Advanced Structural and Chemical Imaging最新文献

Detection of defects in atomic-resolution images of materials using cycle analysis 利用循环分析方法检测材料原子分辨率图像中的缺陷

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2020-03-30 DOI: 10.1186/s40679-020-00070-x

Oleg S. Ovchinnikov, Andrew O’Hara, Stephen Jesse, Bethany M. Hudak, Shi‐Ze Yang, Andrew R. Lupini, Matthew F. Chisholm, Wu Zhou, Sergei V. Kalinin, Albina Y. Borisevich, Sokrates T. Pantelides

{"title":"Detection of defects in atomic-resolution images of materials using cycle analysis","authors":"Oleg S. Ovchinnikov, Andrew O’Hara, Stephen Jesse, Bethany M. Hudak, Shi‐Ze Yang, Andrew R. Lupini, Matthew F. Chisholm, Wu Zhou, Sergei V. Kalinin, Albina Y. Borisevich, Sokrates T. Pantelides","doi":"10.1186/s40679-020-00070-x","DOIUrl":"https://doi.org/10.1186/s40679-020-00070-x","url":null,"abstract":"The automated detection of defects in high-angle annular dark-field Z-contrast (HAADF) scanning-transmission-electron microscopy (STEM) images has been a major challenge. Here, we report an approach for the automated detection and categorization of structural defects based on changes in the material’s local atomic geometry. The approach applies geometric graph theory to the already-found positions of atomic-column centers and is capable of detecting and categorizing any defect in thin diperiodic structures (i.e., “2D materials”) and a large subset of defects in thick diperiodic structures (i.e., 3D or bulk-like materials). Despite the somewhat limited applicability of the approach in detecting and categorizing defects in thicker bulk-like materials, it provides potentially informative insights into the presence of defects. The categorization of defects can be used to screen large quantities of data and to provide statistical data about the distribution of defects within a material. This methodology is applicable to atomic column locations extracted from any type of high-resolution image, but here we demonstrate it for HAADF STEM images.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"6 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2020-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-020-00070-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5160864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Imaging of polymer:fullerene bulk-heterojunctions in a scanning electron microscope: methodology aspects and nanomorphology by correlative SEM and STEM 聚合物成像:富勒烯异质结在扫描电子显微镜下的成像:方法学方面和相关的SEM和STEM纳米形貌

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2020-03-04 DOI: 10.1186/s40679-020-00069-4

Yonghe Li, Erich Müller, Christian Sprau, Alexander Colsmann, Dagmar Gerthsen

{"title":"Imaging of polymer:fullerene bulk-heterojunctions in a scanning electron microscope: methodology aspects and nanomorphology by correlative SEM and STEM","authors":"Yonghe Li, Erich Müller, Christian Sprau, Alexander Colsmann, Dagmar Gerthsen","doi":"10.1186/s40679-020-00069-4","DOIUrl":"https://doi.org/10.1186/s40679-020-00069-4","url":null,"abstract":"Scanning transmission electron microscopy (STEM) at low energies (≤?30?keV) in a scanning electron microscope is well suited to distinguish weakly scattering materials with similar materials properties and analyze their microstructure. The capabilities of the technique are illustrated in this work to resolve material domains in PTB7:PC71BM bulk-heterojunctions, which are commonly implemented for light-harvesting in organic solar cells. Bright-field (BF-) and high-angle annular dark-field (HAADF-) STEM contrast of pure PTB7 and PC71BM was first systematically analyzed using a wedge-shaped sample with well-known thickness profile. Monte-Carlo simulations are essential for the assignment of material contrast for materials with only slightly different scattering properties. Different scattering cross-sections were tested in Monte-Carlo simulations with screened Rutherford scattering cross-sections yielding best agreement with the experimental data. The STEM intensity also depends on the local specimen thickness, which can be dealt with by correlative STEM and scanning electron microscopy (SEM) imaging of the same specimen region yielding additional topography information. Correlative STEM/SEM was applied to determine the size of donor (PTB7) and acceptor (PC71BM) domains in PTB7:PC71BM absorber layers that were deposited from solution with different contents of the processing additive 1,8-diiodooctane (DIO).","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"6 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2020-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-020-00069-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4172507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks mpfit:一个具有多个高斯峰的原子分辨率图像拟合的鲁棒方法

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2020-01-27 DOI: 10.1186/s40679-020-0068-y

Debangshu Mukherjee, Leixin Miao, Greg Stone, Nasim Alem

引用次数: 19

Investigation of hole-free phase plate performance in transmission electron microscopy under different operation conditions by experiments and simulations 通过实验和模拟研究了不同操作条件下透射电镜无孔相板的性能

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2019-10-01 DOI: 10.1186/s40679-019-0067-z

Rebecca Pretzsch, Manuel Dries, Simon Hettler, Martin Spiecker, Martin Obermair, Dagmar Gerthsen

{"title":"Investigation of hole-free phase plate performance in transmission electron microscopy under different operation conditions by experiments and simulations","authors":"Rebecca Pretzsch, Manuel Dries, Simon Hettler, Martin Spiecker, Martin Obermair, Dagmar Gerthsen","doi":"10.1186/s40679-019-0067-z","DOIUrl":"https://doi.org/10.1186/s40679-019-0067-z","url":null,"abstract":"Hole-free phase plates (HFPPs), also known as Volta phase plates, were already demonstrated to be well suited for in-focus transmission electron microscopy imaging of organic objects. However, the underlying physical processes have not been fully understood yet. To further elucidate the imaging properties of HFPPs, phase shift measurements were carried out under different experimental conditions. Both positive and negative phase shifts occur depending on the diameter of the zero-order electron beam and the HFPP film temperature. The analysis of Thon ring patterns of an amorphous carbon test sample reveals that the phase-shifting patch can be significantly larger than the size of the zero-order beam on the HFPP film. An HFPP was used for in-focus phase contrast imaging of carbon nanotube (CNT) bundles under positive and negative phase-shifting conditions. The comparison of experimental and simulated images of CNT bundles gives detailed information on the phase shift profile, which depends on the spatial frequency in the vicinity of the zero-order beam. The shape of the phase shift profile also explains halo-like image artifacts that surround the imaged objects.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"5 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-019-0067-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4056534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Optimal principal component analysis of STEM XEDS spectrum images STEM XEDS光谱图像的优化主成分分析

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2019-04-09 DOI: 10.1186/s40679-019-0066-0

Pavel Potapov, Axel Lubk

引用次数: 20

Unsupervised machine learning applied to scanning precession electron diffraction data 无监督机器学习在扫描进动电子衍射数据中的应用

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2019-03-15 DOI: 10.1186/s40679-019-0063-3

Ben H. Martineau, Duncan N. Johnstone, Antonius T. J. van Helvoort, Paul A. Midgley, Alexander S. Eggeman

{"title":"Unsupervised machine learning applied to scanning precession electron diffraction data","authors":"Ben H. Martineau, Duncan N. Johnstone, Antonius T. J. van Helvoort, Paul A. Midgley, Alexander S. Eggeman","doi":"10.1186/s40679-019-0063-3","DOIUrl":"https://doi.org/10.1186/s40679-019-0063-3","url":null,"abstract":"Scanning precession electron diffraction involves the acquisition of a two-dimensional precession electron diffraction pattern at every probe position in a two-dimensional scan. The data typically comprise many more diffraction patterns than the number of distinct microstructural volume elements (e.g. crystals) in the region sampled. A dimensionality reduction, ideally to one representative diffraction pattern per distinct element, may then be sought. Further, some diffraction patterns will contain contributions from multiple crystals sampled along the beam path, which may be unmixed by harnessing this oversampling. Here, we report on the application of unsupervised machine learning methods to achieve both dimensionality reduction and signal unmixing. Potential artefacts are discussed and precession electron diffraction is demonstrated to improve results by reducing the impact of bending and dynamical diffraction so that the data better approximate the case in which each crystal yields a given diffraction pattern.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"5 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2019-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-019-0063-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4622263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 32

Fast approximate STEM image simulations from a machine learning model 从机器学习模型快速近似STEM图像模拟

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2019-03-12 DOI: 10.1186/s40679-019-0064-2

Aidan H. Combs, Jason J. Maldonis, Jie Feng, Zhongnan Xu, Paul M. Voyles, Dane Morgan

{"title":"Fast approximate STEM image simulations from a machine learning model","authors":"Aidan H. Combs, Jason J. Maldonis, Jie Feng, Zhongnan Xu, Paul M. Voyles, Dane Morgan","doi":"10.1186/s40679-019-0064-2","DOIUrl":"https://doi.org/10.1186/s40679-019-0064-2","url":null,"abstract":"Accurate quantum mechanical scanning transmission electron microscopy image simulation methods such as the multislice method require computation times that are too large to use in applications in high-resolution materials imaging that require very large numbers of simulated images. However, higher-speed simulation methods based on linear imaging models, such as the convolution method, are often not accurate enough for use in these applications. We present a method that generates an image from the convolution of an object function and the probe intensity, and then uses a multivariate polynomial fit to a dataset of corresponding multislice and convolution images to correct it. We develop and validate this method using simulated images of Pt and Pt–Mo nanoparticles and find that for these systems, once the polynomial is fit, the method runs about six orders of magnitude faster than parallelized CPU implementations of the multislice method while achieving a 1???R2 error of 0.010–0.015 and root-mean-square error/standard deviation of dataset being predicted of about 0.1 when compared to full multislice simulations.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"5 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2019-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-019-0064-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4803158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Analysis of crystal defects by scanning transmission electron microscopy (STEM) in a modern scanning electron microscope 用现代扫描电镜扫描透射电镜(STEM)分析晶体缺陷

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2019-03-09 DOI: 10.1186/s40679-019-0065-1

Cheng Sun, Erich Müller, Matthias Meffert, Dagmar Gerthsen

{"title":"Analysis of crystal defects by scanning transmission electron microscopy (STEM) in a modern scanning electron microscope","authors":"Cheng Sun, Erich Müller, Matthias Meffert, Dagmar Gerthsen","doi":"10.1186/s40679-019-0065-1","DOIUrl":"https://doi.org/10.1186/s40679-019-0065-1","url":null,"abstract":"Dislocations and stacking faults are important crystal defects, because they strongly influence material properties. As of now, transmission electron microscopy (TEM) is the most frequently used technique to study the properties of single dislocations and stacking faults. Specifically, the Burgers vector b of dislocations or displacement vector R of stacking faults can be determined on the basis of the g·b?=?n (g·R?=?n) criterion by setting up different two-beam diffraction conditions with an imaging vector g. Based on the reciprocity theorem, scanning transmission electron microscopy (STEM) can also be applied for defect characterization, but has been less frequently used up to now. In this work, we demonstrate g·b?=?n (g·R?=?n) analyses of dislocations and stacking faults in GaN by STEM imaging in a scanning electron microscope. The instrument is equipped with a STEM detector, double-tilt TEM specimen holder, and a charge-coupled-device camera for the acquisition of on-axis diffraction patterns. The latter two accessories are mandatory to control the specimen orientation, which has not been possible before in a scanning electron microscope.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"5 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2019-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-019-0065-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4389389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 22

Protein structural biology using cell-free platform from wheat germ 小麦胚芽无细胞平台蛋白结构生物学研究

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2018-11-10 DOI: 10.1186/s40679-018-0062-9

Irina V. Novikova, Noopur Sharma, Trevor Moser, Ryan Sontag, Yan Liu, Michael J. Collazo, Duilio Cascio, Tolou Shokuhfar, Hanjo Hellmann, Michael Knoblauch, James E. Evans

{"title":"Protein structural biology using cell-free platform from wheat germ","authors":"Irina V. Novikova, Noopur Sharma, Trevor Moser, Ryan Sontag, Yan Liu, Michael J. Collazo, Duilio Cascio, Tolou Shokuhfar, Hanjo Hellmann, Michael Knoblauch, James E. Evans","doi":"10.1186/s40679-018-0062-9","DOIUrl":"https://doi.org/10.1186/s40679-018-0062-9","url":null,"abstract":"One of the biggest bottlenecks for structural analysis of proteins remains the creation of high-yield and high-purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes, while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited many areas of genomic and proteomics research, therapeutics, vaccine development and protein chip constructions. In this work, we demonstrate a versatile and multiscale eukaryotic wheat germ cell-free protein expression pipeline to generate functional proteins of different sizes from multiple host organism and DNA source origins. We also report on a robust purification procedure, which can produce highly pure (>?98%) proteins with no specialized equipment required and minimal time invested. This pipeline successfully produced and analyzed proteins in all three major geometry formats used for structural biology including single particle analysis with electron microscopy, and both two-dimensional and three-dimensional protein crystallography. The flexibility of the wheat germ system in combination with the multiscale pipeline described here provides a new workflow for rapid production and purification of samples that may not be amenable to other recombinant approaches for structural characterization.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0062-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4435169","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: 16

Multiscale higher-order TV operators for L1 regularization 用于L1正则化的多尺度高阶电视算子

IF 3.56

Advanced Structural and Chemical Imaging Pub Date : 2018-10-23 DOI: 10.1186/s40679-018-0061-x

Toby Sanders, Rodrigo B. Platte

{"title":"Multiscale higher-order TV operators for L1 regularization","authors":"Toby Sanders, Rodrigo B. Platte","doi":"10.1186/s40679-018-0061-x","DOIUrl":"https://doi.org/10.1186/s40679-018-0061-x","url":null,"abstract":"In the realm of signal and image denoising and reconstruction, (ell _1) regularization techniques have generated a great deal of attention with a multitude of variants. In this work, we demonstrate that the (ell _1) formulation can sometimes result in undesirable artifacts that are inconsistent with desired sparsity promoting (ell _0) properties that the (ell _1) formulation is intended to approximate. With this as our motivation, we develop a multiscale higher-order total variation (MHOTV) approach, which we show is related to the use of multiscale Daubechies wavelets. The relationship of higher-order regularization methods with wavelets, which we believe has generally gone unrecognized, is shown to hold in several numerical results, although notable improvements are seen with our approach over both wavelets and classical HOTV. These results are presented for 1D signals and 2D images, and we include several examples that highlight the potential of our approach for improving two- and three-dimensional electron microscopy imaging. In the development approach, we construct the tools necessary for MHOTV computations to be performed efficiently, via operator decomposition and alternatively converting the problem into Fourier space.","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0061-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4911685","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: 11