bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first decade of the disector
Authors: Gundersen H.J.G. 
Published: June 2020

Nine years and eleven months ago the disector was described: a complete rule for uniform sampling of 3D structures strictly according to cardinality – and from sections, physical or just imaging planes.Intuitively, the simplest situation is when particlenumber is wanted: with a uniform sample one just counts the number Q−in the sample and estimate numerical density NV or N directly (with the fractionator).Along the way, it has been realized that under certain fortuitous circumstances one may also count other uniquebutnotisolated features of structure, like ’trees’ (ciliae, brush borders and other appendages on surfaces) and the complementary type, exemplied by glands and follicles. All these structures each have exactly one disk of connection to an easily recognizable surface, these disks may be counted in a disector.The most basic mathematical definition of a 0-dimensional quantity or counting measure is that of the Euler number. The Euler number encompasses the number of isolated particles as a part of the definition, but is much more general.
Introduction to emission electron microscopy for the in situ study of surfaces
Authors: Kordesch Martin E. 
Published: June 2020

The Photoelectron Emission Microscope (PEEM) and Low Energy Electron Microscope (LEEM) are parallel-imaging electron microscopes with highly surface-sensitive image contrast mechanisms. In PEEM, the electron yield at the illumination wavelength determines image contrast, in LEEM, the intensity of low energy (< 100 eV) electrons back-diffracted from the surface, as well as interference effects, are responsible for image contrast. Mirror Electron Microscopy is also possible with the LEEM apparatus. In MEM, no electron penetration into the solid occurs, and an image of surface electronic potentials is obtained.While the emission microscope techniques named above are not high resolution methods, the unique contrast mechanisms, the ability to use thick single crystal samples, their compatibility with uhv surface science methods and new material-growth methods, coupled with real-time imaging capability, make them very useful.These microscopes do not depend on scanning probes, and some are compatible with pressures up to 10-3Torr and specimen temperatures above 1300K.
In-situ measurements of scanned probe tip shape with etched nuclear tracks
Authors: Tentschert J. , Fraundorf P. , Armbruster B. 
Published: June 2020

In air based Scanning Tunneling Microscopy (STM), tip geometry is often unknown so effects in images due to tip shape are difficult to quantify. While the importance of tip structure is often discussed, the methods for getting this information tend to be unsatisfactory in that they often involve ad hoc assumptions (seeing carbon atoms means a good tip) or they lack the ability to make measurements necessary to make quantitative assertions about unknowns. By exploiting the reproducibility of etched nuclear track pits, we have measured the tip interaction profile for an STM tip in air to a resolution of better than 4 nm in three dimensions.As a source of nuclear track pits we coated Nuclepore filters to make them conductive for STM. We used holes in both the 50nm and 200nm range. As a height calibration we took an image of 30nm colloidal Au on HOPG. Our method was as follows: We took an image of an area containing several pits. Next, the image was flattened, several holes were cut and averaged, and a standard deviation image was calculated using the programming language Semper 6, see Figure 1.
Stereological ground rules
Authors: DeHoff R.T. 
Published: June 2020

Microstructures have three primary attributes: chemistry; physics; and geometry. The chemical and physical attributes are routinely quantified. The geometry of microstructures is almost never quantified in spite of the existence of a sophisticated but easy to use measuring apparatus for the purpose called stereology.Stereology is a mathematical apparatus that permits statistical inference of the geometric properties of three dimensional microstructures from information obtained from images of the structure that are essentially two dimensional. This tool is not widely used mostly because the ground rules have been presented vaguely, or with limited application, or perhaps because the basic relationships are too simple to be believable.This presentation briefly reviews the geometric properties that may be accessed through the stereological apparatus, the kinds of measurements required, and the expected value theorems that connect the measurements to the three dimensional geometry.Table 1 summarizes these three aspects of the content of stereology.
Image simulation in electron microscopy
Authors: Kilaas Roar 
Published: June 2020

The theoretical calculation of High Resolution Transmission Electron Microscope (HRTEM) images has become a routine operation due largely to the existence of several commercially available computer programs. Associated with these “black box” calculations, exists a danger coming from the ease with which the programs can be used to produce images without any understanding of the underlying physical principles and approximations used in the calculations. While hopefully the majority of users of image simulation take the care to understand the limitations of the technique, there are several basic principles that must be understood in order to use the technique within the limits of its applicability. An example of this is shown in figure 1.Although image simulation is fairly straightforward, and the technique has been applied successfully to many problems in HRTEM, figure 2, it is not an optimum tool for solving unknown structures. Each image depends on many adjustable parameters, the structure itself being the most important, and the task of computing hundreds of images and comparing them visually is a tedious task to say the least.
Image reconstruction using a focus series on thick biological specimens: TEM CTF correction
Authors: Han Karen F. , Sedat John W. , Agard David A. 
Published: June 2020

The primary project of our laboratory is the investigation of chromatin structure by three dimensional electron microscope tomography. Three dimensional tomography involves the reconstruction of an object by combining multiple projection views of the object at different tilt angles. There are two complications that give rise to an inaccurate representation in the image of the projected object mass density: 1) electron-specimen interactions, and 2) electron microscope lens aberrations. In our abstract, “Analysis of Electron-specimen Interactions of Thick Biological Specimens in Transmission Electron Microscopy at 200 keV” elsewhere in these proceedings, we investigated image formation at the level of electron-specimen interactions at 200 keV. We extrapolated that at 300 keV, there is still a significant amount of elastic scattering for thick (up to 0.7 microns) biological specimens . Here, we demonstrate that this allows the correction of the microscope aberration function through multiple focus observations can enhance contrast.For high resolution electron microscopy of crystalline materials, some authors have demonstrated that the focus variation method to reconstruct the specimen exit-surface electron wave can lead to an improvement in resolution.
Automated 3-D cell population analysis in thick tissue sections using laser-scanning confocal-microscopy data
Authors: Ancin Hakan 
Published: June 2020

This paper presents methods for performing detailed quantitative automated three dimensional (3-D) analysis of cell populations in thick tissue sections while preserving the relative 3-D locations of cells. Specifically, the method disambiguates overlapping clusters of cells, and accurately measures the volume, 3-D location, and shape parameters for each cell. Finally, the entire population of cells is analyzed to detect patterns and groupings with respect to various combinations of cell properties. All of the above is accomplished with zero subjective bias.In this method, a laser-scanning confocal light microscope (LSCM) is used to collect optical sections through the entire thickness (100 - 500μm) of fluorescently-labelled tissue slices. The acquired stack of optical slices is first subjected to axial deblurring using the expectation maximization (EM) algorithm. The resulting isotropic 3-D image is segmented using a spatially-adaptive Poisson based image segmentation algorithm with region-dependent smoothing parameters. Extracting the voxels that were labelled as "foreground" into an active voxel data structure results in a large data reduction.
A new method for determining sample thickness: A comparison to experimental results
Authors: Blackson John , Luo Suichu , Joy David C 
Published: June 2020

Sample thickness is an important parameter in quantitative electron microscopy,. Several methods for determining sample thickness have been described previously. A theoretical method presented here utilizes the low loss region of the electron energy loss spectrum to calculate sample thickness. The method avoids many of the limitations of other methods and is applicable to a wide variety of samples. The method is compared to film thicknesses determined experimentally as described below.Chromium films were deposited simultaneously onto collodion supported TEM grids and cured epoxy blanks using a Denton Hi Res 100 coater equipped with a Syton quartz crystal monitor. The cured epoxy blanks were covered with a layer of unpolymerized epoxy that was then cured. The chromium sandwich was cross sectioned using ultramicrotomy techniques employing a diamond knife. Sections were produced which were as thin as possible (<50 nm) to minimize measurement errors. Chromium film thickness was determined directly using transmission electron microscopy (Fig. 1).
Quantitative single-cell fluorescence imaging of indicator dyes
Authors: Gross David J. , Mahoney M礨 G. , Slakey Linda L. 
Published: June 2020

The use of fluorescent molecular probes in combination with quantitative optical microscopy has burgeoned in the past few years due to dramatic advances in both fluorophore design and imaging instrumentation. A number of probes that exhibit fluorescence spectral shifts with ligand binding have been synthesized. Among them is fura-2, which has a high binding affinity for calcium ion and which shows an excitation spectral shift between the calcium-bound and calcium-unbound states. This talk will focus on fura-2-loaded arterial smooth muscle cells (SMC) stimulated to produce temporally and spatially dynamic changes in free cytosolic calcium ion concentration ([Ca2+]i) as measured by a charge-coupled device imaging system.Intracellular Ca2+ is known to play a critical role in the regulation of the contractile state of vascular SMCs. A variety of extracellular agonists have been shown to stimulate transient [Ca2+]i elevation in vascular SMCs; among them are nucleotides that activate specific cell surface receptors.
The NSLS X-1AL scanning x-ray microscope
Authors: Jacobsen Chris , Kirz Janos , Lindaas Steve , Wirick Sue , Zhang Xiaodong , Williams Shawn , Anderson Erik , Kern Dieter , Ade Harald 
Published: June 2020

Soft x rays are well suited to the study of low-Z elements in 0.1-10 μm thick specimens. A variety of soft x-ray microscopes are now under operation, several of which achieve image resolutions of 0.03-0.1 μm. Scanning x-ray microscopes offer some desirable charactistics: they are able to operate in a variety of imaging modes, including transmission, luminescence, dark field, and photoemission, and they enable minimum dose imaging by utilizing highly efficient photon counting detectors and placing moderate efficiency optics between the source and specimen rather than between specimen and detector.The NSLS X-1AL scanning x-ray microscope uses an undulator at the National Synchrotron Light Source at Brookhaven National Laboratory as a tunable, high-brightness soft x-ray source. Monochromatized, spatially coherent illumination is focussed by a Fresnel zone plate fabricated using electron beam lithography. The sample is scanned through the 0.055 μm Rayleigh resolution focal spot using stepping motors (for large scans) and linearized piezos.
Electron diffraction of copper phthalocyanine on the HVEM
Authors: Tivol W. F. , Turner J. N. , McCourt M. P. , Dorset D. L. 
Published: June 2020

The use of high-energy (1200 kV) electrons has been shown to be advantageous in the ab initio structure analysis from electron diffraction of organic compounds. Previous studies showed that ab initio analysis of copper perchlorophthalocyanine could be accomplished ; accelerating voltages at or above 1000 kV, but net at 400 kV for crystals which are about 10 nm thick. Copper perbromophthalocyanine could also be analyzed ab initio at 1200 kV, but the presence of severe dynamical scattering precluded such analysis at lower voltages.A study of copper perchlorophthalocyanine at accelerating voltages from 200 kV to 1200 kV showed that dynamical scattering accounted for the differences among the diffraction patterns which lead the failure of ab initio analysis at the lower voltages. The series of phthalocyanines offers a good model for the study of dynamical scatterin and direct phasing methods, since it consists of relatively radiation-resistant compounds for which high-resolution diffraction patterns can be obtained.
HREM study of strong-metal interaction in Pt/TiO2
Authors: Yao Ming-Hui 
Published: June 2020

The chemisorption ability and catalytic properties of metal particles supported on reducible oxides are often altered by high temperature reduction(HTR) in a process known as strong metal-support interaction(SMSI). Different models have been proposed to explain the SMSI mechanism. In recent years, experimental evidences have favored the "decoration model", which suggests that SMSI is due to the encapsulation of the metal particles by oxide overlayer species dial have migrated from the support. HREM profile imaging was the most useful tool to directly relate these surface decorations to the SMSI effects. The profile imaging can provide atomic-scale information about supported particles and Uieir surfaces without image being obscured by overlapping contrast from the support.In the present work, the SMSI effect in Pt/TiO2 and Pt/CeO2 model catalysts have been studied using HREM profile imaging and multislice simulations. HREM observations were made with a JEM-4000EX microscope, operated at 400 kV. Fig. 1(a) shows a typical profile image of TiO2 after HTR in H2 at 923K.
Crystallographic phase identification in the SEM: Backscattered electron kikuchi patterns
Authors: Michael J. R. , Goehner R. P. 
Published: June 2020

The use of the recently developed charge coupled device (CCD)-based detector for the acquisition of high quality backscattered electron Kikuchi patterns (BEKP) has allowed on-line crystallographic phase identification studies to be conducted in the scanning electron microscope. High quality patterns suitable for analysis have been obtained in a wide variety of materials with little special specimen preparation. Phase identification through a combination of BEKP and energy dispersive x-ray spectrometry (EDS) is demonstrated by the identification of crystals present on ruthenium oxide thin films on Si. The crystals were identified as RuO2, a tetragonal phase.The CCD-based detector has been described previously and will only be briefly described here. The detector consists of a scientific grade slow scan CCD coupled to a YAG scintillator by a fiber optic reducer. During operation the CCD is cooled to -40°C by a thermoelectric cooler. This detector allows high quality patterns to be recorded with beam currents as low as 10-10A and exposure times of 1 to 10 seconds.
Electrochemical atomic layer epitaxy of semiconductor CdTe thin films
Authors: Huang Baoming M. 
Published: June 2020

Semiconductor thin films have important applications in areas such as photovoltaics and luminescent displays. Electrodeposition of these films is a potential low cost, room temperature production technique. Electrochemical atomic layer epitaxy (ECALE) involves alternatively depositing individual element monolayer amount per ECALE cycle, taking advantage of the under-potential deposition (UPD) phenomena.A series of CdTe thin films have been deposited using ECALE methodology in an electrochemical flow cell system. The 0.5 mM Te4+, Te blank, 5mM Cd2+, and Cd blank solutions are made with purasonic grade TeO2 and CdSO4, research grade electrolyte, and 18 M ohm water. The gold foil substrates are cleaned electrochemically before each experiment. An ECALE cycle starts with depositing monolayer amount Te, rinsing with Te blank, then depositing monolayer amount of Cd, and ending with rinsing with Cd blank solution. The whole flow cell system is controlled by a computer with house-written codes, and the deposition process can be fully programmed.
Interfacial properties of GaSb/InAs superlattices
Authors: Twigg M. E. , Bennett B. R. , Waterman J. R. , Davis J. L. , Shanabrook B. V. , Wagner R. J. 
Published: June 2020

Recently, the GaSb/InAs superlattice system has received renewed attention. The interest stems from a model demonstrating that short period Ga1-xInxSb/InAs superlattices will have both a band gap less than 100 meV and high optical absorption coefficients, principal requirements for infrared detector applications. Because this superlattice system contains two species of cations and anions, it is possible to prepare either InSb-like or GaAs-like interfaces. As such, the system presents a unique opportunity to examine interfacial properties.We used molecular beam epitaxy (MBE) to prepare an extensive set of GaSb/InAs superlattices grown on an GaSb buffer, which, in turn had been grown on a (100) GaAs substrate. Through appropriate shutter sequences, the interfaces were directed to assume either an InSb-like or GaAs-like character. These superlattices were then studied with a variety of ex-situ probes such as x-ray diffraction and Raman spectroscopy. These probes confirmed that, indeed, predominantly InSb-like and GaAs-like interfaces had been achieved.
Electron microscopy of ceramic superconductors
Authors: Grant Norton M. , Barry Carter C. 
Published: June 2020

The microstructure of ceramic superconductors plays a crucial role in the transport properties of these materials. For example, it has been shown that high-angle grain boundaries can act as weak links and atomic scale defects can act as pinning centers. The nature and spatial distribution of such defects is related to the way in which the material is processed. Transmission electron microscopy (TEM) is an essential technique for understanding the relationship between microstructure, processing, and properties and for defect characterization. The advantage of TEM is that it is possible to combine various imaging modes with electron diffraction and other analytical techniques such as x-ray energy dispersive spectroscopy in order to obtain both structural and chemical information.Early measurements of critical current densities (Jc) across individual tilt grain boundaries in YBa2Cu3O7-δ (YBCO) thin films demonstrated that Jc decreased with increasing misorientation angle. More recently, however, it has been observed that this phenomenon may not be the case for all high-angle grain boundaries.
Microstructure of dense MgO penetrated by a silicate liquid
Authors: Ramamurthy Sundar , Mallamaci Michael P. , Barry Carter C. , Duncombe Peler R. , Shaw Thomas M. 
Published: June 2020

Grain boundaries control most of the critical properties of ceramic materials and devices. The presence of an intergranular amorphous phase in many polycrystalline ceramic compacts has been reported. Grain boundaries may also involve regions of ordered structure and amorphous (glassy) phase. Dense polycrystalline compacts are processed by liquid-phase sintering routes. The addition of sintering aids such as CaO, MgO and SiO2 influence the densification process substantially. During sintering the grain boundaries are wet by liquid phases, and amorphous films are often found at the grain boundaries and triple junctions in the sintered product. The presence of such films not only influences the sintering behavior but it also affects the final properties in the sintered product. These films have therefore been the subject of intense investigation. Silicate-based compositions are the typical glass phases observed in these materials.In the present study, polycrystalline, dense MgO cubes have been penetrated by liquid monlicellite (CaMgSiO4) at 1700°C.
Microstructure and phase transformation in KNbO3
Authors: Popoola Oludele O. , Kriven Waltraud M. 
Published: June 2020

KNbO3 is a perovskite ferroelectric ceramic material with important electro optical and non linear optical properties. It can be used in an optical parametric oscillator, secondary harmonic generator and photo refractive holographic storage devices. Its macroscopic properties depend on a number of inter-related features such as crystal structure, domain structure, defects and impurity content. KNbO3 has four known solid phases with decreasing symmetry with temperature: Cubic Tetragonal Orthorhombic Monoclinic. The paraelectric to ferroelectric transition occurs during the cubic to tetragonal transformation. The dielectric properties of KNbO3 have been extensively studied and related to the various phase transformations. The aim of this investigation is to study the orthorhombic to tetragonal phase transformations using TEM.Thin slices were cut from a flux grown crystal and mechanically polished to a thickness of 100 μm with a 1 μm surface finish using diamond paste and isopropyl alcohol as the lubricant.
Thickness-dependent annular dark-field STEM
Authors: Hillyard Sean , Silcox John 
Published: June 2020

The demonstration of Z-contrast atom structure images and high spatial resolution using annular dark field STEM has drawn considerable interest. This approach is well suited for quantitative image and diffraction pattern acquisition. Experimental data has been used to validate calculations of convergent beam electron diffraction (CBED) patterns in silicon and ADF STEM images of (100) InP. These procedures can be extended to explore the dependence of images on factors such as thickness.Energy filtered CBED patterns over an angular range of over 150 mrads and covering a range of over four orders of magnitude in intensity from silicon were recorded with a VG HB501A STEM for thicknesses of 217Å, 326Å and 543Å. Simulation using a “frozen phonon” approximation successfully modeled this data provided an accurate phonon amplitude was used. A similar quantitative study for images has been carried out for (100) oriented InP. This sample contains indium columns at the comer of a 2.9Å square and phosphorus atoms at the square center.
Atomic structure of undoped Σ=5 symmetrical-tilt grain boundary in strontium titanate
Authors: Ravikumar V. 
Published: June 2020

Strontium titanate is an important electroceramic material which, under appropriate processing and dopant additions exhibits both varistor and Grain Boundary Layer Capacitor (GBLC) behavior. The presence of electrically active grain boundaries is essential for obtaining these properties. The first step towards correlating the grain boundary structure to properties is to determine the detailed atomic structure of the boundary, which includes its geometric structure, chemistry and electronic structure. We present here our TEM investigation of the atomic structure of an undoped (“pristine”) symmetrical tilt grain boundary in SrTiO3. This provides the basic reference structure, changes to which can be studied as a function of doping and/or processing parameters, and correlated to electrical and dielectric properties.Self-supported TEM samples were made from bicrystals of SrTiO3 through the conventional sample preparation route. Fig. 1 shows a high resolution electron micrograph (Hitachi H9000) of a representative grain boundary region in the sample.