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Bárcena-González G, Guerrero-Lebrero MDLP, Guerrero E, Yañez A, Nuñez-Moraleda B, Fernández-Reyes D, Real P, González D, Galindo PL. CDrift: An Algorithm to Correct Linear Drift From A Single High-Resolution STEM Image. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:913-920. [PMID: 32703333 DOI: 10.1017/s1431927620001774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work, a new method to determine and correct the linear drift for any crystalline orientation in a single-column-resolved high-resolution scanning transmission electron microscopy (HR-STEM) image, which is based on angle measurements in the Fourier space, is presented. This proposal supposes a generalization and the improvement of a previous work that needs the presence of two symmetrical planes in the crystalline orientation to be applicable. Now, a mathematical derivation of the drift effect on two families of asymmetric planes in the reciprocal space is inferred. However, though it was not possible to find an analytical solution for all conditions, a simple formula was derived to calculate the drift effect that is exact for three specific rotation angles. Taking this into account, an iterative algorithm based on successive rotation/drift correction steps is devised to remove drift distortions in HR-STEM images. The procedure has been evaluated using a simulated micrograph of a monoclinic material in an orientation where all the reciprocal lattice vectors are different. The algorithm only needs four iterations to resolve a 15° drift angle in the image.
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Affiliation(s)
| | | | - Elisa Guerrero
- Department of Computer Science and Engineering, University of Cádiz, Puerto Real, Cádiz, Spain
| | - Andres Yañez
- Department of Computer Science and Engineering, University of Cádiz, Puerto Real, Cádiz, Spain
| | - Bernardo Nuñez-Moraleda
- Department of Computer Science and Engineering, University of Cádiz, Puerto Real, Cádiz, Spain
| | - Daniel Fernández-Reyes
- Department of Material Science and Metallurgy Engineering and Inorganic Chemistry, University of Cádiz, Puerto Real, Cádiz, Spain
| | - Pedro Real
- Department of Applied Mathematics I, University of Seville, Seville, Spain
| | - David González
- Department of Material Science and Metallurgy Engineering and Inorganic Chemistry, University of Cádiz, Puerto Real, Cádiz, Spain
| | - Pedro L Galindo
- Department of Computer Science and Engineering, University of Cádiz, Puerto Real, Cádiz, Spain
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Evaluation of different rectangular scan strategies for STEM imaging. Ultramicroscopy 2020; 215:113021. [PMID: 32485392 DOI: 10.1016/j.ultramic.2020.113021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 11/24/2022]
Abstract
STEM imaging is typically performed by raster scanning a focused electron probe over a sample. Here we investigate and compare three different scan patterns, making use of a programmable scan engine that allows to arbitrarily set the sequence of probe positions that are consecutively visited on the sample. We compare the typical raster scan with a so-called 'snake' pattern where the scan direction is reversed after each row and a novel Hilbert scan pattern that changes scan direction rapidly and provides an homogeneous treatment of both scan directions. We experimentally evaluate the imaging performance on a single crystal test sample by varying dwell time and evaluating behaviour with respect to sample drift. We demonstrate the ability of the Hilbert scan pattern to more faithfully represent the high frequency content of the image in the presence of sample drift. It is also shown that Hilbert scanning provides reduced bias when measuring lattice parameters from the obtained scanned images while maintaining similar precision in both scan directions which is especially important when e.g. performing strain analysis. Compared to raster scanning with flyback correction, both snake and Hilbert scanning benefit from dose reduction as only small probe movement steps occur.
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Bárcena-González G, Guerrero-Lebrero MP, Guerrero E, Yañez A, Nuñez-Moraleda B, Kepaptsoglou D, Lazarov VK, Galindo PL. HAADF-STEM Image Resolution Enhancement Using High-Quality Image Reconstruction Techniques: Case of the Fe 3O 4(111) Surface. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2019; 25:1297-1303. [PMID: 31407642 DOI: 10.1017/s1431927619014788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
From simple averaging to more sophisticated registration and restoration strategies, such as super-resolution (SR), there exist different computational techniques that use a series of images of the same object to generate enhanced images where noise and other distortions have been reduced. In this work, we provide qualitative and quantitative measurements of this enhancement for high-angle annular dark-field scanning transmission electron microscopy imaging. These images are compared in two ways, qualitatively through visual inspection in real and reciprocal space, and quantitatively, through the calculation of objective measurements, such as signal-to-noise ratio and atom column roundness. Results show that these techniques improve the quality of the images. In this paper, we use an SR methodology that allows us to take advantage of the information present in the image frames and to reliably facilitate the analysis of more difficult regions of interest in experimental images, such as surfaces and interfaces. By acquiring a series of cross-sectional experimental images of magnetite (Fe3O4) thin films (111), we have generated interpolated images using averaging and SR, and reconstructed the atomic structure of the very top surface layer that consists of a full monolayer of Fe, with topmost Fe atoms in tetrahedrally coordinated sites.
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Affiliation(s)
- G Bárcena-González
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - M P Guerrero-Lebrero
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - E Guerrero
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - A Yañez
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - B Nuñez-Moraleda
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
| | - D Kepaptsoglou
- Department of Physics, University of York, Heslington, York, UK
- SuperSTEM Laboratory, SciTech Daresbury Campus, Daresbury WA4 4AD, UK
| | - V K Lazarov
- Department of Physics, University of York, Heslington, York, UK
| | - P L Galindo
- Department of Computer Science and Engineering, Universidad de Cádiz, 11510 Puerto Real, Spain
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Bárcena-González G, Guerrero-Lebrero M, Guerrero E, Reyes D, Braza V, Yañez A, Nuñez-Moraleda B, González D, Galindo P. Correcting sample drift using Fourier harmonics. Micron 2018; 110:18-27. [DOI: 10.1016/j.micron.2018.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022]
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Bárcena-González G, Guerrero-Lebrero MP, Guerrero E, Yañez A, Fernández-Reyes D, González D, Galindo PL. Evaluation of high-quality image reconstruction techniques applied to high-resolution Z-contrast imaging. Ultramicroscopy 2017; 182:283-291. [PMID: 28783580 DOI: 10.1016/j.ultramic.2017.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/11/2017] [Accepted: 07/25/2017] [Indexed: 10/19/2022]
Abstract
High-quality image reconstruction techniques allow the generation of high pixel density images from a set of low-resolution micrographs. In general, these techniques consist of two main steps, namely, accurate registration, and formulation of an appropriate forward image model via some restoration method. There exist a wide variety of algorithms to cope with both stages and depending on their practical applications, some methods can outperform others, since they can be sensitive to the assumed data model, noise, drift, etc. When dealing with images generated by Z-contrast scanning transmission electron microscopes, a current trend is based on non-rigid approximations in the registration stage. In our work we aimed at reaching similar accuracy but addressing the most complex calculations in the reconstruction stage, instead of in the registration stage (as the non-rigid approaches do), but using a much smaller number of images. We review some of the most significant methods and address their shortcomings when they are applied to the field of microscopy. Simulated images with known targets will be used to evaluate and compare the main approaches in terms of quality enhancement and computing time. In addition, a procedure to determine the reference image will be proposed to minimise the global drift on the series. The best registration and restoration strategies will be applied to experimental images in order to point up the enhanced capability of this high quality image reconstruction methodology in this field.
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Affiliation(s)
- G Bárcena-González
- Department of Computer Science and Engineering, University of Cádiz, Spain.
| | | | - E Guerrero
- Department of Computer Science and Engineering, University of Cádiz, Spain
| | - A Yañez
- Department of Computer Science and Engineering, University of Cádiz, Spain
| | - D Fernández-Reyes
- Department of Material Science and Metallurgy Engineering and Inorganic Chemistry, University of Cádiz, Spain
| | - D González
- Department of Material Science and Metallurgy Engineering and Inorganic Chemistry, University of Cádiz, Spain
| | - P L Galindo
- Department of Computer Science and Engineering, University of Cádiz, Spain
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Cheng S, Li J, Han MG, Deng S, Tan G, Zhang X, Zhu J, Zhu Y. Topologically Allowed Nonsixfold Vortices in a Sixfold Multiferroic Material: Observation and Classification. PHYSICAL REVIEW LETTERS 2017; 118:145501. [PMID: 28430510 DOI: 10.1103/physrevlett.118.145501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 06/07/2023]
Abstract
We report structural transformation of sixfold vortex domains into two-, four-, and eightfold vortices via a different type of topological defect in hexagonal manganites. Combining high-resolution electron microscopy and Landau-theory-based numerical simulations, we investigate the remarkable atomic arrangement and the intertwined relationship between the vortex structures and the topological defects. The roles of their displacement field, formation temperature, and nucleation sites are revealed. All conceivable vortices in the system are topologically classified using homotopy group theory, and their origins are identified.
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Affiliation(s)
- Shaobo Cheng
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, People's Republic of China
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Jun Li
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal 239955, Saudi Arabia
| | - Myung-Geun Han
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Shiqing Deng
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Guotai Tan
- Department of Physics, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Xixiang Zhang
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal 239955, Saudi Arabia
| | - Jing Zhu
- School of Materials Science and Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yimei Zhu
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, USA
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