Advanced Structural and Chemical Imaging最新文献

{"title":"An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data","authors":"Laurent P. René de Cotret,&nbsp;Martin R. Otto,&nbsp;Mark J. Stern,&nbsp;Bradley J. Siwick","doi":"10.1186/s40679-018-0060-y","DOIUrl":"https://doi.org/10.1186/s40679-018-0060-y","url":null,"abstract":"<p>This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, <i>iris</i>, is graphical user-interface program and library for interactive exploration of UES data. Under the hood, <i>iris</i> makes use of <i>npstreams</i>, an extensions of <i>numpy</i> to streaming array-processing, for high-throughput parallel data reduction. Finally, we present <i>scikit-ued</i>, a library of reusable routines and data structures for analysis of UES data, including specialized image processing algorithms, simulation routines, and crystal structure manipulation operations. In this paper, some of the features or all three packages are highlighted, such as parallel data reduction, image registration, interactive exploration. The packages are fully tested and documented and are released under permissive licenses.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0060-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5179117","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}

{"title":"Sub-Ångstrom electric field measurements on a universal detector in a scanning transmission electron microscope","authors":"Jordan A. Hachtel,&nbsp;Juan Carlos Idrobo,&nbsp;Miaofang Chi","doi":"10.1186/s40679-018-0059-4","DOIUrl":"https://doi.org/10.1186/s40679-018-0059-4","url":null,"abstract":"<p>Scanning transmission electron microscopy (STEM) excels in accessing atomic-scale structure and chemistry. Enhancing our ability to directly image the functionalities of local features in materials has become one of the most important topics in the future development of STEM. Recently, differential phase contrast (DPC) imaging has been utilized to map the internal electric and magnetic fields in materials from nanoscale features such as p–n junctions, skyrmions, and even from individual atoms. Here, we use an ultra-low noise SCMOS detector in as the diffraction plane camera to collect four-dimensional (4D) datasets. The high angular resolution, efficient high-SNR acquisition, and modifiability of the camera allow it to function as a universal detector, where STEM imaging configurations, such as DPC, bright field, annular bright field, and annular dark field can all be reconstructed from a single 4D dataset. By examining a distorted perovskite, DyScO₃, which possesses projected lattice spacings as small as 0.83??, we demonstrate DPC spatial resolution almost reaching the information limit of a 100?keV electron beam. In addition, the perovskite has ordered O-coordinations with alternating octahedral tilts, which can be quantitatively measured with single degree accuracy by taking advantage of DPC’s sensitivity to light atoms. The results, acquired on a standard Ronchigram camera as opposed to a specialized DPC detector, open up new opportunities to understand and design functional materials and devices that involve lattice and charge coupling at nano- and atomic-scales.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0059-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4925501","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}

{"title":"Multi-slice frozen phonon simulations of high-angle annular dark field scanning transmission electron microscopy images of the structurally and compositionally complex Mo–V–Nb–Te oxide catalyst","authors":"Douglas A. Blom,&nbsp;Thomas Vogt","doi":"10.1186/s40679-018-0058-5","DOIUrl":"https://doi.org/10.1186/s40679-018-0058-5","url":null,"abstract":"<p>We report frozen phonon multi-slice image simulations for the complex oxidation catalyst M1. Quantitative analysis of the simulations suggests that the detailed order of the cations along the electron propagation direction in a [001] zone axis orientation can lead to different high-angle annular dark field signals from atomic columns with identical composition. The annular dark field signal varies linearly with atomic percent V, and the spread of intensities due to the atomic species order is of similar magnitude to the intensity difference due to ±?5% V.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0058-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5181359","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}

{"title":"Micro-Extinction Spectroscopy (MExS): a versatile optical characterization technique","authors":"Anjli Kumar,&nbsp;Eduardo Villarreal,&nbsp;Xiang Zhang,&nbsp;Emilie Ringe","doi":"10.1186/s40679-018-0057-6","DOIUrl":"https://doi.org/10.1186/s40679-018-0057-6","url":null,"abstract":"<p>Micro-Extinction Spectroscopy (MExS), a flexible, optical, and spatial-scanning hyperspectral technique, has been developed and is described with examples. Software and hardware capabilities are described in detail, including transmission, reflectance, and scattering measurements. Each capability is demonstrated through a case study of nanomaterial characterization, i.e., transmission of transition metal dichalcogenides revealing transition energy and efficiency, reflectance of transition metal dichalcogenides grown on nontransparent substrates identifying the presence of monolayer following electrochemical ablation, and scattering to study single plasmonic nanoparticles and obtain values for the refractive index sensitivity and sensing figure of merit of over a hundred single particles with various shapes and sizes. With the growing integration of nanotechnology in many areas, MExS can be a powerful tool to both characterize and test nanomaterials.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0057-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4498780","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}

{"title":"Maximising the resolving power of the scanning tunneling microscope","authors":"Lewys Jones,&nbsp;Shuqiu Wang,&nbsp;Xiao Hu,&nbsp;Shams ur Rahman,&nbsp;Martin R. Castell","doi":"10.1186/s40679-018-0056-7","DOIUrl":"https://doi.org/10.1186/s40679-018-0056-7","url":null,"abstract":"<p>The usual way to present images from a scanning tunneling microscope (STM) is to take multiple images of the same area, to then manually select the one that appears to be of the highest quality, and then to discard the other almost identical images. This is in contrast to most other disciplines where the signal to noise ratio (SNR) of a data set is improved by taking repeated measurements and averaging them. Data averaging can be routinely performed for 1D spectra, where their alignment is straightforward. However, for serial-acquired 2D STM images the nature and variety of image distortions can severely complicate accurate registration. Here, we demonstrate how a significant improvement in the resolving power of the STM can be achieved through automated distortion correction and multi-frame averaging (MFA) and we demonstrate the broad utility of this approach with three examples. First, we show a sixfold enhancement of the SNR of the Si(111)-(7?×?7) reconstruction. Next, we demonstrate that images with sub-picometre height precision can be routinely obtained and show this for a monolayer of Ti₂O₃ on Au(111). Last, we demonstrate the automated classification of the two chiral variants of the surface unit cells of the (4?×?4) reconstructed SrTiO₃(111) surface. Our new approach to STM imaging will allow a wealth of structural and electronic information from surfaces to be extracted that was previously buried in noise.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0056-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4309038","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}

{"title":"Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform","authors":"R. Kannan,&nbsp;A. V. Ievlev,&nbsp;N. Laanait,&nbsp;M. A. Ziatdinov,&nbsp;R. K. Vasudevan,&nbsp;S. Jesse,&nbsp;S. V. Kalinin","doi":"10.1186/s40679-018-0055-8","DOIUrl":"https://doi.org/10.1186/s40679-018-0055-8","url":null,"abstract":"<p>Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0055-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5138884","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}

{"title":"Accurate lattice parameters from 2D-periodic images for subsequent Bravais lattice type assignments","authors":"P. Moeck,&nbsp;P. DeStefano","doi":"10.1186/s40679-018-0051-z","DOIUrl":"https://doi.org/10.1186/s40679-018-0051-z","url":null,"abstract":"<p>Three different algorithms, as implemented in three different computer programs, were put to the task of extracting direct space lattice parameters from four sets of synthetic images that were per design more or less periodic in two dimensions (2D). One of the test images in each set was per design free of noise and, therefore, genuinely 2D periodic so that it adhered perfectly to the constraints of a Bravais lattice type, Laue class, and plane symmetry group. Gaussian noise with a mean of zero and standard deviations of 10 and 50% of the maximal pixel intensity was added to the individual pixels of the noise-free images individually to create two more images and thereby complete the sets. The added noise broke the strict translation and site/point symmetries of the noise-free images of the four test sets so that all symmetries that existed per design turned into pseudo-symmetries of the second kind. Moreover, motif and translation-based pseudo-symmetries of the first kind, a.k.a. genuine pseudo-symmetries, and a metric specialization were present per design in the majority of the noise-free test images already. With the extraction of the lattice parameters from the images of the synthetic test sets, we assessed the robustness of the algorithms’ performances in the presence of both Gaussian noise and pre-designed pseudo-symmetries. By applying three different computer programs to the same image sets, we also tested the reliability of the programs with respect to subsequent geometric inferences such as Bravais lattice type assignments. Partly due to per design existing pseudo-symmetries of the first kind, the lattice parameters that the utilized computer programs extracted in their default settings disagreed for some of the test images even in the absence of noise, i.e., in the absence of pseudo-symmetries of the second kind, for any reasonable error estimates. For the noisy images, the disagreement of the lattice parameter extraction results from the algorithms was typically more pronounced. Non-default settings and re-interpretations/re-calculations on the basis of program outputs allowed for a reduction (but not a complete elimination) of the differences in the geometric feature extraction results of the three tested algorithms. Our lattice parameter extraction results are, thus, an illustration of Kenichi Kanatani’s dictum that no extraction algorithm for geometric features from images leads to <i>definitive</i> results because they are all aiming at an intrinsically impossible task in all real-world applications (Kanatani in Syst Comput Jpn 35:1–9, 2004). Since 2D-Bravais lattice type assignments are the natural end result of lattice parameter extractions from more or less 2D-periodic images, there is also a section in this paper that describes the intertwined metric relations/holohedral plane and point group symmetry hierarchy of the five translation symmetry types of the Euclidean plane. Because there is no definitive lattice parameter e","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0051-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5090922","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}

{"title":"ASCI: providing a forum for imaging scientists","authors":"Nigel D. Browning","doi":"10.1186/s40679-018-0054-9","DOIUrl":"https://doi.org/10.1186/s40679-018-0054-9","url":null,"abstract":"","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0054-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4733362","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}

{"title":"Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging","authors":"Suhas Somnath,&nbsp;Christopher R. Smith,&nbsp;Sergei V. Kalinin,&nbsp;Miaofang Chi,&nbsp;Albina Borisevich,&nbsp;Nicholas Cross,&nbsp;Gerd Duscher,&nbsp;Stephen Jesse","doi":"10.1186/s40679-018-0052-y","DOIUrl":"https://doi.org/10.1186/s40679-018-0052-y","url":null,"abstract":"<p>We develop an algorithm for feature extraction based on structural similarity and demonstrate its application for atom and pattern finding in high-resolution electron and scanning probe microscopy images. The use of the combined local identifiers formed from an image subset and appended Fourier, or other transform, allows tuning selectivity to specific patterns based on the nature of the recognition task. The proposed algorithm is implemented in Pycroscopy, a community-driven scientific data analysis package, and is accessible through an interactive Jupyter notebook available on GitHub.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0052-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4041838","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}

{"title":"Differentiating the structure of PtNi octahedral nanoparticles through combined ADF–EDX simulations","authors":"Katherine E. MacArthur,&nbsp;Marc Heggen,&nbsp;Rafal E. Dunin-Borkowski","doi":"10.1186/s40679-018-0053-x","DOIUrl":"https://doi.org/10.1186/s40679-018-0053-x","url":null,"abstract":"<p>Advances in catalysis rely on the synthesis and characterisation of nanoparticles that have tailored structures and compositions. Although energy-dispersive X-ray (EDX) spectroscopy can be used to study local variations in the compositions of individual supported nanoparticles on the atomic-scale in the scanning transmission electron microscope, electron beam induced damage and contamination can preclude the use of long exposure times and tomographic approaches. Here, we perform simulations of EDX maps of seven different octahedral PtNi nanoparticles for a selection of crystallographic orientations and tilts, to evaluate which of them can be distinguished from elemental mapping performed in only one orientation.</p>","PeriodicalId":460,"journal":{"name":"Advanced Structural and Chemical Imaging","volume":"4 1","pages":""},"PeriodicalIF":3.56,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40679-018-0053-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4785650","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}