Bulk silicon-germanium (SiGe) alloys and two SiGe thick films (4 and 5 μm) on Si wafers were tested with the electron probe microanalyzer (EPMA) using wavelength dispersive spectrometers (WDS) for heterogeneity and composition for use as reference materials needed by the microelectronics industry. One alloy with a nominal composition of Si0.86Ge0.14 and the two thick films with nominal compositions of Si0.90Ge0.10 and Si0.75Ge0.25 on Si, evaluated for micro- and macroheterogeneity, will make good microanalysis reference materials with an overall expanded heterogeneity uncertainty of 1.1% relative or less for Ge. The bulk Ge composition in the Si0.86Ge0.14 alloy was determined to be 30.228% mass fraction Ge with an expanded uncertainty of the mean of 0.195% mass fraction. The thick films were quantified with WDS-EPMA using both the Si0.86Ge0.14 alloy and element wafers as reference materials. The Ge concentration was determined to be 22.80% mass fraction with an expanded uncertainty of the mean of 0.12% mass fraction for the Si0.90Ge0.10 wafer and 43.66% mass fraction for the Si0.75Ge0.25 wafer with an expanded uncertainty of the mean of 0.25% mass fraction. The two thick SiGe films will be issued as National Institute of Standards and Technology Reference Materials (RM 8905).

Electron-beam-induced carbon film deposition has long been recognized as a side effect of scanning electron microscopy. To characterize the nature of this type of contamination, silicon wafers were subjected to prolonged exposure to 15 kV electron beam energy with a probe current of ∼300 pA. Using Raman spectroscopy, the deposited coating was identified as an amorphous carbon film with an estimated crystallite size of 125 Å. Using atomic force microscopy, the cross-sectional profile of the coating was found to be raised and textured, indicative of the beam raster pattern. A map of the Raman intensity across the coating showed increased intensity along the edges and at the corner of the film. The intensity profile was in excess of that which could be explained by thickness alone. The enhancement was found to correspond with a modeled local field enhancement induced by the coating boundary and showed that the deposited carbon coating generated a localized disturbance in the opto-electrical properties of the substrate, which is compared and contrasted with Raman edge enhancement that is produced by surface structure in silicon.

XFILM is a computer program for determining the thickness and composition of thin films on substrates and multilayers by electron probe microanalysis. In this study, we describe the X-ray emission model implemented in the latest version of XFILM and assess its reliability by comparing measured and calculated k-ratios from thin-film samples available in the literature. We present and discuss examples of applications of XFILM that illustrate the capabilities of the program.

The immunogold technique is a valuable method for labeling cellular macromolecules. However, multiple labeling using colloidal gold (cAu) nanoparticles of different sizes presents certain drawbacks; namely, as particle size increases, there is a decreased labeling efficiency and diminished spatial resolution with respect to the locations of labeled epitopes. Both concerns also limit the utility of heavy metal particles for comparative analysis of labeling densities. To minimize the variables due to differential labeling efficiencies, the best solution would be to conduct multiple labeling with particles of similar size. Consequently, some parameter other than size is necessary to distinguish each label type. In this study, we report the synthesis of colloidal palladium (cPd) nanoparticles of similar size but having two distinct shapes, umbonate and faceted, which are readily distinguishable from spherical colloidal gold particles. Their utility and fidelity as labels using a human platelet whole-mount model is also demonstrated.

Here we evaluate a new grid substrate developed by ProtoChips Inc. (Raleigh, NC) for cryo-transmission electron microscopy. The new grids are fabricated from doped silicon carbide using processes adapted from the semiconductor industry. A major motivating purpose in the development of these grids was to increase the low-temperature conductivity of the substrate, a characteristic that is thought to affect the appearance of beam-induced movement (BIM) in transmission electron microscope (TEM) images of biological specimens. BIM degrades the quality of data and is especially severe when frozen biological specimens are tilted in the microscope. Our results show that this new substrate does indeed have a significant impact on reducing the appearance and severity of beam-induced movement in TEM images of tilted cryo-preserved samples. Furthermore, while we have not been able to ascertain the exact causes underlying the BIM phenomenon, we have evidence that the rigidity and flatness of these grids may play a major role in its reduction. This improvement in the reliability of imaging at tilt has a significant impact on using data collection methods such as random conical tilt or orthogonal tilt reconstruction with cryo-preserved samples. Reduction in BIM also has the potential for improving the resolution of three-dimensional cryo-reconstructions in general.

A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2–3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

Localization microscopy techniques based on localizing single fluorophore molecules now routinely achieve accuracies better than 30 nm. Unlike conventional optical microscopies, localization microscopy experiments do not generate an image but a list of discrete coordinates of estimated fluorophore positions. Data display and analysis therefore generally require visualization methods that translate the position data into conventional images. Here we investigate the properties of several widely used visualization techniques and show that a commonly used algorithm based on rendering Gaussians may lead to a 1.44-fold loss of resolution. Existing methods typically do not explicitly take sampling considerations into account and thus may produce spurious structures. We present two additional visualization algorithms, an adaptive histogram method based on quad-trees and a Delaunay triangulation based visualization of point data that address some of these deficiencies. The new visualization methods are designed to suppress erroneous detail in poorly sampled image areas but avoid loss of resolution in well-sampled regions. A number of criteria for scoring visualization methods are developed as a guide for choosing among visualization methods and are used to qualitatively compare various algorithms.

Tumors are supported by the development of a unique vascular bed. We used fractal dimension (Db) and image analysis to quantify differences in the complexity of the vasculature in normal intestinal submucosa and intestinal polyps. ApcMin/+ mice and wild-type mice were perfused with a curable latex compound, intestines sectioned, and images collected via confocal microscopy. The images were analyzed and area (A), perimeter (P), and integrated optical density (IOD) of the normal and tumor vascular beds were measured. The Db, a quantitative descriptor of morphological complexity, was significantly greater for the polyp vasculature from ApcMin/+ mice than controls. This indicates that the polyp microvasculature is more chaotic than that of the controls, while the IOD and average vascular density values displayed no differences. This suggests the mass of blood volume is equivalent in normal and polyp microvasculature. The lower vascular area-perimeter ratios expressed by the polyp microvasculature suggest it is composed of smaller, more tortuous vessels. These data demonstrate that fractal analysis is applicable for providing a quantitative description of vascular complexity associated with angiogenesis occurring in normal or diseased tissue. Application of Db, IOD, and average density provides a clearer quantification of the complex morphology associated with tissue microvasculature.

Neurodegerative disorders affect millions of people worldwide. Neural cells derived from human embryonic stem cells (hESC) have the potential for cell therapies and/or compound screening for treating affected individuals. While both protein and gene expression indicative of a neural phenotype has been exhibited in these differentiated cells, ultrastuctural studies thus far have been lacking. The objective of this study was to correlate hESC to neural differentiation culture conditions with ultrastructural changes observed in the treated cells. We demonstrate here that in basic culture conditions without growth factors or serum we obtain neural morphology. The addition of brain-derived neurotrophic factor (BDNF) and serum to cultures resulted in more robust neural differentiation. In addition to providing cues such as cell survival or lineage specification, additional factors also altered the intracellular structures and cell morphologies. Even though the addition of BDNF and serum did not increase synaptic formation, altered cellular structures such as abundant polyribosomes and more developed endoplasmic reticulum indicate a potential increase in protein production.

The organic interprismatic layers of the mollusc Pinctada margaritifera are studied using a variety of highly spatially-resolved techniques to establish their composition and structure. Our results show that both the interlamellar sheets of the nacre and interprismatic envelopes form layered structures. Additionally, these organic layers are neither homogeneous in composition, nor continuous in their structure. Both structures play a major role in the biomineralization process and act as a boundary between mineral units.

This article addresses gaps in definitions and a lack of standard measurement techniques to assess the spatial resolution in atom probe tomography. This resolution is known to be anisotropic, being better in-depth than laterally. Generally the presence of atomic planes in the tomographic reconstruction is considered as being a sufficient proof of the quality of the spatial resolution of the instrument. Based on advanced spatial distribution maps, an analysis methodology that interrogates the local neighborhood of the atoms within the tomographic reconstruction, it is shown how both the in-depth and the lateral resolution can be quantified. The influences of the crystallography and the temperature are investigated, and models are proposed to explain the observed results. We demonstrate that the absolute value of resolution is specimen specific.