A simple parameterization is presented for the elastic electron scattering cross sections from single atoms into the annular dark-field (ADF) detector of a scanning transmission electron microscope (STEM). The dependence on atomic number, Z, and inner reciprocal radius of the annular detector, q0, of the cross section σ(Z,q0) is expressed by the empirical relation

where A(q0) is the cross section for hydrogen (Z = 1), and the detector is assumed to have a large outer reciprocal radius. Using electron elastic scattering factors determined from relativistic Hartree-Fock simulations of the atomic electron charge density, values of the exponent n(Z,q0) are tabulated as a function of Z and q0, for STEM probe sizes of 1.0 and 2.0 Å.

Comparison with recently published experimental data for single-atom scattering [Krivanek et al. (2010). Nature464, 571–574] suggests that experimentally measured exponent values are systematically lower than the values predicted for elastic scattering from low-Z atoms. It is proposed that this discrepancy arises from the inelastic scattering contribution to the ADF signal. A simple expression is proposed that corrects the exponent n(Z,q0) for inelastic scattering into the annular detector.

The grain size statistics, commonly derived from the grain map of a material sample, are important microstructure characteristics that greatly influence its properties. The grain map for nanomaterials is usually obtained manually by visual inspection of the transmission electron microscope (TEM) micrographs because automated methods do not perform satisfactorily. While the visual inspection method provides reliable results, it is a labor intensive process and is often prone to human errors. In this article, an automated grain mapping method is developed using TEM diffraction patterns. The presented method uses wide angle convergent beam diffraction in the TEM. The automated technique was applied on a platinum thin film sample to obtain the grain map and subsequently derive grain size statistics from it. The grain size statistics obtained with the automated method were found in good agreement with the visual inspection method.

To analyze nanocrystalline structures quantitatively in 3D, a novel method is presented based on electron diffraction. It allows determination of the average size and morphology of the coherently scattering domains (CSD) in a straightforward way without the need to prepare multiple sections. The method is applicable to all kinds of bulk nanocrystalline materials. As an example, the average size of the CSD in nanocrystalline FeAl made by severe plastic deformation is determined in 3D. Assuming ellipsoidal CSD, it is deduced that the CSD have a width of 19 ± 2 nm, a length of 18 ± 1 nm, and a height of 10 ± 1 nm.

This article simulates highly overlapped projections of spherical particles that are distributed randomly in space. The size and number of the features in the projections are examined as well as how these features change with particle size and concentration. First, there are discernable features in projection even when particles overlap extensively, and the size of these discernable features is the expected size of an individual particle. Second, the number of features increases with specimen thickness at a rate of t0.543 when the specimen thickness is below a critical value and becomes independent of specimen thickness at higher thicknesses. A criterion is established for the critical thickness based on particle size and particle volume fraction. When the specimen thickness is known and smaller than the critical thickness, a single representative transmission electron microscopy (TEM) (or scanning TEM) image exhibiting extensive particle overlap can be used to determine the size and number density of the spherical particles.

Three-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.

A simple plan-view sample preparation technique for transmission electron microscopy (TEM) specimens is proposed for thin films by tearing-off the film with adhesive tape. The demand for very thin samples is highest for nanostructured materials where the structure of 2–5 nm sized features (grains) needs to be resolved; therefore, overlapping of nanometer-sized features should be avoided. The method provides thin areas at the fracture edges of plan-view specimens with thickness in the range of the grain size in the film allowing for artifact free high-resolution TEM imaging. Nanostructured materials typically fracture between the grains providing areas with the thickness of the grain size. Besides the swiftness of the method, the samples are free of surface amorphization artifacts, which can occur in ion beam milling up to 1 nm depth even at low energy ion bombardment. The thin film tear-off technique is demonstrated on a CuMn alloy thin film with grain size of 2 nm.

The ability to prepare multiple cross-section transmission electron microscope (XTEM) samples from one XTEM sample of specific sub-10 nm features was demonstrated. Sub-10 nm diameter Si nanowire (NW) devices were initially cross-sectioned using a dual-beam focused ion beam system in a direction running parallel to the device channel. From this XTEM sample, both low- and high-resolution transmission electron microscope (TEM) images were obtained from six separate, specific site Si NW devices. The XTEM sample was then re-sectioned in four separate locations in a direction perpendicular to the device channel: 90° from the original XTEM sample direction. Three of the four XTEM samples were successfully sectioned in the gate region of the device. From these three samples, low- and high-resolution TEM images of the Si NW were taken and measurements of the NW diameters were obtained. This technique demonstrated the ability to obtain high-resolution TEM images in directions 90° from one another of multiple, specific sub-10 nm features that were spaced 1.1 μm apart.

The quantification of three classes of graphite inclusions in cast iron, namely, nodular, flake, and irregular, is the most important process in the foundry industry. This classification is based on the ISO 945 proposed morphology of graphite inclusions. This work presents a novel solution for automatic quantitative analysis of graphite inclusions into the three mentioned classes. The proposed work comprises three stages, namely, preprocessing of micrographs, classification of graphite inclusions, and then quantification of inclusions in each class. An effort has been made in this work to propose a minimum set of features to represent graphite inclusion morphology. The method employs just two geometric shape descriptors: the diameter ratio and the area ratio. A fuzzy rule based classifier is built using known feature values that are efficient in the classification of the three classes of graphite inclusions. The proposed method is automatic, fast, and provides the basis for determining many more morphological parameters that can be determined with the least effort. The results obtained by the proposed method are compared with the manual method. It is observed that the results obtained from the proposed method are useful in the optimization of cast iron manufacturing in the foundry industry.

Artifacts are the nemesis of trace element analysis in electron-excited energy dispersive X-ray spectrometry. Peaks that result from nonideal behavior in the detector or sample can fool even an experienced microanalyst into believing that they have trace amounts of an element that is not present. Many artifacts, such as the Si escape peak, absorption edges, and coincidence peaks, can be traced to the detector. Others, such as secondary fluorescence peaks and scatter peaks, can be traced to the sample. We have identified a new sample-dependent artifact that we attribute to Compton scattering of energetic X-rays generated in a small feature and subsequently scattered from a low atomic number matrix. It seems likely that this artifact has not previously been reported because it only occurs under specific conditions and represents a relatively small signal. However, with the advent of silicon drift detectors and their utility for trace element analysis, we anticipate that more people will observe it and possibly misidentify it. Though small, the artifact is not inconsequential. Under some conditions, it is possible to mistakenly identify the Compton scatter artifact as approximately 1% of an element that is not present.

The detection of line-like features in images finds many applications in microanalysis. Actin fibers, microtubules, neurites, pilis, DNA, and other biological structures all come up as tenuous curved lines in microscopy images. A reliable tracing method that preserves the integrity and details of these structures is particularly important for quantitative analyses. We have developed a new image transform called the “Coalescing Shortest Path Image Transform” with very encouraging properties. Our scheme efficiently combines information from an extensive collection of shortest paths in the image to delineate even very weak linear features.

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.

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.

We report the first application of multiphoton microscopy (MPM) to generate three-dimensional (3D) images of natural minerals (micron-sized sulfides) in thick (∼120 μm) rock sections. First, reflection mode (RM) using confocal laser scanning microscopy (CLSM), combined with differential interference contrast (DIC), was tested on polished sections. Second, two-photon fluorescence (TPF) and second harmonic signal (SHG) images were generated using a femtosecond-laser on the same rock section without impregnation by a fluorescent dye. CSLM results show that the silicate matrix is revealed with DIC and RM, while sulfides can be imaged in 3D at low resolution by RM. Sulfides yield strong autofluorescence from 392 to 715 nm with TPF, while SHG is only produced by the embedding medium. Simultaneous recording of TPF and SHG images enables efficient discrimination between different components of silicate rocks. Image stacks obtained with MPM enable complete reconstruction of the 3D structure of a rock slice and of sulfide morphology at submicron resolution, which has not been previously reported for 3D imaging of minerals. Our work suggests that MPM is a highly efficient tool for 3D studies of microstructures and morphologies of minerals in silicate rocks, which may find other applications in geosciences.

Atomic force microscopy probe-induced large-area ultrathin SiOx (x ≡ O/Si content ratio and x > 2) protrusions only a few nanometers high on a SiO2 layer were characterized by scanning photoemission microscopy (SPEM) and X-ray photoemission spectroscopy (XPS). SPEM images of the large-area ultrathin SiOx protrusions directly showed the surface chemical distribution and chemical state specifications. The peak intensity ratios of the XPS spectra of the large-area ultrathin SiOx protrusions provided the elemental quantification of the Si 2p core levels and Si oxidation states (such as the Si4+, Si3+, Si2+, and Si1+ species). The O/Si content ratio (x) was evidently determined by the height of the large-area ultrathin SiOx protrusions.

The differences in artifacts associated with voltage-pulsed and laser-pulsed (wavelength = 532 or 355 nm) atom-probe tomographic (APT) analyses of nanoscale precipitation in a high-strength low-carbon steel are assessed using a local-electrode atom-probe tomograph. It is found that the interfacial width of nanoscale Cu precipitates increases with increasing specimen apex temperatures induced by higher laser pulse energies (0.6–2 nJ pulse−1 at a wavelength of 532 nm). This effect is probably due to surface diffusion of Cu atoms. Increasing the specimen apex temperature by using pulse energies up to 2 nJ pulse−1 at a wavelength of 532 nm is also found to increase the severity of the local magnification effect for nanoscale M2C metal carbide precipitates, which is indicated by a decrease of the local atomic density inside the carbides from 68 ± 6 nm−3 (voltage pulsing) to as small as 3.5 ± 0.8 nm−3. Methods are proposed to solve these problems based on comparisons with the results obtained from voltage-pulsed APT experiments. Essentially, application of the Cu precipitate compositions and local atomic density of M2C metal carbide precipitates measured by voltage-pulsed APT to 532 or 355 nm wavelength laser-pulsed data permits correct quantification of precipitation.

Energy dispersive X-ray microanalysis of micron-sized inclusions in steel is of considerable industrial importance. Measured spectra and Monte Carlo simulations show a significant effect of the steel matrix on analysis of CaO-Al2O3-MgO inclusions: the steel matrix filters the softer (Al and Mg) characteristic X-rays, increasing the relative height of the Ca peak. Bulk matrix correction methods would not result in correct inclusion compositions, but operating at a lower acceleration voltage shifts the effect to smaller inclusion sizes.

Persistence of gunshot residue (GSR) simultaneously collected from hands, face and hair, and clothing of the shooting person was examined. Samples were collected from five shooters in nine time intervals after a single shoot with a Luger 9 mm pistol, in the range of 0–4 h and examined with scanning electron microscopy and energy dispersive X-ray spectrometry. Numbers of particles, frequencies of occurrence of certain compositions of particles, and their sizes in function of the time intervals were inspected. The greatest numbers of particles were observed in samples collected from hands right after shooting, but they decrease quickly with time. In samples collected from the face smaller initial numbers of particles were found, but they lasted at a similar level longer. The estimated half-life times of particles were less than 1 h for samples taken from the hands, over 1 h for clothing and about 2–3 h for the face. In samples collected at longer intervals after shooting, there were particles present of small sizes and irregular shapes. The results demonstrate that including evidence collected from the suspect's face and hair may increase the probability of detection of GSR in cases when the suspect has not been apprehended immediately after the investigated incident.

Focused ion beam (FIB) induced damage in nanocrystalline Al thin films has been characterized using advanced transmission electron microscopy techniques. Electron tomography was used to analyze the three-dimensional distribution of point defect clusters induced by FIB milling, as well as their interaction with preexisting dislocations generated by internal stresses in the Al films. The atomic structure of interstitial Frank loops induced by irradiation, as well as the core structure of Frank dislocations, has been resolved with aberration-corrected high-resolution annular dark-field scanning TEM. The combination of both techniques constitutes a powerful tool for the study of the intrinsic structural properties of point defect clusters as well as the interaction of these defects with preexisting or deformation dislocations in irradiated bulk or nanostructured materials.

Using X-ray microscopy and spectromicroscopy, vascular smooth muscle cells (VSMCs) were imaged, prepared without using additional embedding material or staining, but by applying simple, noncryo fixation techniques. The cells were imaged with a compact source transmission X-ray microscope and a scanning transmission X-ray microscope (STXM). With the STXM, spectromicroscopy was performed at the C K-edge and the Ca LIII,II-edges. VSMCs were chosen because of their high amount of actin stress fibers, so that the actin cytoskeleton should be visible. Other parts of the cell, such as the nucleus and organelles, were also identified from the micrographs. Both in the spectra and the images, the effects of the different preparation procedures were observable. Furthermore, Ca hotspots were detected and their density is determined.

Transplantation of spermatogonial stem cells (SSCs), the male germline stem cells, in experimental animal models has been successfully used to study mechanisms involved in SSC self-renewal and to restore fertility. However, there are still many challenges associated with understanding the recipient immune response for SSCs use in clinical therapies. Here, we have undertaken a detailed structural study of macrophages elicited by SSCs transplantation in mice using both high-resolution light microscopy (HRLM) and transmission electron microscopy (TEM). We demonstrate that SSCs transplantation elicits a rapid and potent recruitment of macrophages into the seminiferous epithelium (SE). Infiltrating macrophages were derived from differentiation of peritubular monocyte-like cells into typical activated macrophages, which actively migrate through the SE, accumulate in the tubule lumen, and direct phagocytosis of differentiating germ cells and spermatozoa. Quantitative TEM analyses revealed increased formation of lipid bodies (LBs), organelles recognized as intracellular platforms for synthesis of inflammatory mediators and key markers of macrophage activation, within both infiltrating macrophages and Sertoli cells. LBs significantly increased in number and size in parallel to the augmented macrophage migration during different times post-transplantation. Our findings suggest that LBs may be involved with immunomodulatory mechanisms regulating the seminiferous tubule niche after SSC transplantation.