StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images

A De Backer; K H W van den Bos; W Van den Broek; J Sijbers; S Van Aert

doi:10.1016/j.ultramic.2016.08.018

StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images

Ultramicroscopy. 2016 Dec:171:104-116. doi: 10.1016/j.ultramic.2016.08.018. Epub 2016 Aug 31.

Authors

A De Backer¹, K H W van den Bos¹, W Van den Broek², J Sijbers³, S Van Aert⁴

Affiliations

¹ Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
² AG Strukturforschung/Elektronenmikroskopie, Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, 12489 Berlin, Germany.
³ iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium.
⁴ Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be.

PMID: 27657649
DOI: 10.1016/j.ultramic.2016.08.018

Abstract

An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.

Keywords: Dataprocessing/image processing; General methods in microscopy; High-resolution (scanning) transmission electron microscopy (HR (S)TEM); Model-based fitting; Quantitative electron microscopy; Statistical parameter estimation theory; Tools.