title: Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting.
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.
authors.affiliation: Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.|SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow, UK.
authors.forename: Magnus
authors.identifier: 0000-0001-7981-5293
authors.initials: M
authors.lastname: Nord
authors.affiliation: Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.|Materials and Chemistry, SINTEF, Trondheim, Norway.
authors.forename: Per Erik
authors.initials: PE
authors.lastname: Vullum
authors.affiliation: SUPA, School of Physics and Astronomy, University of Glasgow, Glasgow, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: MacLaren
authors.affiliation: Department of Electronics and Telecommunications, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Thomas
authors.initials: T
authors.lastname: Tybell
authors.affiliation: Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Randi
authors.initials: R
authors.lastname: Holmestad
keywords: Image processing; Non-rigid registration; Oxygen octahedral distortion; Quantitative STEM; Strain mapping