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Journals Advanced Structural and Chemic...

Advanced Structural and Chemical Imaging

https://read.qxmd.com/read/28280683/controlling-residual-hydrogen-gas-in-mass-spectra-during-pulsed-laser-atom-probe-tomography
#21
JOURNAL ARTICLE
R Prakash Kolli
Residual hydrogen (H2) gas in the analysis chamber of an atom probe instrument limits the ability to measure H concentration in metals and alloys. Measuring H concentration would permit quantification of important physical phenomena, such as hydrogen embrittlement, corrosion, hydrogen trapping, and grain boundary segregation. Increased insight into the behavior of residual H2 gas on the specimen tip surface in atom probe instruments could help reduce these limitations. The influence of user-selected experimental parameters on the field adsorption and desorption of residual H2 gas on nominally pure copper (Cu) was studied during ultraviolet pulsed laser atom probe tomography...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261546/prospects-for-atomic-resolution-in-line-holography-for-a-3d-determination-of-atomic-structures-from-single-projections
#22
REVIEW
F-R Chen, C Kisielowski, D Van Dyck
It is now established that the 3D structure of homogeneous nanocrystals can be recovered from in-line hologram of single projections. The method builds on a quantitative contrast interpretation of electron exit wave functions. Since simulated exit wave functions of single and bilayers of graphene reveal the atomic structure of carbon-based materials with sufficient resolution, we explore theoretically how the approach can be expanded beyond periodic carbon-based materials to include non-periodic molecular structures...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261545/nanosurveyor-a-framework-for-real-time-data-processing
#23
JOURNAL ARTICLE
Benedikt J Daurer, Hari Krishnan, Talita Perciano, Filipe R N C Maia, David A Shapiro, James A Sethian, Stefano Marchesini
BACKGROUND: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. RESULTS: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261544/trace-a-high-throughput-tomographic-reconstruction-engine-for-large-scale-datasets
#24
JOURNAL ARTICLE
Tekin Bicer, Doğa Gürsoy, Vincent De Andrade, Rajkumar Kettimuthu, William Scullin, Francesco De Carlo, Ian T Foster
BACKGROUND: Modern synchrotron light sources and detectors produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used imaging techniques that generates data at tens of gigabytes per second is computed tomography (CT). Although CT experiments result in rapid data generation, the analysis and reconstruction of the collected data may require hours or even days of computation time with a medium-sized workstation, which hinders the scientific progress that relies on the results of analysis...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261543/efficient-implementation-of-a-local-tomography-reconstruction-algorithm
#25
JOURNAL ARTICLE
Pierre Paleo, Alessandro Mirone
We propose an efficient implementation of an interior tomography reconstruction method based on a known subregion. This method iteratively refines a reconstruction, aiming at reducing the local tomography artifacts. To cope with the ever increasing data volumes, this method is highly optimized on two aspects: firstly, the problem is reformulated to reduce the number of variables, and secondly, the operators involved in the optimization algorithms are efficiently implemented. Results show that [Formula: see text] slices can be processed in tens of seconds, while being beyond the reach of equivalent exact local tomography method...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261542/syrmep-tomo-project-a-graphical-user-interface-for-customizing-ct-reconstruction-workflows
#26
JOURNAL ARTICLE
Francesco Brun, Lorenzo Massimi, Michela Fratini, Diego Dreossi, Fulvio Billé, Agostino Accardo, Roberto Pugliese, Alessia Cedola
When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261541/data-systems-for-the-linac-coherent-light-source
#27
JOURNAL ARTICLE
J Thayer, D Damiani, C Ford, M Dubrovin, I Gaponenko, C P O'Grady, W Kroeger, J Pines, T J Lane, A Salnikov, D Schneider, T Tookey, M Weaver, C H Yoon, A Perazzo
The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261540/applying-shot-boundary-detection-for-automated-crystal-growth-analysis-during-in-situ-transmission-electron-microscope-experiments
#28
JOURNAL ARTICLE
W A Moeglein, R Griswold, B L Mehdi, N D Browning, J Teuton
In situ scanning transmission electron microscopy is being developed for numerous applications in the study of nucleation and growth under electrochemical driving forces. For this type of experiment, one of the key parameters is to identify when nucleation initiates. Typically, the process of identifying the moment that crystals begin to form is a manual process requiring the user to perform an observation and respond accordingly (adjust focus, magnification, translate the stage, etc.). However, as the speed of the cameras being used to perform these observations increases, the ability of a user to "catch" the important initial stage of nucleation decreases (there is more information that is available in the first few milliseconds of the process)...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28261539/towards-on-the-fly-data-post-processing-for-real-time-tomographic-imaging-at-tomcat
#29
JOURNAL ARTICLE
Federica Marone, Alain Studer, Heiner Billich, Leonardo Sala, Marco Stampanoni
Sub-second full-field tomographic microscopy at third-generation synchrotron sources is a reality, opening up new possibilities for the study of dynamic systems in different fields. Sustained elevated data rates of multiple GB/s in tomographic experiments will become even more common at diffraction-limited storage rings, coming in operation soon. The computational tools necessary for the post-processing of raw tomographic projections have generally not experienced the same efficiency increase as the experimental facilities, hindering optimal exploitation of this new potential...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28251043/atomap-a-new-software-tool-for-the-automated-analysis-of-atomic-resolution-images-using-two-dimensional-gaussian-fitting
#30
JOURNAL ARTICLE
Magnus Nord, Per Erik Vullum, Ian MacLaren, Thomas Tybell, Randi Holmestad
Scanning transmission electron microscopy (STEM) data with atomic resolution can contain a large amount of information about the structure of a crystalline material. Often, this information is hard to extract, due to the large number of atomic columns and large differences in intensity from sublattices consisting of different elements. In this work, we present a free and open source software tool for analysing both the position and shapes of atomic columns in STEM-images, using 2-D elliptical Gaussian distributions...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28018839/a-distributed-astra-toolbox
#31
JOURNAL ARTICLE
Willem Jan Palenstijn, Jeroen Bédorf, Jan Sijbers, K Joost Batenburg
While iterative reconstruction algorithms for tomography have several advantages compared to standard backprojection methods, the adoption of such algorithms in large-scale imaging facilities is still limited, one of the key obstacles being their high computational load. Although GPU-enabled computing clusters are, in principle, powerful enough to carry out iterative reconstructions on large datasets in reasonable time, creating efficient distributed algorithms has so far remained a complex task, requiring low-level programming to deal with memory management and network communication...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28003954/improved-tomographic-reconstruction-of-large-scale-real-world-data-by-filter-optimization
#32
JOURNAL ARTICLE
Daniël M Pelt, Vincent De Andrade
In advanced tomographic experiments, large detector sizes and large numbers of acquired datasets can make it difficult to process the data in a reasonable time. At the same time, the acquired projections are often limited in some way, for example having a low number of projections or a low signal-to-noise ratio. Direct analytical reconstruction methods are able to produce reconstructions in very little time, even for large-scale data, but the quality of these reconstructions can be insufficient for further analysis in cases with limited data...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28003953/the-max-iv-imaging-concept
#33
REVIEW
Zdeněk Matěj, Rajmund Mokso, Krister Larsson, Vincent Hardion, Darren Spruce
The MAX IV Laboratory is currently the synchrotron X-ray source with the beam of highest brilliance. Four imaging beamlines are in construction or in the project phase. Their common characteristic will be the high acquisition rates of phase-enhanced images. This high data flow will be managed at the local computing cluster jointly with the Swedish National Computing Infrastructure. A common image reconstruction and analysis platform is being designed to offer reliable quantification of the multidimensional images acquired at all the imaging beamlines at MAX IV...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/28003952/automatic-software-correction-of-residual-aberrations-in-reconstructed-hrtem-exit-waves-of-crystalline-samples
#34
JOURNAL ARTICLE
Colin Ophus, Haider I Rasool, Martin Linck, Alex Zettl, Jim Ciston
We develop an automatic and objective method to measure and correct residual aberrations in atomic-resolution HRTEM complex exit waves for crystalline samples aligned along a low-index zone axis. Our method uses the approximate rotational point symmetry of a column of atoms or single atom to iteratively calculate a best-fit numerical phase plate for this symmetry condition, and does not require information about the sample thickness or precise structure. We apply our method to two experimental focal series reconstructions, imaging a β-Si3N4 wedge with O and N doping, and a single-layer graphene grain boundary...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27867837/identifying-local-structural-states-in-atomic-imaging-by-computer-vision
#35
JOURNAL ARTICLE
Nouamane Laanait, Maxim Ziatdinov, Qian He, Albina Borisevich
The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27867836/detecting-structural-variances-of-co3o4-catalysts-by-controlling-beam-induced-sample-alterations-in-the-vacuum-of-a-transmission-electron-microscope
#36
JOURNAL ARTICLE
C Kisielowski, H Frei, P Specht, I D Sharp, J A Haber, S Helveg
This article summarizes core aspects of beam-sample interactions in research that aims at exploiting the ability to detect single atoms at atomic resolution by mid-voltage transmission electron microscopy. Investigating the atomic structure of catalytic Co3O4 nanocrystals underscores how indispensable it is to rigorously control electron dose rates and total doses to understand native material properties on this scale. We apply in-line holography with variable dose rates to achieve this goal. Genuine object structures can be maintained if dose rates below ~100 e/Å(2)s are used and the contrast required for detection of single atoms is generated by capturing large image series...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27738593/structural-damage-reduction-in-protected-gold-clusters-by-electron-diffraction-methods
#37
JOURNAL ARTICLE
Eduardo Ortega, Arturo Ponce, Ulises Santiago, Diego Alducin, Alfredo Benitez-Lara, Germán Plascencia-Villa, Miguel José-Yacamán
The present work explores electron diffraction methods for studying the structure of metallic clusters stabilized with thiol groups, which are susceptible to structural damage caused by electron beam irradiation. There is a compromise between the electron dose used and the size of the clusters since they have small interaction volume with electrons and as a consequence weak reflections in the diffraction patterns. The common approach of recording individual clusters using nanobeam diffraction has the problem of an increased current density...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27695667/deceleration-of-probe-beam-by-stage-bias-potential-improves-resolution-of-serial-block-face-scanning-electron-microscopic-images
#38
James C Bouwer, Thomas J Deerinck, Eric Bushong, Vadim Astakhov, Ranjan Ramachandra, Steven T Peltier, Mark H Ellisman
Serial block-face scanning electron microscopy (SBEM) is quickly becoming an important imaging tool to explore three-dimensional biological structure across spatial scales. At probe-beam-electron energies of 2.0 keV or lower, the axial resolution should improve, because there is less primary electron penetration into the block face. More specifically, at these lower energies, the interaction volume is much smaller, and therefore, surface detail is more highly resolved. However, the backscattered electron yield for metal contrast agents and the backscattered electron detector sensitivity are both sub-optimal at these lower energies, thus negating the gain in axial resolution...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27617185/hrtem-low-dose-the-unfold-of-the-morphed-graphene-from-amorphous-carbon-to-morphed-graphenes
#39
H A Calderon, A Okonkwo, I Estrada-Guel, V G Hadjiev, F Alvarez-Ramírez, F C Robles Hernández
We present experimental evidence under low-dose conditions transmission electron microscopy for the unfolding of the evolving changes in carbon soot during mechanical milling. The milled soot shows evolving changes as a function of the milling severity or time. Those changes are responsible for the transformation from amorphous carbon to graphenes, graphitic carbon, and highly ordered structures such as morphed graphenes, namely Rh6 and Rh6-II. The morphed graphenes are corrugated layers of carbon with cross-linked covalently nature and sp(2)- or sp(3)-type allotropes...
2017: Advanced Structural and Chemical Imaging
https://read.qxmd.com/read/27547706/3d-reconstruction-of-biological-structures-automated-procedures-for-alignment-and-reconstruction-of-multiple-tilt-series-in-electron-tomography
#40
JOURNAL ARTICLE
Sébastien Phan, Daniela Boassa, Phuong Nguyen, Xiaohua Wan, Jason Lanman, Albert Lawrence, Mark H Ellisman
Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data from a greater number of tilt series, yielding enhanced data quality and increasing contrast associated with weakly stained structures. This scheme facilitates visualization of nanometer scale details of fine structure in volumes taken from plastic-embedded samples of biological specimens in all dimensions...
2017: Advanced Structural and Chemical Imaging
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