With the development of affordable aberration correctors, analytical scanning transmission electron microscopy (STEM) studies of complex interfaces can now be conducted at high spatial resolution at laboratories worldwide. Energy-dispersive X-ray spectroscopy (EDS) in particular has grown in popularity, as it enables elemental mapping over a wide range of ionization energies. However, the interpretation of atomically resolved data is greatly complicated by beam–sample interactions that are often overlooked by novice users. Here we describe the practical factors—namely, sample thickness and the choice of ionization edge—that affect the quantification of a model perovskite oxide interface. Our measurements of the same sample, in regions of different thickness, indicate that interface profiles can vary by as much as 2–5 unit cells, depending on the spectral feature. This finding is supported by multislice simulations, which reveal that on-axis maps of even perfectly abrupt interfaces exhibit significant delocalization. Quantification of thicker samples is further complicated by channeling to heavier sites across the interface, as well as an increased signal background. We show that extreme care must be taken to prepare samples to minimize channeling effects and argue that it may not be possible to extract atomically resolved information from many chemical maps.

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

Secondary fluorescence, the final term in the familiar matrix correction triumvirate Z·A·F, is the most challenging for Monte Carlo models to simulate. In fact, only two implementations of Monte Carlo models commonly used to simulate electron probe X-ray spectra can calculate secondary fluorescence—PENEPMA and NIST DTSA-IIa (DTSA-II is discussed herein). These two models share many physical models but there are some important differences in the way each implements X-ray emission including secondary fluorescence. PENEPMA is based on PENELOPE, a general purpose software package for simulation of both relativistic and subrelativistic electron/positron interactions with matter. On the other hand, NIST DTSA-II was designed exclusively for simulation of X-ray spectra generated by subrelativistic electrons. NIST DTSA-II uses variance reduction techniques unsuited to general purpose code. These optimizations help NIST DTSA-II to be orders of magnitude more computationally efficient while retaining detector position sensitivity. Simulations execute in minutes rather than hours and can model differences that result from detector position. Both PENEPMA and NIST DTSA-II are capable of handling complex sample geometries and we will demonstrate that both are of similar accuracy when modeling experimental secondary fluorescence data from the literature.

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

A method for automatic classification of the shape of graphite particles in cast iron is proposed. In a typical supervised classification procedure, the standard charts from the ISO-945 standard are used as a training and validation population. Several shape and size parameters are described and used as discriminants. A new parameter, the average internal angle, is proposed and is shown to be relevant for accurate classification. The ideal parameter sets are determined, leading to validation success rates above 90%. The classifier is then applied to real cast iron samples and provides results that are consistent with visual examination. The method provides classification results per particle, different from the traditional per field chart comparison methods. The full procedure can run automatically without user interference.

Roughness increases significantly after finishing procedures. The aim of this study was to assess by the atomic force microscope (AFM) the effect of finishing instruments on the surface roughness of composite resins. A nanofiller composite resin (Filtek Supreme, 3M–F) and a microhybrid composite resin (Point 4, Kerr–P) were selected. The finishing procedures were done with a 30-blade carbide bur (C) and a 30-μm finishing diamond bur (D). Standardized specimens were produced and divided into six experimental groups (n = 4) according to (1) composite resin, (2) absence of finishing (Mylar matrix–M), and (3) finishing instrument (FM, PM, FC, FD, PC, PD). The mean surface roughness was evaluated by AFM in the contact mode. FM and PM groups were assessed statistically by the Student's T test, and FC, FD, PC, PD groups were submitted to variance analysis (ANOVA), both at 5% significance. The mean surface roughness values, in nanometers, were FM, 23.63 (b); FC, 283.88 (c); FD, 510.55 (d); PM, 12.52 (a); PC, 343.98 (c); PD, 531.64 (d). Microhybrid composite displayed less roughness than nanofiller composite in the absence of finishing procedures. The 30-blade carbide bur produced less roughness compared to the extra fine diamond bur.

The soft X-ray energy range provides important detection capabilities for a wide range of material systems, e.g., the K-edge behavior of biological materials or magnetic contrast imaging at the L2,3- and M4,5-edges, respectively, using the X-ray magnetic circular dichroism effect. The need for thinned samples due to the short penetration depth of soft X-rays is a limiting factor for microscopic imaging in transmission microscopy. In contrast, the more surface sensitive photoelectron emission microscopy allows the X-ray microscopic investigation of nontransparent bulk samples, but only small magnetic fields and very smooth surfaces are possible. As both high magnetic fields as well as bulk samples are important for magnetic imaging, we present total electron yield (TEY) microscopy results using the total sample current detection performed at the new ultra high vacuum scanning microscope “MAXYMUS” at HZB/BESSY II. We compare synchronous measurements in TEY and transmission mode to demonstrate the capabilities of TEY microscopy. Pictures and spectra with high absorption contrast and three-dimensional-like edge enhancement are observed as known for scanning electron microscopy. This unveils details on smallest length scales of the surface morphology. Furthermore, surface sensitive in- and out-of-plane magnetic TEY measurements at nontransparent samples are shown.

Fluorescence resonance energy transfer (FRET) microscopy is a powerful technique to quantify dynamic protein-protein interactions in live cells. Total internal reflection fluorescence (TIRF) microscopy can selectively excite molecules within about 150 nm of the glass-cell interface. Recently, these two approaches were combined to enable high-resolution FRET imaging on the adherent surface of living cells. Here, we show that interference fringing of the coherent laser excitation used in TIRF creates lateral heterogeneities that impair quantitative TIRF-FRET measurements. We overcome this limitation by using a two-dimensional scan head to rotate laser beams for donor and acceptor excitation around the back focal plane of a high numerical aperture objective. By setting different radii for the circles traced out by each laser in the back focal plane, the penetration depth was corrected for different wavelengths. These modifications quell spatial variations in illumination and permit calibration for quantitative TIRF-FRET microscopy. The capability of TIRF-FRET was demonstrated by imaging assembled cyan and yellow fluorescent protein–tagged HIV-Gag molecules in single virions on the surfaces of living cells. These interactions are shown to be distinct from crowding of HIV-Gag in lipid rafts.

Abundant charcoalified seed fern (pteridosperm) pollen organs and ovules have been recovered from Late Viséan (Mississippian 330 Ma) limestones from Kingswood, Fife, Scotland. To overcome limitations of data collection from these tiny, sometimes unique, fossils, we have combined low vacuum scanning electron microscopy on uncoated specimens with backscatter detector and synchrotron radiation X-ray tomographic microscopy utilizing the Materials Science and TOMCAT beamlines at the Swiss Light Source of the Paul Scherrer Institut. In combination these techniques improve upon traditional cellulose acetate peel sectioning because they enable study of external morphology and internal anatomy in multiple planes of section on a single specimen that is retained intact. The pollen organ Melissiotheca shows a basal parenchymatous cushion bearing more than 100 sporangia on the distal face. Digital sections show the occurrence of pollen in some sporangia. The described ovule is new and has eight integumentary lobes that are covered in spirally arranged glandular hairs. Virtual longitudinal sections reveal the lobes are free above the pollen chamber. Results are applied in taxonomy and will subsequently contribute to our understanding of the former diversity and evolution of ovules, seeds, and pollen organs in the seed ferns, the first seed-bearing plants to conquer the land.

We have developed a microwave protocol for a paraffin-embedding microtechnique of the shoot apical meristem of Zea mays and have successfully applied this protocol to other plant tissues. This protocol decreases the time required for all aspects of microtechnique tissue processing, including fixation (24 hr to 15 min), dehydration (73 hr to 10 min), and infiltration (96 hr to 3 hr). Additionally, the time required to adhere paraffin ribbons to gelatin-coated slides and for the Johanson's safranin O, fast green FCF staining protocol has been significantly decreased. Using this technique, the quality of tissue preservation and subsequent in situ localization of knotted mRNA was increased by using microwaves.

Electron backscatter diffraction (EBSD) is one of the primary tools in materials development and analysis. The technique can perform simultaneous analyses at multiple length scales, providing local sub-micron information mapped globally to centimeter scale. Recently, a series of technological revolutions simultaneously increased diffraction pattern quality and collection rate. After collection, current EBSD pattern indexing techniques (whether Hough-based or dictionary pattern matching based) are capable of reliably differentiating between a “user selected” set of phases, if those phases contain sufficiently different crystal structures. EBSD is currently less well suited for the problem of phase identification where the phases in the sample are unknown. A pattern analysis technique capable of phase identification, utilizing the information-rich diffraction patterns potentially coupled with other data, such as EDS-derived chemistry, would enable EBSD to become a high-throughput technique replacing many slower (X-ray diffraction) or more expensive (neutron diffraction) methods. We utilize a machine learning technique to develop a general methodology for the space group classification of diffraction patterns; this is demonstrated within the $\lpar 4/m\comma \;\bar{3}\comma \;\;2/m\rpar$ point group. We evaluate the machine learning algorithm's performance in real-world situations using materials outside the training set, simultaneously elucidating the role of atomic scattering factors, orientation, and pattern quality on classification accuracy.

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

Nanophase aluminum powder was characterized in a field-emission-gun transmission electron microscope (TEM). Different techniques were used to investigate the structure of the particles, including conventional bright-field and dark-field imaging, scanning transmission electron microscopy (STEM), high-resolution lattice imaging, diffraction studies, energy dispersive X-ray spectroscopy (EDS) analysis and mapping, and electron energy loss spectroscopy (EELS) analysis and mapping. It has been established that the particle cores consist of aluminum single crystals that sometimes contain crystal lattice defects. The core is covered by a passivating layer of aluminum oxide a few nanometers thick. The alumina is mostly amorphous, but evidences of partial crystallinity of the oxide were also found. The thickness of this layer was measured using different techniques, and the results are in good agreement with each other. The particles are agglomerated in two distinct ways. Some particles were apparently bonded together during processing before oxidation. These mostly form dumbbells covered by a joint oxide layer. Also, oxidized particles are loosely assembled into relatively large clusters.

Electron correlation microscopy (ECM) is a new technique that utilizes time-resolved coherent electron nanodiffraction to study dynamic atomic rearrangements in materials. It is the electron scattering equivalent of photon correlation spectroscopy with the added advantage of nanometer-scale spatial resolution. We have applied ECM to a Pd40Ni40P20 metallic glass, heated inside a scanning transmission electron microscope into a supercooled liquid to measure the structural relaxation time τ between the glass transition temperature Tg and the crystallization temperature, Tx. τ determined from the mean diffraction intensity autocorrelation function g2(t) decreases with temperature following an Arrhenius relationship between Tg and Tg+25 K, and then increases as temperature approaches Tx. The distribution of τ determined from the g2(t) of single speckles is broad and changes significantly with temperature.

Calcium regulates many intracellular events such as growth and differentiation during different stages of gamete development. The aim of this study was to localize and quantify the intracellular distribution of calcium during different developmental stages of spermatogenesis in sterlet, Acipenser ruthenus, using a combined oxalate–pyroantimonate technique. The distribution of calcium was described in spermatogonium, spermatocyte, spermatid, and spermatozoon stages. In the spermatogonium and spermatocyte, calcium deposits were mainly localized in the nucleus and cytoplasm. The spermatid had calcium in the nucleus, developing acrosomal vesicle, and cytoplasm. Intracellular calcium transformed from scattered deposits in spermatogonia and spermatocyte stages into an unbound form in spermatid and the spermatozoon. The proportion of area covered by calcium increased significantly (p<0.05) from early to late stages of spermatogenesis. The largest proportion of area covered by calcium was observed in the nucleus of the spermatozoon. In conclusion, although most of the intracellular calcium is deposited in limited areas of the spermatogonium and spermatocyte, it is present an unbound form in the larger area of spermatids and spermatozoa which probably reflects changes in its physiological function and homeostasis during the process of male gamete production in spermatogenesis.

This paper reports an unusual green pigment, brochantite (Cu4(SO4)(OH)6), on 16th-century Portuguese-Flemish paintings, attributed to the Master Frei Carlos workshop. This green mineral is usually identified as an impurity or alteration product in the green pigments verdigris (Cu(CH3COO)2nCu(OH)2) or malachite (CuCO3 Cu(OH)2). However, after thorough investigation with a broad range of analytical techniques, it became clear that, in this case, brochantite was applied as a pigment. The abundance, pigment granulometry, and pigment morphology suggest intentional use by this Portuguese-Flemish Master as a natural pigment rather than its accidental use as an alteration product. This seems to be a distinguishable feature to other painters (Flemish and Portuguese) working in Portugal at the beginning of the 16th century.

The multi-analytical study of these easel paintings was first performed by physical imaging techniques and material characterization was carried out by optical microscopy, micro-Fourier-transform infrared-spectroscopy, micro-Raman spectroscopy, scanning electron microscopy coupled with energy dispersive X-ray spectrometry, and micro-X-ray diffraction analysis (XRD).

A multiscale approach combining phase-contrast X-ray micro- and nanotomography is applied for imaging a Cretaceous fossil inflorescence in the resolution range from 0.75 μm to 50 nm. The wide range of scale views provides three-dimensional reconstructions from the external gross morphology of the inflorescence fragment to the finest exine sculptures of in situ pollen. This approach enables most of the characteristics usually observed under light microscopy, or with low magnification under scanning and transmission electron microscopy, to be obtained nondestructively. In contrast to previous tomography studies of fossil and extant flowers that used resolutions down to the micron range, we used voxels with a 50 nm side in local tomography scans. This high level of resolution enables systematic affinities of fossil flowers to be established without breaking or slicing specimens.

Aberration correction reduces the depth of field in scanning transmission electron microscopy (STEM) and thus allows three-dimensional (3D) imaging by depth sectioning. This imaging mode offers the potential for sub-Ångstrom lateral resolution and nanometer-scale depth sensitivity. For biological samples, which may be many microns across and where high lateral resolution may not always be needed, optimizing the depth resolution even at the expense of lateral resolution may be desired, aiming to image through thick specimens. Although there has been extensive work examining and optimizing the probe formation in two dimensions, there is less known about the probe shape along the optical axis. Here the probe shape is examined in three dimensions in an attempt to better understand the depth resolution in this mode. Examples are presented of how aberrations change the probe shape in three dimensions, and it is found that off-axial aberrations may need to be considered for focal series of large areas. It is shown that oversized or annular apertures theoretically improve the vertical resolution for 3D imaging of nanoparticles. When imaging nanoparticles of several nanometer size, regular STEM can thereby be optimized such that the vertical full-width at half-maximum approaches that of the aberration-corrected STEM with a standard aperture.

Multielemental X-ray maps collected by a remote scanning system of the electron beam are processed by a dedicated software program performing accurate modal determination of geological samples. The classification of different mineral phases is based on elemental concentrations. The software program Petromod loads the maps into a database and computes a matrix consisting of numerical values proportional to the elemental concentrations. After an initial calibration, the program can perform the chemical composition calculated on the basis of a fixed number of oxygens for a selected area. In this way, it is possible to identify all the mineral phases occurring in the sample. Up to three elements can be selected to calculate the modal percentage of the identified mineral. An automated routine scans the whole set of maps and assigns each pixel that satisfies the imposed requirements to the selected phase. Repeating this procedure for every mineral phase occurring in the mapped area, a modal distribution of the rock-forming minerals can be performed. The final output consists of a digitized image, which can be further analyzed by common image analysis software, and a table containing the calculated modal percentages. The method is here applied to a volcanic and a metamorphic rock sample.