The dictionary-based approach to the indexing of diffraction patterns is applied to electron channeling patterns (ECPs). The main ingredients of the dictionary method are introduced, including the generalized forward projector (GFP), the relevant detector model, and a scheme to uniformly sample orientation space using the “cubochoric” representation. The GFP is used to compute an ECP “master” pattern. Derivative free optimization algorithms, including the Nelder–Mead simplex and the bound optimization by quadratic approximation are used to determine the correct detector parameters and to refine the orientation obtained from the dictionary approach. The indexing method is applied to poly-silicon and shows excellent agreement with the calibrated values. Finally, it is shown that the method results in a mean disorientation error of 1.0° with 0.5° SD for a range of detector parameters.

We present a computational method for pseudo-circular object detection and quantitative characterization in digital images, using the gradient accumulation matrix as a basic tool. This Gradient Accumulation Transform (GAT) was first introduced in 1992 by Kierkegaard and recently used by Kaytanli & Valentine. In the present article, we modify the approach by using the phase coding studied by Cicconet, and by adding a “local contributor list” (LCL) as well as a “used contributor matrix” (UCM), which allow for accurate peak detection and exploitation. These changes help make the GAT algorithm a robust and precise method to automatically detect pseudo-circular objects in a microscopic image. We then present an application of the method to cell counting in microbiological images.

Quantitative analysis of multicellular organization, cell–cell junction integrity, and substrate properties is essential to understand the mechanisms underlying collective cell migration. However, spatially and temporally defining these properties is difficult within collectively migrating cell groups due to challenges in accurate cell segmentation within the monolayer. In this paper, we present Matlab®-based algorithms to spatially quantify multicellular organization (migration distance, interface roughness, and cell alignment, area, and morphology), cell–cell junction integrity, and substrate features in confocal microscopy images of two-dimensional collectively migrating endothelial monolayers. We used novel techniques, including measuring the migrating front roughness using a parametric curve formulation, automatically binning cells to obtain data as a function of distance from the migrating front, using iterative morphological closings to fully define cell boundaries, quantifying β-catenin localization as a measure of cell–cell junction integrity, and skeletonizing fibronectin to determine fiber length and orientation. These algorithms are widely accessible, as they use common fluorescent markers and Matlab® functions, and provide high-throughput critical feature quantification within collectively migrating cell groups. These image analysis algorithms can help standardize feature quantification among different experimental techniques, cell types, and research groups studying collective cell migration.

The concept of atomic-scale tomography has been proposed in the past decade as a technique that could deliver the position of all atoms with high precision and their elemental (isotopic) identity. The technique was never intended to be limited to merely structural information and there is clearly a rich array of additional analytical information that can be brought to bear on such tomographs. In this paper, some of these types of information are considered and the implications are explored. The fuller realm of this analytical and structural information may be called atomic-scale analytical tomography.

We present liquid-cell transmission electron microscopy (liquid-cell TEM) imaging of fixed and non-fixed prostate cancer cells (PC3 and LNCaP) with high resolution in a custom developed silicon nitride liquid cell. Fixed PC3 cells were imaged for 90–120 min without any discernable damage. High contrast on the cellular structures was obtained even at low electron doses (~2.5 e−/nm2 per image). The images show distinct structures of cell compartments (nuclei and nucleoli) and cell boundaries without any further sample embedding, dehydration, or staining. Furthermore, we observed dynamics of vesicles trafficking from the cell membrane in consecutive still frames in a non-fixed cell. Our findings show that liquid-cell TEM, operated at low electron dose, is an excellent tool to investigate dynamic events in non-fixed cells with enough spatial resolution (few nm) and natural amplitude contrast to follow key intracellular processes.

The bulk of the major core protein VP7 in African horse sickness virus (AHSV) self-assembles into flat, hexagonal crystalline particles in a process appearing unrelated to viral replication. Why this unique characteristic of AHSV VP7 is genetically conserved, and whether VP7 aggregation and particle formation have an effect on cellular biology or the viral life cycle, is unknown. Here we investigated how different small peptide and enhanced green fluorescent protein (eGFP) insertions into the VP7 top domain affected VP7 localization, aggregation, and particle formation. This was done using a dual laser scanning confocal and transmission electron microscopy approach in conjunction with analyses of the solubility, aggregation, and fluorescence profiles of the proteins. VP7 top domain modifications did not prevent trimerization, or intracellular trafficking, to one or two discrete sites in the cell. However, modifications that resulted in a misfolded and insoluble VP7-eGFP component blocked trafficking, and precluded protein accumulation at a single cellular site, perhaps by interfering with normal trimer–trimer interactions. Furthermore, the modifications disrupted the stable layering of the trimers into characteristic AHSV VP7 crystalline particles. It was concluded that VP7 trafficking is driven by a balance between VP7 solubility, trimer forming ability, and trimer–trimer interactions.

Cyclin E1 (CCNE1) is a core component of cell cycle regulation that drives the transition into the S phase. CCNE1 plays critical roles in cell cycle, cell proliferation, and cellular functions. However, the function of CCNE1 in early embryonic development is limited. In the present study, the function and expression of Ccne1 in porcine early parthenotes were examined. Immunostaining experiments showed that CCNE1 localized in the nucleus, starting at the four-cell stage. Knockdown of Ccne1 by double-stranded RNA resulted in the failure of blastocyst formation and induced blastocyst apoptosis. Ccne1 depletion increased expression of the pro-apoptotic gene Bax, and decreased the expression of Oct4 and the rate of inner cell mass (ICM)/trophectoderm formation. The results indicated that CCNE1 affects blastocyst formation by inducing cell apoptosis and ICM formation during porcine embryonic development.

Development of collateral vessels, arteriogenesis, may protect against tissue ischemia, however, quantitative data on this process remain scarce. We have developed a technique for replicating the entire arterial network of ischemic rat hindlimbs in three dimensions (3D) based on vascular casting and automated sequential cryo-imaging. Various dilutions of Batson’s No. 17 with methyl methacrylate were evaluated in healthy rats, with further protocol optimization in ischemic rats. Penetration of the resin into the vascular network greatly depended on dilution; the total length of casted vessels below 75 µm was 13-fold higher at 50% dilution compared with the 10% dilution. Dilutions of 25–30%, with transient clamping of the healthy iliac artery, were optimal for imaging the arterial network in unilateral ischemia. This protocol completely filled the lumina of small arterioles and collateral vessels. These appeared as thin anastomoses in healthy legs and increasingly larger vessels during ligation (median diameter 1 week: 63 µm, 4 weeks: 127 µm). The presented combination of quality casts with high-resolution cryo-imaging enables automated, detailed 3D analysis of collateral adaptation, which furthermore can be combined with co-registered 3D distributions of fluorescent molecular imaging markers reflecting biological activity or perfusion.

The purpose of this work was to determine whether the morphology of the oral mucosa epithelium (OME) of patients with xerostomia differ from patients without xerostomia. In total, 34 patients with dry eye disease (DED) with or without xerostomia were examined at The Norwegian Dry Eye Disease Clinic with in vivo confocal microscopy of the lower lip. In addition, age- and gender-matched healthy controls (HC) were included. DED patients with xerostomia had a higher superficial to deep backscatter ratio compared with DED patients without xerostomia (p=0.002) and HC (p=0.001). Regression analysis demonstrated that this ratio was related to xerostomia independently of gender and age (p<0.001). Sensitivity and specificity of detecting xerostomia were 0.78 and 0.85, respectively, when using a superficial to deep backscatter ratio cut-off value of 0.995 (p=0.004). The mean nucleus to cytosol backscatter ratio in the superficial OME was lower in patients with xerostomia than in those without xerostomia (p=0.034). In vivo confocal microscopy is a potential tool for evaluating the oral cavity and to assess changes in the OME associated with xerostomia, objectively and quantitatively. The cause of the increased backscatter in the superficial OME in xerostomia, however, remains to be elucidated.

Supported lipid bilayer systems were evaluated following various experimental procedures in an effort to determine their appropriateness for visualization using total internal reflection fluorescence (TIRF) microscopy. The incorporation and distribution of Texas Red® 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (TR-DHPE) was studied when incorporated into bilayers of variable lipid composition using different forms of mechanical shearing. Results showed that 0.8 mol% TR-DHPE provides the most optimum TIRF images. At this concentration, a sufficient level of photostability can be achieved without an undesirable increase in TR-DHPE aggregates caused by excess probe molecules. Solutions composed of a 3:1 molar ratio of DOPC:DPPC with 0.8 mol% TR-DHPE produce bilayers that consistently display clear, distinct, rounded domains, whereas other lipid compositions did not. This optimum phase separation appears to be influenced by an increase in mechanical shearing during the vesicle formation process, when the lipid solutions were exposed to sonication and extrusion processes. The combination of a sonication and extrusion process also helped with eliminating the presence of TR-DHPE aggregates within the model membranes. It was also shown that bilayers formed on conditioned glass, placed on a slide, produced more highly detailed bilayers in which distinct lipid phase separation could be optimally visualized using TIRF microscopy.

The rapidity with which epithelial cells cover a wound surface helps determine whether scarring or scar-less healing results. As methylene blue is a vital dye that is absorbed by damaged tissue but not undamaged epidermis, it can be used to assess wound closure. We sought to develop a quantitative methylene blue exclusion assay to estimate the timeframe for re-epithelialization in regenerating appendages in zebrafish and axolotls, two classic model systems of regeneration. Following application of methylene blue to the amputation plane and extensive washing, the regenerating tail was imaged in vivo until staining was no longer visible. The percent area of the amputation plane positive for methylene blue, representing the area of the amputation plane not yet re-epithelialized, was measured for each time point. The loss of methylene blue occurred rapidly, within ~2.5 h in larval and juvenile axolotls and <1 h in adult zebrafish, consistent with high rates of re-epithelialization in these models of regeneration. The assay allows simple, rapid estimation of the time course for regenerative re-epithelialization without affecting subsequent regenerative ability. This technique will permit comparison of re-epithelialization across different strains and stages, as well as under the influence of various pharmacological inhibitors that affect regeneration.

Fluorescent dyes like Rhodamine B (RB) have been used to identify the spatial distribution of adhesive restorative materials in the tooth/restoration interface. Potential effects of the addition of RB to dental adhesives were addressed in the past, but no further information is available on how to determine suitable concentrations of RB in these bonding agents for imaging in the confocal laser scanning microscope. This study provides systematical strategies for adding RB to viscous dental adhesive resins, focusing on the determination of the lowest range of dye concentrations necessary to achieve an acceptable image of the dentin/adhesive interface. It was demonstrated that optimized images of the resin distribution in dentin can be produced with 0.1–0.02 mg/mL of RB in the (tested) adhesives. Our approaches took into account aspects related to the dye concentration, photophysical parameters in different host media, specimen composition and morphology to develop a rational use of the fluorescent agent with the resin-based materials. Information gained from this work can help optimize labeling methods using dispersions of low-molecular-weight dyes in different monomer blend systems.

The aim of this study was to investigate if load cycling affects interfacial integrity of glass ionomer cements bonded to sound- or caries-affected dentin. A conventional glass ionomer, Ketac Bond, and a resin-modified glass ionomer (Vitrebond Plus), were applied to dentin. Half of the specimens were load cycled. The interfaces were submitted to dye-assisted confocal microscopy evaluation. The unloaded specimens of sound and carious dentin were deficiently hybridized when Ketac Bond was used. Ketac Bond samples showed an absorption layer and an adhesive layer that were scarcely affected by fluorescein penetration (nanoleakage), in sound dentin. Nevertheless, a higher degree of micropermeability was found in carious dentin. In Ketac Bond specimens, load cycling improves the sealing capability and remineralization at the cement–dentin interface as porosity and nanoleakage was reduced. In contrast, samples treated with Vitrebond Plus exhibited a Rhodamine B-labeled absorption layer with scarce nanoleakage in both sound and carious unloaded dentin. The adhesive layer was affected by dye sorption throughout the porous cement–dentin interface. Samples treated with Vitrebond Plus had significant increases in nanoleakage and cement–dye sorption after load cycling. Within the limitations of an in vitro study, it is expected that conventional glass ionomers will provide major clinical efficacy when applied to carious-affected or sound dentin.

Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm2 with the acquisition time of ~2 s or less. Here we report the details of this method, and, in particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO3 in [001] projection for 200 keV electrons.

Lithium sulfur (Li–S) batteries have the potential to provide higher energy storage density at lower cost than conventional lithium ion batteries. A key challenge for Li–S batteries is the loss of sulfur to the electrolyte during cycling. This loss can be mitigated by sequestering the sulfur in nanostructured carbon–sulfur composites. The nanoscale characterization of the sulfur distribution within these complex nanostructured electrodes is normally performed by electron microscopy, but sulfur sublimates and redistributes in the high-vacuum conditions of conventional electron microscopes. The resulting sublimation artifacts render characterization of sulfur in conventional electron microscopes problematic and unreliable. Here, we demonstrate two techniques, cryogenic transmission electron microscopy (cryo-TEM) and scanning electron microscopy in air (airSEM), that enable the reliable characterization of sulfur across multiple length scales by suppressing sulfur sublimation. We use cryo-TEM and airSEM to examine carbon–sulfur composites synthesized for use as Li–S battery cathodes, noting several cases where the commonly employed sulfur melt infusion method is highly inefficient at infiltrating sulfur into porous carbon hosts.

The potential of electrospray deposition, for the controlled preparation of particles for imaging in electron microscopes, is evaluated on various materials: from mono-modal suspensions of spherical particles to multimodal suspensions and to real-world industrial materials. It is shown that agglomeration is reduced substantially on the sample carrier, compared with conventional sample preparation techniques. For the first time, it is possible to assess the number concentration of a tri-modal polystyrene suspension by electron microscopy, due to the high deposition efficiency of the electrospray. We discovered that some suspension stabilizing surfactants form artifact particles during electrospraying. These can be avoided by optimizing the sprayed suspension.

Formation of a nanometer-scale oxide surface layer is common when a material is exposed to oxygen-containing environment. Employing aberration-corrected analytical transmission electron microscopy and using single crystal SnSe as an example, we show that for an alloy, a second thin amorphous layer can appear underneath the outmost oxide layer. This inner amorphous layer is not oxide based, but instead originates from solid-state amorphization of the base alloy when its free energy rises to above that of the metastable amorphous state; which is a result of the composition shift due to the preferential depletion of the oxidizing species, in our case, the outgoing Sn reacting with the oxygen atmosphere.

We report a systematic spectroscopical investigation of three plagioclase particles (RB-QD04-0022, RA-QD02-0025-01, and RA-QD02-0025-02) returned by the Hayabusa spacecraft from the asteroid Itokawa, by means of scanning electron microscopy, cathodoluminescence microscopy/spectroscopy, and micro-Raman spectroscopy. The cathodoluminescence properties are used to evaluate the crystallization effects and the degree of space weathering processes, especially the shock-wave history of Itokawa. They provide new insights regarding spectral changes of asteroidal bodies due to space weathering processes. The cathodoluminescence spectra of the plagioclase particles from Itokawa show a defect-related broad band centered at around 450 nm, with a shoulder peak at 425 nm in the blue region, but there are no Mn- or Fe-related emission peaks. The absence of these crystal field-related activators indicates that the plagioclase was formed during thermal metamorphism at subsolidus temperature and extreme low oxygen fugacity. Luminescence characteristics of the selected samples do not show any signatures of the shock-induced microstructures or amorphization, indicating that these plagioclase samples suffered no (or low-shock pressure regime) shock metamorphism. Cathodoluminescence can play a key role as a powerful tool to determine mineralogy of fine-grained astromaterials.