Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting

Nord, M., Vullum, P. E., MacLaren, I. , Tybell, T. and Holmestad, R. (2017) Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting. Advanced Structural and Chemical Imaging, 3, 9. (doi:10.1186/s40679-017-0042-5)

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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.

Item Type:Articles
Additional Information:Funding: The Research Council of Norway (RCN) is acknowledged for the support to the Norwegian Micro- and Nano-Fabrication Facility, NorFab (197413/V30). Partial funding for this work was obtained from the Norwegian PhD Network on Nanotechnology for Microsystems, which is sponsored by the RCN, Division for Science, under Contract No. 190086/S10. Funding for TEM time is partly funded by the project NORTEM (Grant 197405) within the program INFRASTRUCTURE of the RCN. NORTEM was co-funded by the RCN and the project partners NTNU, UiO and SINTEF.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:MacLaren, Dr Ian and Nord, Dr Magnus
Authors: Nord, M., Vullum, P. E., MacLaren, I., Tybell, T., and Holmestad, R.
College/School:College of Science and Engineering > School of Physics and Astronomy
Journal Name:Advanced Structural and Chemical Imaging
Publisher:Springer
ISSN:2198-0926
ISSN (Online):2198-0926
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Advanced Structural and Chemical Imaging 3: 9
Publisher Policy:Reproduced under a Creative Commons License

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