Electron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

Automatic qualitative analysis for peak identification is a standard feature of virtually all modern computer-aided analysis software for energy dispersive X-ray spectrometry with electron excitation. Testing of recently installed systems from four different manufacturers has revealed the occasional occurrence of misidentification of peaks of major constituents whose concentrations exceeded 0.1 mass fraction (10 wt%). Test materials where peak identification failures were observed included ZnS, KBr, FeS2, tantalum-niobium alloy, NIST Standard Reference Material 482 (copper–gold alloy), Bi2Te3, uranium–rhodium alloys, platinum–chromium alloy, GaAs, and GaP. These misidentifications of major constituents were exacerbated when the incident beam energy was 10 keV or lower, which restricted or excluded the excitation of the high photon energy K- and L-shell X-rays where multiple peaks, for example, Kα (K-L2,3)–Kβ (K-M2,3); Lα (L3-M4,5)–Lβ (L2-M4)–Lγ (L2-N4), are well resolved and amenable to identification with high confidence. These misidentifications are so severe as to properly qualify as blunders that present a serious challenge to the credibility of this critical analytical technique. Systematic testing of a peak identification system with a suite of diverse materials can reveal the specific elements and X-ray peaks where failures are likely to occur.

The biomechanical response of tissues serves as a valuable marker in the prediction of disease and in understanding the related behavior of the body under various disease and age states. Alterations in the macroscopic biomechanical response of diseased tissues are well documented; however, a thorough understanding of the microstructural events that lead to these changes is poorly understood. In this article we introduce a novel microbiaxial optomechanical device that allows two-photon imaging techniques to be coupled with macromechanical stimulation in hydrated planar tissue specimens. This allows that the mechanical response of the microstructure can be quantified and related to the macroscopic response of the same tissue sample. This occurs without the need to fix tissue in strain states that could introduce a change in the microstructural configuration. We demonstrate the passive realignment of fibrous proteins under various types of loading, which demonstrates the ability of tissue microstructure to reinforce itself in periods of high stress. In addition, the collagen and elastin response of tissue during viscoelastic behavior is reported showing interstitial fluid movement and fiber realignment potentially responsible for the temporal behavior. We also demonstrate that nonhomogeneities in fiber strain exist over biaxial regions of assumed homogeneity.

The synaptic ribbon is a unique presynaptic structure with an intricate morphology in photoreceptors. Because of the resolution limit in conventional fluorescence microscopy, investigating ribbon protein locations has been challenging, especially in the early development stages of model animals. Here, we used stimulated emission depletion microscopy, a super-resolution imaging technique, to look at retina sections in 4 days post-fertilization (dpf) zebrafish. We observed that in photoreceptor cells, RIBEYE and RIM2 are expressed along the synaptic ribbon, with RIM2 consistently located inside of the horseshoe-shaped synaptic ribbon structure with RIBEYE located on the outside. The L-type calcium channel subunit, CACNA1F, exhibited small spot-like staining beneath the RIM2 and RIBEYE structures. Using morpholino antisense oligonucleotides to knock down RIBEYE expression, we observed fewer and shorter ribbons in the photoreceptor outer plexiform layers of 4 dpf fish retina as well as a reduction in RIM2 expression. The clustering of CACNA1F in these blind fish was no longer observed, but instead showed a diffuse expression in the photoreceptor terminal.

Electron-excited X-ray maps recorded with the scanning electron microscope (SEM)/electron probe X-ray microanalyzer (EPMA) are a major method of presenting compositional information. Digitally recorded maps are processed in a variety of ways to improve the visibility of features. Scaling of the recorded signal to match the 8-bit gray-scale intensity range of a typical computer display system is almost always necessary. Inherent limitations of gray-scale displays have led to other intensity-encoding methods for X-ray maps, including clipping, histogram normalization, and pseudocolor scales. While feature visibility is improved by applying these scales, comparisons among image sets are difficult. Quantitative comparisons must be based on standardized intensities corrected for background to produce intensity ratio (k-value) maps. We have developed a new logarithmic, multiband color-encoding method to view these k-value maps more effectively. Three color bands are defined, starting with a dark primary color and grading to a bright pastel: blue = trace (0.001 to 0.01); green = minor (0.01 to 0.1); and red = major (0.1 to 1.0). Within each band, the color is assigned according to a logarithmic scale that depends on intensity ratio or compositional measurements. Logarithmic multiband color encoding permits direct comparisons of maps, such as maps of different elements in the same field of view or maps of the same element in different areas, because the color scale is identical for all maps.

The evolution of liquid lead (Pb) inclusions at grain boundaries in aluminum (Al) was investigated by direct in situ TEM observation in the temperature range from 330°–643°C, In agreement with earlier reports on quenched alloys, the characteristic contact angle of the lens-shaped grain boundary inclusions was found to be near 120°. This angle remained approximately constant over the entire temperature range, ruling out the possibility of a wetting transition. Coarsening of grain boundary inclusions was observed to proceed mainly by Ostwald ripening, although coalescence could also be observed. Inclusions at grain boundaries, at triple junctions, and at the intersection of grain boundaries with the foil surfaces adopted characteristic shapes that were shown to be equilibrium forms. At the highest temperatures, the grain boundaries were observed to detach from the inclusions and the interaction of a migrating grain boundary with inclusions could be observed.

In this paper, we have observed an atomic-scale structure and compositional variation at the interface of the InGaN/GaN multi-quantum wells (MQW) by both scanning transmission electron microscopy (STEM) using high-angle annular dark-field mode and atom probe tomography (APT). The iso-concentration analysis of APT results revealed that the roughness of InGaN/GaN interface increased as the MQW layers were filled up, and that the upper interface of MQW (GaN/InGaN to the p-GaN side) was much rougher than that of the lower interface (InGaN/GaN tot he n-GaN side). On the basis of experimental results, it is suggested that the formation of interface roughness can affect the quantum efficiency of InGaN-based light-emitting diodes.

In conventional X-ray microtomography (μCT), the three-dimensional (3D) distribution of the attenuation coefficient of X-rays is measured and reconstructed in a 3D volume. As spatial resolution increases, the refraction of X-rays becomes a significant phenomenon in the imaging process. Although this so-called phase contrast was initially a cumbersome feature in lab-based μCT, special phase retrieval algorithms were developed to exploit these effects. Clear advantages in terms of visualization and analysis can be seen when phase retrieval algorithms are applied, including an increased signal-to-noise ratio. In this work, this is demonstrated both on simulated and measured data.

The anterior–posterior and dorsal–ventral progression of heart organogenesis is well illustrated by the patterning and activity of two members of different families of cell adhesion molecules: the calcium-dependent cadherins, specifically N-cadherin, and the extracellular matrix glycoproteins, fibronectin. N-cadherin by its binding to the intracellular molecule β-catenin and fibronectin by its binding to integrins at focal adhesion sites, are involved in regulation of gene expression by their association with the cytoskeleton and through signal transduction pathways. The ventral precardiac mesoderm cells epithelialize and become stably committed by the activation of these cell–matrix and intracellular signaling transduction pathways. Cross talk between the adhesion signaling pathways initiates the characteristic phenotypic changes associated with cardiomyocyte differentiation: electrical activity and organization of myofibrils. The development of both organ form and function occurs within a short interval thereafter. Mutations in any of the interacting molecules, or environmental insults affecting either of these signaling pathways, can result in embryonic lethality or fetuses born with severe heart defects. As an example, we have defined that exposure of the embryo temporally to lithium during an early sensitive developmental period affects a canonical Wnt pathway leading to β-catenin stabilization. Lithium exposure results in an anterior–posterior progression of severe cardiac defects.

The glomerular basement membrane and its associated cells are critical elements in the renal ultrafiltration process. Traditionally the anionic charge associated with several carbohydrate moieties in the glomerular basement membrane are thought to form a charge selective barrier that restricts the transmembrane flux of anionic proteins across the glomerular basement membrane into the urinary space. The charge selective function, along with the size selective component of the basement membrane, serves to limit the efflux of plasma proteins from the capillary lumen. Heparan sulfate glycosaminoglycans are anionically charged carbohydrate structures attached to proteoglycan core proteins and have a role in establishing the charge selective function of the glomerular basement membrane. Although there are a large number of studies in the literature that support this concept, the results of several recent studies using molecular genetic approaches to minimize the anionic charge of the glomerular basement membrane would suggest that the role of heparan sulfate glycosaminoglycans in the glomerular capillary wall are still not yet entirely resolved, suggesting that this research area still requires new and novel exploration.

Nanosized incubational domain was observed in 10 at.% gadolinium-doped ceria (GDC) using high-resolution transmission electron microscopy. Dislocations were extensively observed in 10 at.% GDC instead of heavily doped 25 at.% GDC. By Fast Fourier Transform and Inverse Fast Fourier Transform analysis, it was noticed that the incubational domain existing in 10 at.% GDC has different lattice spacing and orientation from the neighboring ceria matrix. Furthermore, dislocations were usually observed in the interface region between the incubational domain and the ceria matrix. Based on experimental results, the formation mechanism of dislocation associated incubational domain in lightly gadolinium-doped ceria is rationalized.

Atom probe is a nanoscale technique for creating three-dimensional spatially and chemically resolved point datasets, primarily of metallic or semiconductor materials. While atom probe can achieve local high-level resolution, the spatial coherence of the technique is highly dependent upon the evaporative physics in the material and can often result in large geometric distortions in experimental results. The distortions originate from uncertainties in the projection function between the field evaporating specimen and the ion detector. Here we explore the possibility of continuum numerical approximations to the evaporative behavior during an atom probe experiment, and the subsequent propagation of ions to the detector, with particular emphasis placed on the solution of axisymmetric systems, such as isolated particles and multilayer systems. Ultimately, this method may prove critical in rapid modeling of tip shape evolution in atom probe tomography, which itself is a key factor in the rapid generation of spatially accurate reconstructions in atom probe datasets.

We present a fast and simple method to prepare specimens for transmission electron microscopy studies of oxide thin films deposited on silicon substrates. The method consists of scratching the film surface using a pointed diamond tip, in a special manner. Small and thin fragments are then detached from the film and its substrate. Depending on the scratching direction, the fragments can be used for plan-view or cross-section imaging. High-resolution images can be also obtained from thin edges of the film fragments. The method is demonstrated in the case of HfO2 sol-gel films deposited on [100] Si wafer substrates.

Methods for creating speckle patterns on mouse arteries for use in deformation and strain field measurements in a stereomicroscope digital image correlation (DIC) system are described. Both fluorescent microsphere binding and ethidium bromide (EB) nuclear staining were used to generate high contrast, random patterns on mouse carotid arteries. To quantify the quality of each pattern, several metrics are used including (a) histogram distribution for each intensity pattern and (b) pixel-level variance in intensity pattern noise. Results demonstrate that both approaches provide sufficient pattern contrast for use in image-based methods to measure deformations in soft tissue. While fluorescent nuclear staining generates higher pixel-level intensity noise, this method provides better overall pattern quality (greater spatial uniformity and broader histogram) for automated DIC analysis when used at the appropriate magnification. Using recently developed theoretical predictions, estimates for the standard deviation in image-correlation-based displacements due to the measured intensity pattern variance are presented for fluorescent microsphere binding and EB nuclear staining patterns. Results confirm that both patterning approaches provide relatively small standard deviation in displacement measurements and hence are appropriate for measurement of deformations in small artery specimens.

The teeth of the marine mollusk Acanthopleura hirtosa are an excellent example of a complex, organic, matrix-mediated biomineral, with the fully mineralized teeth comprising layers of iron oxide and iron oxyhydroxide minerals around a calcium apatite core. To investigate the relationship between the various mineral layers and the organic matrix fibers on which they grew, sections have been prepared from specific features in the teeth at controlled orientations using focused ion beam processing. Compositional and microstructural details of heterophase interfaces, and the fate of the organic matrix fibers within the mineral layers, can then be analyzed by a range of transmission electron microscopy (TEM) techniques. Energy-filtered TEM highlights the interlocking nature of the various mineral phases, while high-angle annular dark-field scanning TEM imaging demonstrates that the organic matrix continues to exist in the fully mineralized teeth. These new insights into the structure of this complex biomaterial are an important step in understanding the relationship between its structural and physical properties and may help explain its high strength and crack-resistance behavior.

In this article, a new scanning electron microscopy (SEM) image composition technique is described, which can significantly reduce drift related image corruptions. Drift distortion commonly causes blur and distortions in the SEM images. Such corruption ordinarily appears when conventional image-acquisition methods, i.e., “slow scan” and “fast scan,” are applied. The damage is often very significant; it may render images unusable for metrology applications, especially where subnanometer accuracy is required. The described correction technique works with a large number of quickly taken frames, which are properly aligned and then composed into a single image. Such image contains much less noise than the individual frames, while the blur and deformation is minimized. This technique also provides useful information about changes of the sample position in time, which may be applied to investigate the drift properties of the instrument without a need of additional equipment.

Crystal structure of nano-scale precipitates in age-hardening aluminum alloys is a challenge to crystallography. The utility of selected area electron diffraction intensities from embedded precipitates is limited by double scattering via matrix reflections. This effect can be signally reduced by the precession technique, which we have used to collect extensive intensity data from the semicoherent, metastable η′-precipitate in the Al-Zn-Mg alloy system. A structure model in the space group P-62c is proposed from high-resolution microscopy and electron diffraction intensities. The advantages of using the precession technique for quantitative electron diffraction is discussed.