the posterior stroma.

In this study the nanomorphology of P3HT:PC61BM absorber layers of organic solar cells was studied as a function of the processing parameters and for P3HT with different molecular weight. For this purpose we apply scanning transmission electron microscopy (STEM) at low electron energies in a scanning electron microscope. This method exhibits sensitive material contrast in the high-angle annular dark-field (HAADF) mode, which is well suited to distinguish materials with similar densities and mean atomic numbers. The images taken with low-energy HAADF STEM are compared with conventional transmission electron microscopy and atomic force microscopy images to illustrate the capabilities of the different techniques. For the interpretation of the low-energy HAADF STEM images, a semiempirical equation is used to calculate the image intensities. The experiments show that the nanomorphology of the P3HT:PC61BM blends depends strongly on the molecular weight of the P3HT. Low-molecular-weight P3HT forms rod-like domains during annealing. In contrast, only small globular features are visible in samples containing high-molecular-weight P3HT, which do not change significantly after annealing at 150°C up to 30 min.

Abstract: Films of Fe3O4 were prepared by sputter deposition onto MgO substrates of both 〈100〉 and 〈110〉 orientations. The films used in this study were mainly 50 nm thick. X-ray diffraction, Mössbauer spectroscopy, and other techniques revealed that the films were stoichiometric single crystals. Electron microscopy showed that the films were essentially dislocation free. Despite this high degree of perfection, the magnetic properties of the films were inconsistent with bulk single crystal properties. For example, the magnetization of the films did not saturate in fields as large as 7 Tesla, while bulk single crystals saturate by 0.1 Tesla.