Advanced Structural and Chemical Imaging最新文献_第3页

A non-rigid registration method for the analysis of local deformations in the wood cell wall 木材细胞壁局部变形分析的非刚性配准方法

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Advanced Structural and Chemical Imaging Pub Date : 2018-01-22 DOI: 10.1186/s40679-018-0050-0

Alessandra Patera, Stephan Carl, Marco Stampanoni, Dominique Derome, Jan Carmeliet

{"title":"A non-rigid registration method for the analysis of local deformations in the wood cell wall","authors":"Alessandra Patera, Stephan Carl, Marco Stampanoni, Dominique Derome, Jan Carmeliet","doi":"10.1186/s40679-018-0050-0","DOIUrl":"https://doi.org/10.1186/s40679-018-0050-0","url":null,"abstract":"This paper concerns the problem of wood cellular structure image registration. Given the large variability of wood geometry and the important changes in the cellular organization due to moisture sorption, an affine-based image registration technique is not exhaustive to describe the overall hygro-mechanical behaviour of wood at micrometre scales. Additionally, free tools currently available for non-rigid image registration are not suitable for quantifying the structural deformations of complex hierarchical materials such as wood, leading to errors due to misalignment. In this paper, we adapt an existing non-rigid registration model based on B-spline functions to our case study. The so-modified algorithm combines the concept of feature recognition within specific regions locally distributed in the material with an optimization problem. Results show that the method is able to quantify local deformations induced by moisture changes in tomographic images of wood cell wall with high accuracy. The local deformations provide new important insights in characterizing the swelling behaviour of wood at the cell wall level.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0050-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4857105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Correction to: Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles 修正:纳米颗粒透射电子显微镜图像表面应变测量的准确性

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Advanced Structural and Chemical Imaging Pub Date : 2017-11-07 DOI: 10.1186/s40679-017-0049-y

Jacob Madsen, Pei Liu, Jakob B. Wagner, Thomas W. Hansen, Jakob Schiøtz

引用次数: 3

Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles 纳米颗粒透射电子显微镜图像表面应变测量的准确性

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-10-25 DOI: 10.1186/s40679-017-0047-0

Jacob Madsen, Pei Liu, Jakob B. Wagner, Thomas W. Hansen, Jakob Schiøtz

引用次数: 18

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy 流式多gpu实现的扫描透射电子显微镜图像仿真算法

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-10-25 DOI: 10.1186/s40679-017-0048-z

Alan Pryor Jr., Colin Ophus, Jianwei Miao

{"title":"A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy","authors":"Alan Pryor Jr., Colin Ophus, Jianwei Miao","doi":"10.1186/s40679-017-0048-z","DOIUrl":"https://doi.org/10.1186/s40679-017-0048-z","url":null,"abstract":"Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"3 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2017-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-017-0048-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4988185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 89

A fast image simulation algorithm for scanning transmission electron microscopy 扫描透射电子显微镜快速图像模拟算法

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-05-10 DOI: 10.1186/s40679-017-0046-1

Colin Ophus

引用次数: 128

An environmental transfer hub for multimodal atom probe tomography 多模态原子探针层析成像的环境传递中心

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-05-02 DOI: 10.1186/s40679-017-0045-2

Daniel E. Perea, Stephan S. A. Gerstl, Jackson Chin, Blake Hirschi, James. E. Evans

{"title":"An environmental transfer hub for multimodal atom probe tomography","authors":"Daniel E. Perea, Stephan S. A. Gerstl, Jackson Chin, Blake Hirschi, James. E. Evans","doi":"10.1186/s40679-017-0045-2","DOIUrl":"https://doi.org/10.1186/s40679-017-0045-2","url":null,"abstract":"Environmental control during transfer between instruments is required for samples sensitive to air or thermal exposure to prevent morphological or chemical changes prior to analysis. Atom probe tomography is a rapidly expanding technique for three-dimensional structural and chemical analysis, but commercial instruments remain limited to loading specimens under ambient conditions. In this study, we describe a multifunctional environmental transfer hub allowing controlled cryogenic or room-temperature transfer of specimens under atmospheric or vacuum pressure conditions between an atom probe and other instruments or reaction chambers. The utility of the environmental transfer hub is demonstrated through the acquisition of previously unavailable mass spectral analysis of an intact organic molecule made possible via controlled cryogenic transfer into the atom probe using the hub. The ability to prepare and transfer specimens in precise environments promises a means to access new science across many disciplines from untainted samples and allow downstream time-resolved in situ atom probe studies.\u0000","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"3 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2017-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-017-0045-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4096387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 47

Dynamic X-ray diffraction imaging of the ferroelectric response in bismuth ferrite 铋铁氧体铁电响应的动态x射线衍射成像

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-03-21 DOI: 10.1186/s40679-017-0044-3

Nouamane Laanait, Wittawat Saenrang, Hua Zhou, Chang-Beom Eom, Zhan Zhang

{"title":"Dynamic X-ray diffraction imaging of the ferroelectric response in bismuth ferrite","authors":"Nouamane Laanait, Wittawat Saenrang, Hua Zhou, Chang-Beom Eom, Zhan Zhang","doi":"10.1186/s40679-017-0044-3","DOIUrl":"https://doi.org/10.1186/s40679-017-0044-3","url":null,"abstract":"X-ray diffraction imaging is rapidly emerging as a powerful technique by which one can capture the local structure of crystalline materials at the nano- and meso-scale. Here, we present investigations of the dynamic structure of epitaxial monodomain BiFeO3 thin-films using a novel full-field Bragg diffraction imaging modality. By taking advantage of the depth penetration of hard X-rays and their exquisite sensitivity to the atomic structure, we imaged in situ and in operando, the electric field-driven structural responses of buried BiFeO3 epitaxial thin-films in micro-capacitor devices, with sub-100?nm lateral resolution. These imaging investigations were carried out at acquisition frame rates that reached up to 20?Hz and data transfer rates of 40?MB/s, while accessing diffraction contrast that is sensitive to the entire three-dimensional unit cell configuration. We mined these large datasets for material responses by employing matrix decomposition techniques, such as independent component analysis. We found that this statistical approach allows the extraction of the salient physical properties of the ferroelectric response of the material, such as coercive fields and transient spatiotemporal modulations in their piezoelectric response, and also facilitates their decoupling from extrinsic sources that are instrument specific.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"3 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2017-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-017-0044-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4828377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography 脉冲激光原子探针层析成像质谱中残余氢气的控制

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-02-22 DOI: 10.1186/s40679-017-0043-4

R. Prakash Kolli

{"title":"Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography","authors":"R. Prakash Kolli","doi":"10.1186/s40679-017-0043-4","DOIUrl":"https://doi.org/10.1186/s40679-017-0043-4","url":null,"abstract":"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. The results indicate that the total residual hydrogen concentration, H\u0000 TOT, in the mass spectra exhibits a generally decreasing trend with increasing laser pulse energy and increasing laser pulse frequency. Second-order interaction effects are also important. The pulse energy has the greatest influence on the quantity H\u0000 TOT, which is consistently less than 0.1?at.% at a value of 80?pJ.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"3 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2017-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-017-0043-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4850379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 25

Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting Atomap:一个使用二维高斯拟合自动分析原子分辨率图像的新软件工具

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-02-13 DOI: 10.1186/s40679-017-0042-5

Magnus Nord, Per Erik Vullum, Ian MacLaren, Thomas Tybell, Randi Holmestad

{"title":"Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting","authors":"Magnus Nord, Per Erik Vullum, Ian MacLaren, Thomas Tybell, Randi Holmestad","doi":"10.1186/s40679-017-0042-5","DOIUrl":"https://doi.org/10.1186/s40679-017-0042-5","url":null,"abstract":"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. The software is tested on variants of the perovskite oxide structure. By first fitting the most intense atomic columns and then subtracting them, information on all the projected sublattices can be obtained. From this, we can extract changes in the lattice parameters and shape of A-cation columns from annular dark field images of perovskite oxide heterostructures. Using annular bright field images, shifts in oxygen column positions are also quantified in the same heterostructure. The precision of determining the position of atomic columns is compared between STEM data acquired using standard acquisition, and STEM-images obtained as an image stack averaged after using non-rigid registration.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"3 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2017-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-017-0042-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4534134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 154

Prospects for atomic resolution in-line holography for a 3D determination of atomic structures from single projections 原子分辨率在线全息技术在单投影原子结构三维测定中的应用前景

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2017-02-06 DOI: 10.1186/s40679-017-0041-6

F. -R. Chen, C. Kisielowski, D. Van Dyck

引用次数: 14