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Microscopy and Microanalysis

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https://read.qxmd.com/read/30761977/quantifying-uncertainty-from-mass-peak-overlaps-in-atom-probe-microscopy
#1
Andrew J London
There are many sources of random and systematic error in composition quantification by atom probe microscopy, often, however, only statistical error is reported. Significantly larger errors can occur from the misidentification of ions and overlaps or interferences of peaks in the mass spectrum. These overlaps can be solved using maximum likelihood estimation (MLE), improving the accuracy of the result, but with an unknown effect on the precision. An analytical expression for the uncertainty of the MLE solution is presented and it is demonstrated to be much more accurate than the existing methods...
February 14, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30761973/new-insight-into-the-development-of-the-respiratory-acini-in-rabbits-morphological-electron-microscopic-studies-and-tunel-assay
#2
Doaa M Mokhtar, Manal T Hussein, Marwa M Hussein, Enas A Abd-Elhafez, Gamal Kamel
This study investigated the histomorphological features of developing rabbit respiratory acini during the postnatal period. On the 1st day of postnatal life, the epithelium of terminal bronchiole consisted of clear cells which intercalated between few ciliated and abundant non-ciliated (Clara) cells. At this age, the rabbit lung was in the alveolar stage. The terminal bronchioles branched into several alveolar ducts, which opened into atria that communicated to alveolar sacs. All primary and secondary inter-alveolar septa were thick and showed a double-capillary network (immature septa)...
February 14, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30757984/simplified-sample-embedding-and-polishing-methods-for-preparing-hydrophilic-fragile-or-solvent-susceptible-materials-for-thin-sections-for-microscopic-analyses
#3
Masato Ueshima, Hirofumi Sakanakura
In the preparation of thin sections for microscopy, embedding and polishing processes in particular can change the composition and morphologies of samples. Soils and ashes are very fragile and solvent-susceptible, and appropriate sample preparation procedures have not been well-established. To improve the existing preparation methods and make them easier and faster, we embedded freeze-dried blocks, polished, and then examined these thin-section samples using polarization microscopy, laser microscopy, and field emission scanning electron microscopy with energy-dispersive X-ray spectrometry, and electron backscattered diffraction (EBSD)...
February 13, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30757983/automatic-counting-of-intra-cellular-ribonucleo-protein-aggregates-in-saccharomyces-cerevisiae-using-a-textural-approach
#4
Ambroise Marin, Emmanuel Denimal, Lucie Bertheau, Stéphane Guyot, Ludovic Journaux, Paul Molin
In the context of microbiology, recent studies show the importance of ribonucleo-protein aggregates (RNPs) for the understanding of mechanisms involved in cell responses to specific environmental conditions. The assembly and disassembly of aggregates is a dynamic process, the characterization of the stage of their evolution can be performed by the evaluation of their number. The aim of this study is to propose a method to automatically determine the count of RNPs. We show that the determination of a precise count is an issue by itself and hence, we propose three textural approaches: a classical point of view using Haralick features, a frequency point of view with generalized Fourier descriptors, and a structural point of view with Zernike moment descriptors (ZMD)...
February 13, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30757982/a-gas-phase-reaction-cell-for-modern-atom-probe-systems
#5
Daniel Haley, Ingrid McCarroll, Paul A J Bagot, Julie M Cairney, Michael P Moody
In this work, we demonstrate a new system for the examination of gas interactions with surfaces via atom probe tomography. This system provides capability of examining the surface and subsurface interactions of gases with a wide range of specimens, as well as a selection of input gas types. This system has been primarily developed to aid the investigation of hydrogen interactions with metallurgical samples, to better understand the phenomenon of hydrogen embrittlement. In its current form, it is able to operate at pressures from 10-6 to 1000 mbar (abs), can use a variety of gasses, and is equipped with heating and cryogenic quenching capabilities...
February 13, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30757980/statistically-rigorous-silver-nanowire-diameter-distribution-quantification-by-automated-electron-microscopy-and-image-analysis
#6
Clifford S Todd, William A Heeschen, Peter Y Eastman, Ellen C Keene
Silver nanowire (AgNW) diameters are typically characterized by manual measurement from high magnification electron microscope images. Measurement is monotonous and has potential ergonomic hazards. Because of this, statistics regarding wire diameter distribution can be poor, costly, and low-throughput. In addition, manual measurements are of unknown uncertainty and operator bias. In this paper we report an improved microscopy method for diameter and yield measurement of nanowires in terms of speed/automation and reduction of analyst variability...
February 13, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30757977/spatial-and-compositional-biases-introduced-by-position-sensitive-detection-systems-in-apt-a-simulation-approach
#7
C Bacchi, G Da Costa, F Vurpillot
Due to the low capacity of contemporary position-sensitive detectors in atom probe tomography (APT) to detect multiple events, material analyses that exhibit high numbers of multiple events are the most subject to compositional biases. To solve this limitation, some researchers have developed statistical correction algorithms. However, those algorithms are only efficient when one is confronted with homogeneous materials having nearly the same evaporation field between elements. Therefore, dealing with more complex materials must be accompanied by a better understanding of the signal loss mechanism during APT experiments...
February 13, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30744721/multipoint-background-analysis-gaining-precision-and-accuracy-in-microprobe-trace-element-analysis
#8
Julien M Allaz, Michael L Williams, Michael J Jercinovic, Karsten Goemann, John Donovan
Electron microprobe trace element analysis is a significant challenge. Due to the low net intensity of peak measurements, the accuracy and precision of such analyses relies critically on background measurements, and on the accuracy of any pertinent peak interference corrections. A linear regression between two points selected at appropriate background positions is a classical approach for electron probe microanalysis (EPMA). However, this approach neglects the accurate assessment of background curvature (exponential or polynomial), and the presence of background interferences, a hole in the background, or an absorption edge can dramatically affect the results if underestimated or ignored...
February 12, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30744709/a-gill-histopathology-study-in-two-native-fish-species-from-the-hydrographic-douro-basin
#9
Dércia Santos, Ana Luzio, Ana M Coimbra, Simone Varandas, António Fontaínhas-Fernandes, Sandra M Monteiro
Gill histopathology is a valuable tool to evaluate ecosystems health, because the gill is a key site of waterborne pollutant uptake and the first target organ to their toxicity. Consequently, this makes it important in biomonitoring programs. This study aims to evaluate gill histopathological differences in Douro basin native fish species and determine possible associations with water quality and the ecological status classifications. Two native fish species (Pseudochondrostoma duriense and Luciobarbus bocagei) were sampled in four points of the Douro basin: two reference points, Ameixiosa (Paiva River) and Covelas (Bestança River), both classified with an excellent ecological status; and two disturbed points, Castro Daire (Paiva River) and Alvações do Corgo (Corgo River), categorized with a good and a moderate ecological status, respectively...
February 12, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30722807/tracking-microscope-performance-a-workflow-to-compare-point-spread-function-evaluations-over-time
#10
Anna H Klemm, Andreas W Thomae, Katarina Wachal, Steffen Dietzel
Routine system checks are essential for supervising the performance of an advanced light microscope. Recording and evaluating the point spread function (PSF) of a given system provides information about the resolution and imaging. We compared the performance of fluorescent and gold beads for PSF recordings. We then combined the open-source evaluation software PSFj with a newly developed KNIME pipeline named PSFtracker to create a standardized workflow to track a system's performance over several measurements and thus over long time periods...
February 6, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30722805/an-automated-computational-approach-for-complete-in-plane-compositional-interface-analysis-by-atom-probe-tomography
#11
Zirong Peng, Yifeng Lu, Constantinos Hatzoglou, Alisson Kwiatkowski da Silva, Francois Vurpillot, Dirk Ponge, Dierk Raabe, Baptiste Gault
We introduce an efficient, automated computational approach for analyzing interfaces within atom probe tomography datasets, enabling quantitative mapping of their thickness, composition, as well as the Gibbsian interfacial excess of each solute. Detailed evaluation of an experimental dataset indicates that compared with the composition map, the interfacial excess map is more robust and exhibits a relatively higher resolution to reveal compositional variations. By field evaporation simulations with a predefined emitter mimicking the experimental dataset, the impact of trajectory aberrations on the measurement of the thickness, composition, and interfacial excess of the decorated interface are systematically analyzed and discussed...
February 6, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714566/calibration-of-atom-probe-tomography-reconstructions-through-correlation-with-electron-micrographs
#12
Isabelle Mouton, Shyam Katnagallu, Surendra Kumar Makineni, Oana Cojocaru-Mirédin, Torsten Schwarz, Leigh Thomas Stephenson, Dierk Raabe, Baptiste Gault
Although atom probe tomography (APT) reconstructions do not directly influence the local elemental analysis, any structural inferences from APT volumes demand a reliable reconstruction of the point cloud. Accurate estimation of the reconstruction parameters is crucial to obtain reliable spatial scaling. In the current work, a new automated approach of calibrating atom probe reconstructions is developed using only one correlative projection electron microscopy (EM) image. We employed an algorithm that implements a 2D cross-correlation of microstructural features observed in both the APT reconstructions and the corresponding EM image...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714562/application-of-gray-level-co-occurrence-matrix-analysis-as-a-new-method-for-enzyme-histochemistry-quantification
#13
Milorad Dragić, Marina Zarić, Nataša Mitrović, Nadežda Nedeljković, Ivana Grković
Enzyme histochemistry is a valuable histological method which provides a connection between morphology, activity, and spatial localization of investigated enzymes. Even though the method relies purely on arbitrary evaluations performed by the human eye, it is still wildly accepted and used in histo(patho)logy. Texture analysis emerged as an excellent tool for image quantification of subtle differences reflected in both spatial discrepancies and gray level values of pixels. The current study of texture analysis utilizes the gray-level co-occurrence matrix as a method for quantification of differences between ecto-5'-nucleotidase activities in healthy hippocampal tissue and tissue with marked neurodegeneration...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714561/mineralization-of-sialoliths-investigated-by-ex-vivo-and-in-vivo-x-ray-computed-tomography
#14
Pedro Nolasco, Paulo V Coelho, Carla Coelho, David F Angelo, J R Dias, Nuno M Alves, António Maurício, Manuel F C Pereira, António P Alves de Matos, Raul C Martins, Patrícia A Carvalho
The fraction of organic matter present affects the fragmentation behavior of sialoliths; thus, pretherapeutic information on the degree of mineralization is relevant for a correct selection of lithotripsy procedures. This work proposes a methodology for in vivo characterization of salivary calculi in the pretherapeutic context. Sialoliths were characterized in detail by X-ray computed microtomography (μCT) in combination with atomic emission spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, and transmission electron microscopy...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714554/cd81-promotes-a-migratory-phenotype-in-neuronal-like-cells
#15
Soraia A Martins, Patrícia D Correia, Roberto A Dias, Odete A B da Cruz E Silva, Sandra I Vieira
Tetraspanins, such as CD81, can form lateral associations with each other and with other transmembrane proteins. These interactions may underlie CD81 functions in multiple cellular processes, such as adhesion, morphology, migration, and differentiation. Since CD81's role in neuronal cells' migration has not been established, we here evaluated effects of CD81 on the migratory phenotype of SH-SY5Y neuroblastoma cells. CD81 was found enriched at SH-SY5Y cell's membrane, co-localizing with its interactor filamentous-actin (F-actin) in migratory relevant structures of the leading edge (filopodia, stress fibers, and adhesion sites)...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714553/fabrication-of-atom-probe-tomography-specimens-from-nanoparticles-using-a-fusible-bi-in-sn-alloy-as-an-embedding-medium
#16
Se-Ho Kim, Ji Yeong Lee, Jae-Pyoung Ahn, Pyuck-Pa Choi
We propose a new method for preparing atom probe tomography specimens from nanoparticles using a fusible bismuth-indium-tin alloy as an embedding medium. Iron nanoparticles synthesized by the sodium borohydride reduction method were chosen as a model system. The as-synthesized iron nanoparticles were embedded within the fusible alloy using focused ion beam milling and ion-milled to needle-shaped atom probe specimens under cryogenic conditions. An atom probe analysis revealed boron atoms in a detected iron nanoparticle, indicating that boron from the sodium borohydride reductant was incorporated into the nanoparticle during its synthesis...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714545/the-f-ratio-quantification-method-for-x-ray-microanalysis-applied-to-mg-al-zn-alloys
#17
Chaoyi Teng, Hendrix Demers, Xin Chu, Raynald Gauvin
The f-ratio quantitative X-ray microanalysis method has been recently developed for binary systems based on a scanning electron microscope/energy dispersive spectroscopy (SEM/EDS) system. This method incorporates traditional EDS experiments and Monte Carlo simulations, and calibration factors are calculated with standard samples to evaluate the differences between them. In this work, the f-ratio method was extended to Mg-Al-Zn multi-element systems using a cold field emission SEM and a tungsten emission SEM...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30714543/charge-state-field-evaporation-behavior-in-cu-v-nanocrystalline-alloys
#18
Xuyang Zhou, Gregory B Thompson
Atom probe tomography (APT) of a nanocrystalline Cu-7 at.% V thin film annealed at 400°C for 1 h revealed chemical partitioning in the form of solute segregation. The vanadium precipitated along high angle grain boundaries and at triple junctions, determined by cross-correlative precession electron diffraction of the APT specimen. Upon field evaporation, the V2+/(V1+ + VH1+) ratio from the decomposed ions was ~3 within the matrix grains and ~16 within the vanadium precipitates. It was found that the VH1+ complex was prevalent in the matrix, with its presence explained in terms of hydrogen's ability to assist in field evaporation...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30712530/improved-accuracy-for-trace-element-analysis-of-al-and-ti-in-quartz-by-electron-probe-microanalysis
#19
Ji-Qiang Cui, Shui-Yuan Yang, Shao-Yong Jiang, Jing Xie
The trace elements in quartz, Al and Ti, contain considerable information about mineral genesis, and determining their concentrations is of great importance in geology. Electron probe microanalysis has the advantages of non-destructive testing and high spatial resolution; however, it is a challenge to improve the accuracy and precision of trace element detection using this method. The important factors affecting accuracy include the fragility of quartz lattices at high beam currents and the methods used to determine the background...
February 4, 2019: Microscopy and Microanalysis
https://read.qxmd.com/read/30712529/surface-diffusion-of-fe-and-cu-on-fe-001-under-electric-field-using-first-principles-calculations
#20
Toshiharu Ohnuma
First-principles calculations were performed to determine the Fe on Fe (001) evaporation field and to characterize the surface diffusion of Fe and Cu on Fe (001) and on a step structure under an applied electric field. The evaporation field of Fe on Fe (001) was calculated by the nudged elastic band (NEB) method, using the combination of the effective screening medium and constant electrode potential methods to obtain a condition of constant electric field. The calculated evaporation field of Fe on Fe (001) was 32...
February 4, 2019: Microscopy and Microanalysis
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