P-glycoprotein is implicated in clinical drug resistance; thus, rapid quantitative analysis of its expression and activity is of paramout importance to the design and success of novel therapeutics. The scope for the application of quantitative imaging and image analysis tools in this field is reported here at “proof of concept” level. P-glycoprotein expression was utilized as a model for quantitative immunofluorescence and subsequent spatial intensity distribution analysis (SpIDA). Following expression studies, p-glycoprotein inhibition as a function of verapamil concentration was assessed in two cell lines using live cell imaging of intracellular Calcein retention and a routine monolayer fluorescence assay. Intercellular and sub-cellular distributions in the expression of the p-glycoprotein transporter between parent and MDR1-transfected Madin–Derby Canine Kidney cell lines were examined. We have demonstrated that quantitative imaging can provide dose–response parameters while permitting direct microscopic analysis of intracellular fluorophore distributions in live and fixed samples. Analysis with SpIDA offers the ability to detect heterogeniety in the distribution of labeled species, and in conjunction with live cell imaging and immunofluorescence staining may be applied to the determination of pharmacological parameters or analysis of biopsies providing a rapid prognostic tool.

Attempts to elucidate chromosome structure have long remained elusive. Electron microscopy is useful for chromosome structure research because of its high resolution and magnification. However, biological samples such as chromosomes need to be subjected to various preparation steps, including dehydration, drying, and metal/carbon coating, which may induce shrinkage and artifacts. The ionic liquid technique has recently been developed and it enables sample preparation without dehydration, drying, or coating, providing a sample that is closer to the native condition. Concurrently, focused ion beam/scanning electron microscopy (FIB/SEM) has been developed, allowing the investigation and direct analysis of chromosome interiors. In this study, we investigated chromosome interiors by FIB/SEM using plant and human chromosomes prepared by the ionic liquid technique. As a result, two types of chromosomes, with and without cavities, were visualized, both for barley and human chromosomes prepared by critical point drying. However, chromosome interiors were revealed only as a solid structure, lacking cavities, when prepared by the ionic liquid technique. Our results suggest that the existence and size of cavities depend on the preparation procedures. We conclude that combination of the ionic liquid technique and FIB/SEM is a powerful tool for chromosome study.

Biofilms are three-dimensional communities of bacteria distributed in a highly hydrated extracellular matrix (ECM). They can be visualized by scanning electron microscopy (SEM), but the requisite SEM sample preparation can modify the biofilm morphology. Here, four different approaches to prepare biofilms of hydrated Staphylococcus aureus for SEM imaging are compared. In order of increasing cooling effectiveness these are: (1) drying in air; (2) plunging in liquid nitrogen; (3) plunging in liquid ethane; and (4) high pressure freezing with liquid nitrogen. These different methods give rise to markedly different biofilm morphologies, which are revealed by cryo-SEM imaging. Significantly, high-pressure frozen biofilms exhibit a rich network of nanoscale ECM fibers surrounding individual bacteria throughout the biofilm thickness. This structure is entirely lost when similar biofilms are dried in air, and it is substantially modified when these biofilms are plunged into liquid nitrogen or liquid ethane.

We evaluate the usefulness of digital volume data produced with the high-resolution episcopic microscopy (HREM) method for visualizing the three-dimensional (3D) arrangement of components of human skin, and present protocols designed for processing skin biopsies for HREM data generation. A total of 328 biopsies collected from normally appearing skin and from a melanocytic nevus were processed. Cuboidal data volumes with side lengths of ~2×3×6 mm3 and voxel sizes of 1.07×1.07×1.5 µm3 were produced. HREM data fit ideally for visualizing the epidermis at large, and for producing highly detailed volume and surface-rendered 3D representations of the dermal and hypodermal components at a structural level. The architecture of the collagen fiber bundles and the spatial distribution of nevus cells can be easily visualized with volume-rendering algorithms. We conclude that HREM has great potential to serve as a routine tool for researching and diagnosing skin pathologies.

This study evaluated the effect of fluoride solutions on surface roughness and morphology of composites in the short and long term. Specimens were randomly assigned to experimental groups (n=5) according to type of composite (nanofilled, microhybrid, microfilled) and immersion media (artificial saliva, 0.05% sodium fluoride solution, Fluordent Reach, Oral-B, and Fluorgard). Roughness was evaluated at time intervals: T0 after 24 h in artificial saliva (baseline); T60 after being in assigned immersion media for 1 min daily over 60 days; and Tfinal after artificial aging (20,000 thermal cycles, 1,200,000 mechanical loading cycles, and continuous immersion for 1,825 min). Surface morphology was qualitatively analyzed by scanning electron microscopy (SEM) at T60 and Tfinal. Roughness data were submitted to analysis of variance for mixed repeated measures, Sidak, and Tukey tests at α=0.05. Micro-filled resin showed the highest roughness values. Fluoride solutions had no influence on roughness. Higher roughness values were observed after artificial aging. In SEM observations after the artificial aging, the specimens showed surface degradation, irrespective of immersion medium or type of composite. Nano-filled resin showed higher loss of resin matrix and protrusion of filler particles. Roughness was not influenced by fluoride solutions; however, it is material dependent and increases over time.

This aim of this study was to assess the discriminatory value of fractal and grey level co-occurrence matrix (GLCM) analysis methods in standard microscopy analysis of two histologically similar brain white mass regions that have different nerve fiber orientation. A total of 160 digital micrographs of thionine-stained rat brain white mass were acquired using a Pro-MicroScan DEM-200 instrument. Eighty micrographs from the anterior corpus callosum and eighty from the anterior cingulum areas of the brain were analyzed. The micrographs were evaluated using the National Institutes of Health ImageJ software and its plugins. For each micrograph, seven parameters were calculated: angular second moment, inverse difference moment, GLCM contrast, GLCM correlation, GLCM variance, fractal dimension, and lacunarity. Using the Receiver operating characteristic analysis, the highest discriminatory value was determined for inverse difference moment (IDM) (area under the receiver operating characteristic (ROC) curve equaled 0.925, and for the criterion IDM≤0.610 the sensitivity and specificity were 82.5 and 87.5%, respectively). Most of the other parameters also showed good sensitivity and specificity. The results indicate that GLCM and fractal analysis methods, when applied together in brain histology analysis, are highly capable of discriminating white mass structures that have different axonal orientation.

Image pre-processing is highly significant in automated analysis of microscopy images. In this work, non-uniform illumination correction has been attempted using the surface fitting method (SFM), multiple regression method (MRM), and bidirectional empirical mode decomposition (BEMD) in digital microscopy images of tuberculosis (TB). The sputum smear positive and negative images recorded under a standard image acquisition protocol were subjected to illumination correction techniques and evaluated by error and statistical measures. Results show that SFM performs more efficiently than MRM or BEMD. The SFM produced sharp images of TB bacilli with better contrast. To further validate the results, multifractal analysis was performed that showed distinct variation before and after implementation of illumination correction by SFM. Results demonstrate that after illumination correction, there is a 26% increase in the number of bacilli, which aids in classification of the TB images into positive and negative, as TB positivity depends on the count of bacilli.

Transmission electron microscopy (TEM) is an important tool for studies in cell biology, and is essential to address research questions from bacteria to animals. Recent technological innovations have advanced the entire field of TEM, yet classical techniques still prevail for most present-day studies. Indeed, the majority of cell and developmental biology studies that use TEM do not require cutting-edge methodologies, but rather fast and efficient data generation. Although access to state-of-the-art equipment is frequently problematic, standard TEM microscopes are typically available, even in modest research facilities. However, a major unmet need in standard TEM is the ability to quickly prepare and orient a sample to identify a region of interest. Here, I provide a detailed step-by-step method for a positional correlative anatomy approach to flat-embedded samples. These modifications make the TEM preparation and analytic procedures faster and more straightforward, supporting a higher sampling rate. To illustrate the modified procedures, I provide numerous examples addressing research questions in Caenorhabditis elegans and Drosophila. This method can be equally applied to address questions of cell and developmental biology in other small multicellular model organisms.

The study uses microscopy to analyze damage caused to the ovaries of a fresh water fish, Cyprinus carpio L., owing to its exposure to municipal wastes in a polluted reservoir, Umiam in Meghalaya, India. Histological analysis of the ovary showed atretic oocytes, detached ovarian wall, detached follicular linings, and necrosis of nuclei. Scanning electron microscopy revealed deformed oocytes with a rough and distorted surface. Transmission electron microscopy showed a poorly developed chorion, presence of relatively less electron-dense materials as compared with control, multinucleation in some cells surrounding the oocytes, and distorted and condensed mitochondria. The importance of microscopy in its different forms in analyzing histological, surface microstructural and fine structural damage to fish ovaries in response to environmental pollution owing to municipal wastes and city garbage is discussed with the help of available literature.

The in vitro effect of cadmium (Cd) on apical segments of Pterocladiella capillacea was examined. Over a period of 7 days, the segments were cultivated with the combination of different salinities (25, 35, and 45 practical salinity units) and Cd concentrations, ranging from 0.17 to 0.70 ppm. The effects of Cd on growth rates and content of photosynthetic pigments were analyzed. In addition, metabolic profiling was performed, and samples were processed for microscopy. Serious damage to physiological performance and ultrastructure was observed under different combinations of Cd concentrations and salinity values. Elementary infrared spectroscopy revealed toxic effects registered on growth rate, photosynthetic pigments, chloroplast, and mitochondria organization, as well as changes in lipids and carbohydrates. These alterations in physiology and ultrastructure were, however, coupled to activation of such defense mechanisms as cell wall thickness, reduction of photosynthetic harvesting complex, and flavonoid. In conclusion, P. capillacea is especially sensitive to Cd stress when intermediate concentrations of this pollutant are associated with low salinity values. Such conditions resulted in metabolic compromise, reduction of primary productivity, i.e., photosynthesis, and carbohydrate accumulation in the form of starch granules. Taken together, these findings improve our understanding of the potential impact of this metal in the natural environment.

Dried leaves of Satureja khuzestanica Jamzad are a popular herbal medicine and dental anesthetic among the nomadic inhabitants of southwestern Iran. The present study establishes criteria for identification of S. khuzestanica dried whole, fragmented and powdered leaves for specification as a herbal substance using macroscopic and microscopic characterization. Quantitative microscopy techniques were also considered. Macroscopically leaves exhibit a grayish-green color, are broadly ovate in shape with an acute apex, attenuate base, and ciliate margin and have a surface covered by an indumentum of glandular and non-glandular trichomes. Microscopically leaves have an isobilateral amphistomatic structure containing peltate glandular trichomes consisting of a multiseriate stalk (five cells) and an enlarged secretory head composed of 12 cells, capitate glandular trichomes of variable morphology together with two types of non-glandular trichomes. Oval-shaped hygromorphic diacytic stomata with an adaxial stomatal index of 13.54, collateral vascular bundles consisting of xylem, and three layers of sclerenchymatous tissue close to phloem together with cluster, prismatic and raphide calcium oxalate crystals were also identified as useful pharmacognostic parameters for identification of S. khuzestanica dried leaves.

Recently, the use of different types of natural fibers to produce paper and textiles from agave plants has been proposed. Agave atrovirens can be a good source of cellulose and lignin; nevertheless, the microstructural changes that happen during delignification have scarcely been studied. The aim of this work was to study the microstructural changes that occur during the delignification of agave fibers by means of microscopy techniques and image analysis. The fibers of A. atrovirens were obtained from leaves using convective drying, milling, and sieving. Fibers were processed using the Acetosolv pulping method at different concentrations of acetic acid; increasing acid concentration promoted higher levels of delignification, structural damage, and the breakdown of fiber clumps. Delignification followed by spectrometric analysis and microstructural studies were carried out by light, confocal laser scanning and scanning electron microscopy and showed that the delignification process follows three stages: initial, bulk, and residual. Microscopy techniques and image analysis were efficient tools for microstructural characterization during delignification of agave fibers, allowing quantitative evaluation of the process and the development of linear prediction models. The data obtained integrated numerical and microstructural information that could be valuable for the study of pulping of lignocellulosic materials.

High precision determination of atomic position is necessary for quantitative electron microscopy so that small width of peaks, which represent atoms in structural images, adequate resolution, and sufficiently strong image contrast are needed. The width of peak is usually determined by the point spread (PS) of instruments, but the PS of objects should also be taken into consideration in aberration-corrected transmission electron microscopy when point resolution of a microscope reaches the sub-angstrom scale, and thus the PS of the instrument is comparable with that of the object. In this article, PS is investigated by studying peak width with variation of atomic number, sample thickness, and spherical aberration coefficients in both negative Cs (NCSI) and positive Cs imaging (PCSI) modes by means of dynamical image simulation. Through comparing the peak width with various atomic number, thickness, and values of spherical aberration, NCSI mode is found to be superior to PCSI considering the smaller width.

The atomic structure of Cs0.44[Nb2.54W2.46O14] closely resembles the structure of the most active catalyst for the synthesis of acrylic acid, the M1 phase of ${\rm Mo}_{{{\rm 10}}} {\rm V}_{{\rm 2}}^{{{\rm 4{\plus}}}} {\rm Nb}_{2} {\rm TeO}_{{{\rm 42}{\minus}x}} $ . Consistently with observations made for the latter compound, the high-angle electron scattering signal recorded by scanning transmission electron microscopy shows a significant intensity variation, which repeats periodically with the projected crystallographic unit cell. The occupation factors for the individual mixed Nb/W atomic columns are extracted from the observed intensity variations. For this purpose, experimental images and simulated images are compared on an identical intensity scale, which enables a quantification of the cation distribution. According to our analysis specific sites possess low tungsten concentrations of 25%, whereas other sites have tungsten concentrations above 70%. These findings allow us to refine the existing structure model of the target compound, which has until now described a uniform distribution of the niobium and tungsten atoms in the unit cell, showing that the similarity between Cs0.44[Nb2.54W2.46O14] and the related catalytic compounds also extends to the level of the cation segregation.

In an earlier publication Rosenauer et al. introduced a method for determination of composition in AlGaN/GaN heterostructures from high-angle annular dark field (HAADF) images. Static atomic displacements (SADs) were neglected during simulation of reference data because of the similar covalent radii of Al and Ga. However, SADs have been shown (Grillo et al.) to influence the intensity in HAADF images and therefore could be the reason for an observed slight discrepancy between measured and nominal concentrations. In the present study parameters of the Stillinger–Weber potential were varied in order to fit computed elastic constants, lattice parameters and bonding energies to experimental ones. A reference data set of HAADF images was simulated, in which the new parameterization was used to account for SADs. Two reference samples containing AlGaN layers with different Al concentrations were investigated and Al concentrations in the layers determined based on the new data set. We found that these concentrations were in good agreement with nominal concentrations as well as concentrations determined using alternative techniques such as strain state analysis and energy dispersive X-ray spectroscopy.

We discuss observations of InN nanowires (NWs) by plan-view high-resolution transmission electron microscopy (TEM). The main difficulties arise from suitable methods available for plan-view specimen preparation. We explore different approaches and find that the best results are obtained using a refined preparation method based on the conventional procedure for plan-view TEM of thin films, specifically modified for the NW morphology. The fundamental aspects of such a preparation are the initial mechanical stabilization of the NWs and the minimization of the ion-milling process after dimpling the samples until perforation. The combined analysis by plan-view and cross-sectional TEM of the NWs allows determination of the degree of strain relaxation and reveals the formation of an unintentional shell layer (2–3-nm thick) around the InN NWs. The shell layer is composed of bcc In2O3 nanocrystals with a preferred orientation with respect to the wurtzite InN: In2O3 [111] || InN [0001] and In2O3 <110> || InN< $$ 11\bar 20 $$ >.

Carbon nanotubes (CNT) have proven to be materials with great potential for the construction of biosensors. Development of fast, simple, and low cost biosensors to follow reactions in bioprocesses, or to detect food contaminants such as toxins, chemical compounds, and microorganisms, is presently an important research topic. This report includes microscopy and spectroscopy to characterize raw and chemically modified multiwall carbon nanotubes (MWCNTs) synthesized by chemical vapor deposition with the intention of using them as the active transducer in bioprocessing sensors. MWCNT were simultaneously purified and functionalized by an acid mixture involving HNO3–H2SO4 and amyloglucosidase attached onto the chemically modified MWCNT surface. A 49.0% decrease in its enzymatic activity was observed. Raw, purified, and enzyme-modified MWCNTs were analyzed by scanning and transmission electron microscopy and Raman and X-ray photoelectron spectroscopy. These studies confirmed purification and functionalization of the CNTs. Finally, cyclic voltammetry electrochemistry was used for electrical characterization of CNTs, which showed promising results that can be useful for construction of electrochemical biosensors applied to biological areas.

A microstructural characterization study was performed on high-pressure die cast specimens extracted from escalator steps manufactured from an Al-12 wt.% Si alloy designed for structural applications. Black and white, color light optical imaging and scanning electron microscopy techniques were used to conduct the microstructural analysis. Most regions in the samples studied contained globular-rosette primary α-Al grains surrounded by an Al-Si eutectic aggregate, while primary dendritic α-Al grains were present in the surface layer. This dendritic microstructure was observed in the regions where the melt did not impinge directly on the die surface during cavity filling. Consequently, microstructures in the surface layer were nonuniform. Utilizing physical metallurgy principles, these results were analyzed in terms of the applied pressure and filling velocity during high-pressure die casting. The effects of these parameters on solidification at different locations of the casting are discussed.

A contactless method of probing and analyzing multifunctional oxide interfaces using an electron energy analyzer inside a scanning electron microscope is presented. High contrast experimental secondary electron analyzer signals are used to detect changes in the interface conductivity of a LaAlO3/SrTiO3 sample. Monte Carlo simulations of the primary beam/specimen interaction are carried out and correlated with the experimental results in order to help understand the role of the primary beam energy and adjust it to enhance contrast.

The electron channeling contrast imaging technique was used to investigate the microstructure of copper coatings fabricated by cold gas dynamic spray. The high velocity impact characteristics for cold spray led to the formation of many substructures, such as high density dislocation walls, dislocation cells, deformation twins, and ultrafine equiaxed subgrains/grains. A schematic model is proposed to explain structure refinement of Cu during cold spray, where an emphasis is placed on the role of dislocation configurations and twinning.