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

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.

[1]  David A Muller,et al.  Room design for high-performance electron microscopy. , 2006, Ultramicroscopy.

[2]  W. Sigle,et al.  Oxygen octahedra picker: A software tool to extract quantitative information from STEM images. , 2016, Ultramicroscopy.

[3]  Sergei V. Kalinin,et al.  Mapping octahedral tilts and polarization across a domain wall in BiFeO3 from Z-contrast scanning transmission electron microscopy image atomic column shape analysis. , 2010, ACS nano.

[4]  J Sijbers,et al.  StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images. , 2016, Ultramicroscopy.

[5]  Lewys Jones,et al.  Smart Align—a new tool for robust non-rigid registration of scanning microscope data , 2015, Advanced Structural and Chemical Imaging.

[6]  R. Takahashi,et al.  Effect of Polar (111)-Oriented SrTiO3 on Initial Perovskite Growth , 2016 .

[7]  D. Revin,et al.  Artefacts in geometric phase analysis of compound materials. , 2015, Ultramicroscopy.

[8]  P. Vullum,et al.  Assessing electron beam sensitivity for SrTiO3 and La0.7Sr0.3MnO3 using electron energy loss spectroscopy. , 2016, Ultramicroscopy.

[9]  S. Pennycook,et al.  Lattice mismatch accommodation via oxygen vacancy ordering in epitaxial La 0.5 Sr 0.5 CoO 3-δ thin films , 2013 .

[10]  Dan Zhou,et al.  Sample Tilt Effects on Atom Column Position Determination in ABF-STEM Imaging , 2016, Microscopy and Microanalysis.

[11]  Lewys Jones,et al.  Identifying and Correcting Scan Noise and Drift in the Scanning Transmission Electron Microscope , 2013, Microscopy and Microanalysis.

[12]  Andrés Yáñez,et al.  The Peak Pairs algorithm for strain mapping from HRTEM images. , 2007, Ultramicroscopy.

[13]  Stijn Lichtert,et al.  Statistical consequences of applying a PCA noise filter on EELS spectrum images. , 2013, Ultramicroscopy.

[14]  Martin Hÿtch,et al.  Quantitative measurement of displacement and strain fields from HREM micrographs , 1998 .

[15]  J D Burton,et al.  Suppression of octahedral tilts and associated changes in electronic properties at epitaxial oxide heterostructure interfaces. , 2010, Physical review letters.

[16]  Jian-Min Zuo,et al.  Lattice and strain analysis of atomic resolution Z-contrast images based on template matching. , 2014, Ultramicroscopy.

[17]  A. Peláiz‐Barranco,et al.  Atomic‐Scale Imaging and Quantification of Electrical Polarisation in Incommensurate Antiferroelectric Lanthanum‐Doped Lead Zirconate Titanate , 2012 .

[18]  Q. Ramasse,et al.  Local stabilisation of polar order at charged antiphase boundaries in antiferroelectric (Bi0.85Nd0.15)(Ti0.1Fe0.9)O3 , 2013 .

[19]  Haiyan Wang,et al.  Interface lattice displacement measurement to 1 pm by geometric phase analysis on aberration-corrected HAADF STEM images , 2013 .

[20]  Liang Qiao,et al.  Towards 3D Mapping of BO6 Octahedron Rotations at Perovskite Heterointerfaces, Unit Cell by Unit Cell. , 2015, ACS nano.

[21]  Wolfgang Dahmen,et al.  Optimized imaging using non-rigid registration , 2014, Ultramicroscopy.

[22]  J. Silcox,et al.  Detector geometry, thermal diffuse scattering and strain effects in ADF STEM imaging , 1995 .

[23]  H. Kurata,et al.  Octahedral tilt propagation controlled by A-site cation size at perovskite oxide heterointerfaces , 2014 .

[24]  Ondrej L. Krivanek,et al.  Towards sub-Å electron beams , 1999 .

[25]  Maxim Ziatdinov,et al.  Identifying local structural states in atomic imaging by computer vision , 2016, Advanced Structural and Chemical Imaging.

[26]  C. Eom,et al.  Surface stability of epitaxial La0.7Sr0.3MnO3 thin films on (111)-oriented SrTiO3 , 2013 .

[27]  A. M. Glazer,et al.  The classification of tilted octahedra in perovskites , 1972 .

[28]  A. J. D’Alfonso,et al.  Quantitative comparisons of contrast in experimental and simulated bright-field scanning transmission electron microscopy images , 2009 .

[29]  Akira Ohtomo,et al.  Atomic-scale imaging of nanoengineered oxygen vacancy profiles in SrTiO3 , 2004, Nature.

[30]  P. Vullum,et al.  Structural phases driven by oxygen vacancies at the La0.7Sr0.3MnO3/SrTiO3 hetero-interface , 2015 .

[31]  M. Hÿtch,et al.  Measurement of the displacement field of dislocations to 0.03 Å by electron microscopy , 2003, Nature.

[32]  Nick Barnes.  Publish your computer code: it is good enough , 2010, Nature.

[33]  A. Bleloch,et al.  Atomic structure of a (2 x 1) reconstructed NiSi2/Si(001) interface. , 2004, Physical review letters.

[34]  Q. Ramasse,et al.  Novel Nanorod Precipitate Formation in Neodymium and Titanium Codoped Bismuth Ferrite , 2013 .

[35]  M. Willinger,et al.  Direct imaging of octahedral distortion in a complex molybdenum vanadium mixed oxide. , 2015, Angewandte Chemie.

[36]  Susanne Stemmer,et al.  Standardless atom counting in scanning transmission electron microscopy. , 2010, Nano letters.

[37]  Stephen J. Pennycook,et al.  High-resolution Z-contrast imaging of crystals , 1991 .

[38]  N. Shibata,et al.  Dynamics of annular bright field imaging in scanning transmission electron microscopy. , 2010, Ultramicroscopy.

[39]  Steve Granick,et al.  Image analysis with rapid and accurate two-dimensional Gaussian fitting. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[40]  L. Houben,et al.  Atomic-precision determination of the reconstruction of a 90 degree tilt boundary in YBa2Cu3O7-delta by aberration corrected HRTEM. , 2006, Ultramicroscopy.

[41]  C. L. Jia,et al.  Atomic-Resolution Imaging of Oxygen in Perovskite Ceramics , 2003, Science.