Electron microscopy has a pivotal role as an analytical tool in pharmaceutical research. However, digital image data have proven to be too large for efficient quantitative analysis. We describe here the development and application of an automated image processing (AIP) program that rapidly quantifies shape measurements of recombinant adenovirus (rAd) obtained from digitized field emission scanning electron microscope (FESEM) images. The program was written using the macro-recording features within Image-Pro® Plus software. The macro program, which is linked to a Microsoft Excel spreadsheet, consists of a series of subroutines designed to automatically measure rAd vector objects from the FESEM images. The application and utility of this macro program has enabled us to rapidly and efficiently analyze very large data sets of rAd samples while minimizing operator time.

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Nanoscale resolution in microscopy characterization has become crucial for state-of-the-art science and technology. We have developed a Magneto-optical Scanning Near-Field Optical Microscope (MO-SNOM), and it has demonstrated to be a powerful tool to study local magnetic properties [1,2]. One of the critical steps in producing a reliable instrument and consistent images is the fabrication of the microscope tip. This work presents concepts and results on tip processing by chemical etching on FS-SN-3224 optical fibers from 3M. The quality of the tips produced was tested on magnetic multilayers presenting exchange-bias coupling.

Confocal microscopy allows for optical sectioning of tissues, thus obviating the need for physical sectioning and subsequent registration to obtain a three-dimensional representation of tissue architecture. However, practicalities such as tissue opacity, light penetration, and detector sensitivity have usually limited the available depth of imaging to 200 μm. With the emergence of newer, more powerful systems, we attempted to push these limits to those dictated by the working distance of the objective. We used whole-mount immunohistochemical staining followed by clearing with benzyl alcohol-benzyl benzoate (BABB) to visualize three-dimensional myocardial architecture. Confocal imaging of entire chick embryonic hearts up to a depth of 1.5 mm with voxel dimensions of 3 μm was achieved with a 10× dry objective. For the purpose of screening for congenital heart defects, we used endocardial painting with fluorescently labeled poly-L-lysine and imaged BABB-cleared hearts with a 5× objective up to a depth of 2 mm. Two-photon imaging of whole-mount specimens stained with Hoechst nuclear dye produced clear images all the way through stage 29 hearts without significant signal attenuation. Thus, currently available systems allow confocal imaging of fixed samples to previously unattainable depths, the current limiting factors being objective working distance, antibody penetration, specimen autofluorescence, and incomplete clearing.

The novel crystallization properties of nano-materials represent a great challenge to researchers across all disciplines of materials science. Simple binary solids can be found to adopt unprecedented structures, when confined into nanometer-sized cavities, such as the inner cylindrical bore of single-walled carbon nanotubes (SWNT). Lanthanum iodide was encapsulated within SWNTs and the resulting encapsulation composite was analyzed using energy-dispersive X-ray microanalysis (EDX) and high-resolution transmission electron microscopy (HRTEM) imaging techniques, to reveal a one-dimensional crystal fragment, with the stoichiometry of LaI2, crystallizing in the structure of LaI3 with one third of the iodine positions unoccupied. A complete characterization of the encapsulation composite was achieved using an enhanced image restoration technique, which restores the object wave from a focal series of HRTEM images, providing information about the precise structural data of both filling material and host SWNT, and thereby enabling the identification of the SWNT chirality.

Extended abstract of a paper presented at Microscopy and Microanalysis 2005 in Honolulu, Hawaii, USA, July 31--August 4, 2005

Osmium postfixation is established as a routine procedure for transmission electron microscopy (TEM). On the one hand, this routine procedure leads to good results for TEM, but on the other hand results in blackened tissue samples that do not allow examination of any structures within the embedded tissue sample by a light microscope. Equivalent fixation results for TEM are achieved with imidazole–osmium postfixation, and with this postfixation method tissue is not blackened and can be transilluminated with point light sources. This allows easier recognition of histological details within tissue samples and makes it possible to screen embedded samples for appropriate ultrastructural processing. Jejunum is used to demonstrate the method.

This work proposes a parallel implementation for image restoration, applied to biological images, obtained from an Atomic Force Microscope (AFM) [1]. Depending on the scanning dimensions, any image obtained from this technique can present either poor signal/noise ratios and blurred contents. In order to restore or, at least, decrease the effects of such degradations, image restoration methods are usually employed. The algorithm of restoration is based on the use of the Tikhonov methodology, described elsewhere, known here as the serial approach [2].

The extracellular matrix (ECM) is a dynamic component of tissues that influences cellular phenotype and behavior. We sought to determine the role of specific ECM substrates in the regulation of protein kinase C (PKC) isozyme expression and function in cardiac myocyte attachment, cell volume, and myofibril formation. PKC isozyme expression was ECM substrate specific. Increasing concentrations of the PKC δ inhibitor rottlerin attenuated myocyte attachment to randomly organized collagen (1, 5, and 10 μM), laminin (5 and 10 μM), aligned collagen (5 and 10 μM), and fibronectin (10 μM). Rottlerin significantly decreased cell volume on laminin and randomly organized collagen, and inhibited myofibril formation on laminin. The PKC α inhibitor Gö 6976 inhibited attachment to randomly organized collagen at 6 nM but did not affect cell volume. The general PKC inhibitor Bisindolylmalemide I (10 and 30 μM) did not affect myocyte attachment; however, it significantly decreased cell volume on randomly organized collagen. Our data indicate that PKC isozymes are expressed and utilized by neonatal cardiac myocytes during attachment, cell growth, and myofibril formation. Specifically, it appears that PKC δ and/or its downstream effectors play an important role in the interaction between cardiac myocytes and laminin, providing further evidence that the ECM influences cardiac myocyte behavior.

The structural properties of β-phase tantalum nanocrystallites prepared by room temperature magnetron sputter deposition on amorphous carbon substrates are investigated at atomic resolution. For these purposes spherical aberration-corrected high-resolution transmission electron microscopy is applied in tandem with the numerical retrieval of the exit-plane wavefunction as obtained from a through-focus series of experimental micrographs. We demonstrate that recent improvements in the resolving power of electron microscopes enable the imaging of the atomic structure of β-tantalum with column spacings of solely 0.127 nm with directly interpretable contrast features. For the first time ever, we substantiate the existence of grain boundaries of 30° tilt type in β-Ta whose formation may be well explained by atomic agglomeration processes taking place during sputter deposition.

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A comparative study of scanning electron microscopy (SEM) and atomic force microscopy (AFM) imaging of the healthy human optic nerve was carried out to determine the similarities and the differences. In this study we compared the fine optic nerve structures as observed by SEM and AFM. The fibers of the right optic nerve of a 61-year-old man show different arrangements in transverse sections taken from the same individual 5 mm central to the optic canal and 5 mm peripheral to the optic chiasma; this difference can be recognized by light microscopy (LM), SEM, and AFM. AFM revealed such typical optic nerve fibers (taken from a point 5 mm central to the optic canal) with annular and longitudinal orientations, which were not visible by SEM in this form. By contrast, LM and SEM visualized other structures, such as pia mater and optic nerve fibers loosely arranged in bundles, none of which was visualized by AFM. The images, however, taken 5 mm peripheral from the optic chiasma show shapeless nerve fibers having a wavy course. Our results reveal that more detailed information on optic nerve morphology is obtained by exploiting the advantages of both SEM and AFM. These are the first SEM and AFM images of healthy human optic nerve fibers, containing clear representations of the three dimensions of the optic nerve.

Practical analyses of the structures of ultrathin multilayers in tunneling magneto resistance (TMR) and Magnetic Random Access Memory (MRAM) devices have been a challenging task because layers are very thin, just 1–2 nm thick. Particularly, the thinness (∼1 nm) and chemical properties of the AlOx barrier layer are critical to its magnetic tunneling property. We focused on evaluating the current TEM analytical methods by measuring the thickness and composition of an AlOx layer using several TEM instruments, that is, a round robin test, and cross-checked the thickness results with an X-ray reflectometry (XRR) method. The thickness measured by using HRTEM, HAADF-STEM, and zero-loss images was 1.1 nm, which agreed with the results from the XRR method. On the other hand, TEM-EELS measurements showed 1.8 nm for an oxygen 2D-EELS image and 3.0 nm for an oxygen spatially resolved EELS image, whereas the STEM-EDS line profile showed 2.5 nm in thickness. However, after improving the TEM-EELS measurements by acquiring time-resolved images, the measured thickness of the AlOx layer was improved from 1.8 nm to 1.4 nm for the oxygen 2D-EELS image and from 3.0 nm to 2.0 nm for the spatially resolved EELS image, respectively. Also the observed thickness from the EDS line profile was improved to 1.4 nm after more careful optimization of the experimental parameters. We found that EELS and EDS of one-dimensional line scans or two-dimensional elemental mapping gave a larger AlOx thickness even though much care was taken. The reasons for larger measured values can be found from several factors such as sample drift, beam damage, probe size, beam delocalization, and multiple scattering for the EDS images, and chromatic aberration, diffraction limit due to the aperture, delocalization, alignment between layered direction in samples, and energy dispersion direction in the EELS instrument for EELS images. In the case of STEM-EDS mapping with focused nanoprobes, it is always necessary to reduce beam damage and sample drift while trying to maintain the signal-to-noise (S/N) ratio as high as possible. Also we confirmed that the time-resolved TEM-EELS acquisition technique improves S/N ratios of elemental maps without blurring the images.

The intracellular distribution of the elements carbon, nitrogen, and oxygen was measured in cultured rat hepatocytes by energy dispersive electron probe X-ray microanalysis of 100-nm-thick freeze-dried cryosections. Electron irradiation with a dose up to 106 e/nm2 caused no or merely negligible mass loss in mitochondria and in cytoplasm. Cell nuclei lost carbon, nitrogen, and—to a clearly higher extent—oxygen with increasing electron irradiation. Therefore, electron doses less than 3 × 105 e/nm2 were used to measure the subcellular compartmentation of carbon, nitrogen, and oxygen in cytoplasm, mitochondria, and nuclei of the cells. The subcellular distribution of carbon, nitrogen, and oxygen reflects the intracellular compartmentation of various biomolecules. Cells exposed to inorganic mercury before cryofixation showed an increase of oxygen in nuclei and cytoplasm. Concomitantly the phosphorus/nitrogen ratio decreased in mitochondria. The data suggest mercury-induced production of ribonucleic acid (RNA) and decrease of adenosine triphosphate (ATP). Although biomolecules cannot be identified by X-ray microanalysis, measurements of the whole element spectrum including the light elements carbon, nitrogen, and oxygen can be useful to study specific biomolecular activity in cellular compartments depending on the functional state of the cell.

The damage layers generated in III–V compounds exposed to energetic gallium ions in a focused ion beam (FIB) instrument have been characterized by transmission electron microscopy (TEM). The damage on the side walls of the milled trenches is in the form of amorphous layers associated with direct amorphization from the gallium beam, rather than from redeposition of milled material. However, the damage on the bottom of the milled trenches is more complex. For InP and InAs the damage layers include the presence of crystalline phases resulting from recrystallization associated heating from the incident beam and gallium implantation. In contrast, such crystalline phases are not present in GaAs. The thicknesses of the damage layers are greater than those calculated from theoretical models of ion implantation. These differences arise because the dynamic nature of FIB milling means that the energetic ion beams pass through already damaged layers. In InP recoil phosphorus atoms also cause significant damage.

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.

Altered intracellular Ca2+ dynamics are characteristically observed in cardiomyocytes from failing hearts. Studies of Ca2+ handling in myocytes predominantly use Fluo-3 AM, a visible light excitable Ca2+ chelating fluorescent dye in conjunction with rapid line-scanning confocal microscopy. However, Fluo-3 AM does not allow for traditional ratiometric determination of intracellular Ca2+ concentration and has required the use of mathematic correction factors with values obtained from separate procedures to convert Fluo-3 AM fluorescence to appropriate Ca2+ concentrations. This study describes methodology to directly measure intracellular Ca2+ levels using inactivated, Fluo-3-AM-loaded cardiomyocytes equilibrated with Ca2+ concentration standards. Titration of Ca2+ concentration exhibits a linear relationship to increasing Fluo-3 AM fluorescence intensity. Images obtained from individual myocyte confocal scans were recorded, average pixel intensity values were calculated, and a plot is generated relating the average pixel intensity to known Ca2+ concentrations. These standard plots can be used to convert transient Ca2+ fluorescence obtained with experimental cells to Ca2+ concentrations by linear regression analysis. Standards are determined on the same microscope used for acquisition of unknown Ca2+ concentrations, simplifying data interpretation and assuring accuracy of conversion values. This procedure eliminates additional equipment, ratiometric imaging, and mathematic correction factors and should be useful to investigators requiring a straightforward method for measuring Ca2+ concentrations in live cells using Ca2+-chelating dyes exhibiting variable fluorescence intensity.

We have explored the possibility of measuring small changes of orientation within grains by electron backscattering diffraction (EBSD), in the scanning electron microscope. Conventional orientation maps (using EBSD) index the orientation of each position on the sample separately. This does not give accurate results for small differences of orientation. We have studied methods of measuring small changes in orientation by measuring the change from one EBSD pattern to the next directly, without indexing either. Previous workers have measured the change of position of a zone axis in the EBSD pattern. We have compared this with an alternative method, which we show to be superior, of measuring the shift of the peaks in the Hough transform from one diffraction pattern to the next. This means that we are measuring the change of orientation of sets of crystal planes within the grain, rather than measuring the change of orientation of zone axes. We show that it is possible, with a standard EBSD configuration, to measure the shift of the Kikuchi bands to a precision of about a 10th of a pixel, which corresponds to a change of orientation in the sample of about 0.1 mrad (0.006°).

One of the pillars of Nanotechnology is the possibility of matter manipulation on nanometer scale. At the basis of such pillar, the importance of Scanning Probe Microscopy (SPM) is twofold: surface visualization and material manipulation at a sub-molecular level. There is a myriad of reports in the literature showing astonishing cases of high resolution imaging and manipulation carried out by different SPM techniques [1]. Within such examples, anodic oxidation nanolithography (AON) appears as one of the most promising tools due to its simplicity and applicability to a large variety of materials [1,2]. Therefore, this work reports on a detailed study of possibilities and limitations of AON towards the fabrication of semiconductor- and/or metal-based devices.

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