DOI: 10.1186/s40679-017-0042-5. Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting

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

10.1186/s40679-017-0042-5

Crossref journal-article

Springer Science and Business Media LLC

Advanced Structural and Chemical Imaging (297)

Abstract

AbstractScanning 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.

Bibliography

Nord, M., Vullum, P. E., MacLaren, I., Tybell, T., & 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(1).

Authors 5

Magnus Nord (first)
Per Erik Vullum (additional)
Ian MacLaren (additional)
Thomas Tybell (additional)
Randi Holmestad (additional)

References 43 Referenced 224

Krivanek, O.L., Dellby, N., Lupini, A.R.: Towards sub-Å electron beams. Ultramicroscopy 78(1–4), 1–11 (1999) (10.1016/S0304-3991(99)00013-3) / Ultramicroscopy by OL Krivanek (1999)
Falke, U., Bleloch, A., Falke, M., Teichert, S.: Atomic structure of a (2 × 1) reconstructed NiSi$$_2$$/Si(001) interface. Phys. Rev. Lett. 92, 116103 (2004) (10.1103/PhysRevLett.92.116103) / Phys. Rev. Lett. by U Falke (2004)
Lunkenbein, T., Girgsdies, F., Wernbacher, A., Noack, J., Auffermann, G., Yasuhara, A., Klein-Hoffmann, A., Ueda, W., Eichelbaum, M., Trunschke, A., Schlögl, R., Willinger, M.G.: Direct imaging of octahedral distortion in a complex molybdenum vanadium mixed oxide. Angew. Chem. Int. Ed. 54(23), 6828–6831 (2015) (10.1002/anie.201502236) / Angew. Chem. Int. Ed. by T Lunkenbein (2015)
MacLaren, I., Villaurrutia, R., Schaffer, B., Houben, L., Peláiz-Barranco, A.: Atomic-scale imaging and quantification of electrical polarisation in incommensurate antiferroelectric lanthanum-doped lead zirconate titanate. Adv. Func. Mater. 22(2), 261–266 (2012) (10.1002/adfm.201101220) / Adv. Func. Mater. by I MacLaren (2012)
Nord, M., Vullum, P.E., Moreau, M., Boschker, J.E., Selbach, S.M., Holmestad, R., Tybell, T.: Structural phases driven by oxygen vacancies at the La$$_{0.7}$$Sr$$_{0.3}$$MnO$$_{3}$$/SrTiO$$_{3}$$ hetero-interface. Appl. Phys. Lett. 106(4), 041604 (2015) (10.1063/1.4906920) / Appl. Phys. Lett. by M Nord (2015)
Gazquez, J., Bose, S., Sharma, M., Torija, M.A., Pennycook, S .J., Leighton, C.: Lattice mismatch accommodation via oxygen vacancy ordering in epitaxial La$$_{0.5}$$Sr$$_{0.5}$$CoO$$_{3-\delta }$$ thin films. APL. Mater. 1(1), 012105 (2013) (10.1063/1.4809547) / APL. Mater. by J Gazquez (2013)
MacLaren, I., Wang, L.Q., Schaffer, B., Ramasse, Q.M., Craven, A.J., Selbach, S.M., Spaldin, N.A., Miao, S., Kalantari, K., Reaney, I.M.: Novel nanorod precipitate formation in neodymium and titanium codoped bismuth ferrite. Adv. Funct. Mater. 23(6), 683–689 (2013) (10.1002/adfm.201201835) / Adv. Funct. Mater. by I MacLaren (2013)
Borisevich, A.Y., Chang, H.J., Huijben, M., Oxley, M.P., Okamoto, S., Niranjan, M.K., Burton, J.D., Tsymbal, E.Y., Chu, Y.H., Yu, P., Ramesh, R., Kalinin, S.V., Pennycook, S.J.: Suppression of octahedral tilts and associated changes in electronic properties at epitaxial oxide heterostructure interfaces. Phys. Rev. Lett. 105(8), 087204 (2010) (10.1103/PhysRevLett.105.087204) / Phys. Rev. Lett. by AY Borisevich (2010)
Pennycook, S.J., Jesson, D.E.: High-resolution Z-contrast imaging of crystals. Ultramicroscopy 37(1), 14–38 (1991) (10.1016/0304-3991(91)90004-P) / Ultramicroscopy by SJ Pennycook (1991)
LeBeau, J.M., Findlay, S.D., Allen, L.J., Stemmer, S.: Standardless atom counting in scanning transmission electron microscopy. Nano. Lett. 10(11), 4405–4408 (2010) (10.1021/nl102025s) / Nano. Lett. by JM LeBeau (2010)
Muller, D.A., Nakagawa, N., Ohtomo, A., Grazul, J.L., Hwang, H.Y.: Atomic-scale imaging of nanoengineered oxygen vacancy profiles in SrTiO3. Nature 430(7000), 657–661 (2004) (10.1038/nature02756) / Nature by DA Muller (2004)
Hillyard, S., Silcox, J.: Detector geometry, thermal diffuse scattering and strain effects in ADF STEM imaging. Ultramicroscopy 58(1), 6–17 (1995) (10.1016/0304-3991(94)00173-K) / Ultramicroscopy by S Hillyard (1995)
Borisevich, A., Ovchinnikov, O.S., Chang, H.J., Oxley, M.P., Yu, P., Seidel, J., Eliseev, E.A., Morozovska, A.N., Ramesh, R., Pennycook, S.J., Kalinin, S.V.: Mapping octahedral tilts and polarization across a domain wall in BiFeO$$_3$$ from Z-contrast scanning transmission electron microscopy image atomic column shape analysis. ACS. Nano. 4(10), 6071–6079 (2010) (10.1021/nn1011539) / ACS. Nano. by A Borisevich (2010)
Jia, C.L., Lentzen, M., Urban, K.: Atomic-resolution imaging of oxygen in perovskite ceramics. Science 299(5608), 870–873 (2003) (10.1126/science.1079121) / Science by CL Jia (2003)
LeBeau, J.M., D’Alfonso, A.J., Findlay, S.D., Stemmer, S., Allen, L.J.: Quantitative comparisons of contrast in experimental and simulated bright-field scanning transmission electron microscopy images. Phys. Rev. B 80, 174106 (2009) (10.1103/PhysRevB.80.174106) / Phys. Rev. B by JM LeBeau (2009)
MacLaren, I., Wang, L., Morris, O., Craven, A.J., Stamps, R.L., Schaffer, B., Ramasse, Q.M., Miao, S., Kalantari, K., Sterianou, I., Reaney, I.M.: Local stabilisation of polar order at charged antiphase boundaries in antiferroelectric (Bi$$_{0.85}$$Nd$$_{0.15}$$)(Ti$$_{0.1}$$Fe$$_{0.9}$$)O$$_3$$. APL. Mater. 1(2), 021102 (2013) (10.1063/1.4818002) / APL. Mater. by I MacLaren (2013)
Findlay, S.D., Shibata, N., Sawada, H., Okunishi, E., Kondo, Y., Ikuhara, Y.: Dynamics of annular bright field imaging in scanning transmission electron microscopy. Ultramicroscopy 110(7), 903–923 (2010) (10.1016/j.ultramic.2010.04.004) / Ultramicroscopy by SD Findlay (2010)
Aso, R., Kan, D., Shimakawa, Y., Kurata, H.: Octahedral tilt propagation controlled by A-site cation size at perovskite oxide heterointerfaces. Cryst. Growth. Des. 14(5), 2128–2132 (2014) (10.1021/cg500285m) / Cryst. Growth. Des. by R Aso (2014)
He, Q., Ishikawa, R., Lupini, A.R., Qiao, L., Moon, E.J., Ovchinnikov, O., May, S.J., Biegalski, M.D., Borisevich, A.Y.: Towards 3D mapping of BO6 octahedron rotations at perovskite heterointerfaces, unit cell by unit cell. ACS. Nano. 9(8), 8412–8419 (2015) (10.1021/acsnano.5b03232) / ACS. Nano. by Q He (2015)
Glazer, A.M.: The classification of tilted octahedra in perovskites. Acta. Crystallogr. Sect. B. 28(11), 3384–3392 (1972) (10.1107/S0567740872007976) / Acta. Crystallogr. Sect. B. by AM Glazer (1972)
Hÿtch, M .J., Snoeck, E., Kilaas, R.: Quantitative measurement of displacement and strain fields from HREM micrographs. Ultramicroscopy 74(3), 131–146 (1998) (10.1016/S0304-3991(98)00035-7) / Ultramicroscopy by M J H++tch (1998)
Martin, J., Putaux, J.L., Pénisson, J.M.: Measurement of the displacement field of dislocations to 0.03 Å by electron microscopy. Nature 423(6937), 270–273 (2003) (10.1038/nature01638) / Nature by J Martin (2003)
Zhu, Y., Ophus, C., Ciston, J., Wang, H.: Interface lattice displacement measurement to 1 pm by geometric phase analysis on aberration-corrected HAADF STEM images. Acta. Mater. 61(15), 5646–5663 (2013) (10.1016/j.actamat.2013.06.006) / Acta. Mater. by Y Zhu (2013)
Jonathan, J.P., et al.: Artefacts in geometric phase analysis of compound materials. Ultramicroscopy 157, 91–97 (2015) (10.1016/j.ultramic.2015.05.020) / Ultramicroscopy by JP Jonathan (2015)
Anthony, S.M., Granick, S.: Image analysis with rapid and accurate two-dimensional Gaussian fitting. Langmuir 25(14), 8152–8160 (2009) (10.1021/la900393v) / Langmuir by SM Anthony (2009)
Jones, L., Nellist, P.D.: Identifying and correcting scan noise and drift in the scanning transmission electron microscope. Microsc. Microanal. 19(04), 1050 (2013) (10.1017/S1431927613001402) / Microsc. Microanal. by L Jones (2013)
Galindo, P.L., Kret, S., Sanchez, A.M., Laval, J.Y., Yáñez, A., Pizarro, J., Guerrero, E., Ben, T., Molina, S.: The peak pairs algorithm for strain mapping from HRTEM images. Ultramicroscopy 107(12), 1186–1193 (2007) (10.1016/j.ultramic.2007.01.019) / Ultramicroscopy by PL Galindo (2007)
Imtools. http://www.er-c.org/centre/software/imtools.htm. 2016. Accessed 1 Sept 2016
De Backer, A., van den Bos, K.H.W., Van den Broek, W., Sijbers, J., Van Aert, S.: StatSTEM: an efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images. Ultramicroscopy 171, 104–116 (2016) (10.1016/j.ultramic.2016.08.018) / Ultramicroscopy by A De Backer (2016)
Wang, Y., Salzberger, U., Sigle, W., Suyolcu, Y.E., van Aken, P.A.: Oxygen octahedra picker: a software tool to extract quantitative information from STEM images. Ultramicroscopy. 168, 46–52 (2016) (10.1016/j.ultramic.2016.06.001) / Ultramicroscopy. by Y Wang (2016)
Zuo, J.M., Shah, A.B., Kim, H., Meng, Y., Gao, W.: Lattice and strain analysis of atomic resolution Z-contrast images based on template matching. Ultramicroscopy. 136, 50–60 (2014) (10.1016/j.ultramic.2013.07.018) / Ultramicroscopy. by JM Zuo (2014)
Houben, L., Thust, A., Urban, K.: Atomic-precision determination of the reconstruction of a tilt boundary in by aberration corrected HRTEM. Ultramicroscopy 106(3), 200–214 (2006) (10.1016/j.ultramic.2005.07.009) / Ultramicroscopy by L Houben (2006)
Laanait, N., Ziatdinov, M., He, Q., Borisevich, A.: Identifying local structural states in atomic imaging by computer vision. Adv. Struc. Chem. Imag. 2(1), 14 (2016) (10.1186/s40679-016-0028-8) / Adv. Struc. Chem. Imag. by N Laanait (2016)
Barnes, N.: Publish your computer code: it is good enough. Nature 467(7317), 753–753 (2010) (10.1038/467753a) / Nature by N Barnes (2010)
Hallsteinsen, I., Boschker, J.E., Nord, M., Lee, S., Rzchowski, M., Vullum, P.E., Grepstad, J.K., Holmestad, R., Eom, C.B., Tybell, T.: Surface stability of epitaxial La0.7 Sr0.3 MnO3 thin films on (111)-oriented SrTiO3. J. Appl. Phys. 113(18), 183512 (2013) (10.1063/1.4804312) / J. Appl. Phys. by I Hallsteinsen (2013)
Hallsteinsen, I., Nord, M., Bolstad, T., Vullum, P., Boschker, J.E., Longo, P., Takahashi, R., Holmestad, R., Lippmaa, M., Tybell, T.: Effect of polar (111)-oriented SrTiO$$_3$$ on initial perovskite growth. Cryst. Growth. Des. 16(4), 2357–2362 (2016) (10.1021/acs.cgd.6b00143) / Cryst. Growth. Des. by I Hallsteinsen (2016)
Nord, M., Vullum, P.E., Hallsteinsen, I., Tybell, T., Holmestad, R.: Assessing electron beam sensitivity for SrTiO3 and La0.7 Sr0.3 MnO3 using electron energy loss spectroscopy. Ultramicroscopy. 169, 98–106 (2016) (10.1016/j.ultramic.2016.07.004) / Ultramicroscopy. by M Nord (2016)
Lichtert, S., Verbeeck, J.: Statistical consequences of applying a PCA noise filter on EELS spectrum images. Ultramicroscopy 125, 35–42 (2013) (10.1016/j.ultramic.2012.10.001) / Ultramicroscopy by S Lichtert (2013)
de la Peña, F., Burdet, P., Fauske, V.T., Ostasevicius, T., Sarahan, M., Nord, M., Taillon, J., Johnstone, D., Eljarrat, A., Mazzucco, S., Caron, J., Prestat, E., Donval, G., Zagonel, L.F., Walls, M., and iygr. hyperspy: HyperSpy 0.8.4. (2016)
Muller, D.A., Kirkland, E.J., Thomas, M.G., Grazul, J.L., Fitting, L., Weyland, M.: Room design for high-performance electron microscopy. Ultramicroscopy 106(11–12), 1033–1040 (2006) (10.1016/j.ultramic.2006.04.017) / Ultramicroscopy by DA Muller (2006)
Berkels, B., Binev, P., Blom, D.A., Dahmen, W., Sharpley, R.C., Vogt, T.: Optimized imaging using non-rigid registration. Ultramicroscopy 138, 46–56 (2014) (10.1016/j.ultramic.2013.11.007) / Ultramicroscopy by B Berkels (2014)
Jones, L., Yang, H., Pennycook, T.J., Marshall, M.S., Aert, S., Browning, N.D., Castell, M.R., Nellist, P.D.: Smart Align a new tool for robust non-rigid registration of scanning microscope data. Adv. Struct. Chem. Imag. 1(1), 8 (2015) (10.1186/s40679-015-0008-4) / Adv. Struct. Chem. Imag. by L Jones (2015)
Zhou, D., Müller-Caspary, K., Sigle, W., Krause, F.F., Rosenauer, A., van Aken, P.A.: Sample tilt effects on atom column position determination in ABF STEM imaging. Ultramicroscopy 160, 110–117 (2016) (10.1016/j.ultramic.2015.10.008) / Ultramicroscopy by D Zhou (2016)

Dates

Type	When
Created	8 years, 6 months ago (Feb. 13, 2017, 8:19 a.m.)
Deposited	4 years ago (July 30, 2021, 4:09 a.m.)
Indexed	1 day, 16 hours ago (Aug. 19, 2025, 6:28 a.m.)
Issued	8 years, 6 months ago (Feb. 13, 2017)
Published	8 years, 6 months ago (Feb. 13, 2017)
Published Online	8 years, 6 months ago (Feb. 13, 2017)
Published Print	7 years, 8 months ago (Dec. 1, 2017)

Funders 2

Norges Forskningsråd 10.13039/501100005416
Region: Europe
gov (National government)
Labels3
1. Forskningsrådet
2. Norwegian Research Council
3. Research Council of Norway
Awards2
1. 190086/S10
2. 197413/V30
Norges Forskningsråd 10.13039/501100005416
Region: Europe
gov (National government)
Labels3
1. Forskningsrådet
2. Norwegian Research Council
3. Research Council of Norway
Awards1
1. 197405

BibTeX

@article{Nord_2017, title={Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting}, volume={3}, ISSN={2198-0926}, url={http://dx.doi.org/10.1186/s40679-017-0042-5}, DOI={10.1186/s40679-017-0042-5}, number={1}, journal={Advanced Structural and Chemical Imaging}, publisher={Springer Science and Business Media LLC}, author={Nord, Magnus and Vullum, Per Erik and MacLaren, Ian and Tybell, Thomas and Holmestad, Randi}, year={2017}, month=feb }

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