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

Magnus Nord,Ian Maclaren,Per Erik Vullum,Thomas Tybell,Randi Holmestad

doi:10.1186/s40679-017-0042-5

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.

Highlights

Scanning transmission electron microscopy (STEM) together with correction of geometric aberrations in the probe forming optics allows routine acquisition of atomic resolution images with sub-Å resolutions [1, 2]
A better approach is to perform rigid registration to remove the effects of drift, followed by non-rigid registration to remove the effects of short period instabilities in the scanning system [41, 42]
To investigate the effect of short acquisition and alignment, as opposed to recording a single scan at a longer dwell time, we analysed two different STEM-annular dark field (ADF) images from the same session taken along the [110] cubic direction of a sample of STO: (i) acquired as a single image using a pixel dwell time of 38.5 μs with the image shown in Fig. 3a. (ii) Acquired as an image stack of 20 images with dwell time of 2 μs per pixel which is processed using Smart Align [42]

Summary

Introduction

Scanning transmission electron microscopy (STEM) together with correction of geometric aberrations in the probe forming optics allows routine acquisition of atomic resolution images with sub-Å resolutions [1, 2]. We present Atomap, a new free and open source software package for automatic analysis of the position and shape of atomic columns in STEM-images.

Results

Conclusion