Hostname: page-component-586b7cd67f-gb8f7 Total loading time: 0 Render date: 2024-11-25T17:00:13.621Z Has data issue: false hasContentIssue false
  • English
  • Français

TopoTEM: A Python Package for Quantifying and Visualizing Scanning Transmission Electron Microscopy Data of Polar Topologies

Published online by Cambridge University Press:  23 March 2022

Eoghan N. O'Connell ,
Kalani Moore ,
Elora McFall ,
Michael Hennessy Open the ORCID record for Michael Hennessy [Opens in a new window] ,
Eoin Moynihan ,
Ursel Bangert  and
Michele Conroy Open the ORCID record for Michele Conroy [Opens in a new window]
Eoghan N. O'Connell
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Kalani Moore
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Elora McFall
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Michael Hennessy
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Eoin Moynihan
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Ursel Bangert
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
Michele Conroy*
Affiliation:
Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland Department of Materials, Faculty of Engineering, London Centre of Nanotechnology, Imperial College London, London, UK
*
*Corresponding author: Michele Conroy, E-mail: [email protected]
Get access

Abstract

The exotic internal structure of polar topologies in multiferroic materials offers a rich landscape for materials science research. As the spatial scale of these entities is often subatomic in nature, aberration-corrected transmission electron microscopy (TEM) is the ideal characterization technique. Software to quantify and visualize the slight shifts in atomic placement within unit cells is of paramount importance due to the now routine acquisition of images at such resolution. In the previous ~decade since the commercialization of aberration-corrected TEM, many research groups have written their own code to visualize these polar entities. More recently, open-access Python packages have been developed for the purpose of TEM atomic position quantification. Building on these packages, we introduce the TEMUL Toolkit: a Python package for analysis and visualization of atomic resolution images. Here, we focus specifically on the TopoTEM module of the toolkit where we show an easy to follow, streamlined version of calculating the atomic displacements relative to the surrounding lattice and thus plotting polarization. We hope this toolkit will benefit the rapidly expanding field of topology-based nano-electronic and quantum materials research, and we invite the electron microscopy community to contribute to this open-access project.

Keywords

open sourcepolarizationpythonSTEMtopology
Type
Software and Instrumentation
Information
Microscopy and Microanalysis , Volume 28 , Issue 4 , August 2022 , pp. 1444 - 1452
Check for updates
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of the Microscopy Society of America

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

Current address: Max-Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany.

References

Borisevich, A, Ovchinnikov, OS, Chang, HJ, Oxley, MP, Yu, P, Seidel, J, Eliseev EA, Morozovska AN, Ramesh R, Pennycook SJ, & Kalinin, SV (2010). Mapping octahedral tilts and polarization across a domain wall in BiFeO3 from Z-contrast scanning transmission electron microscopy image atomic column shape analysis. ACS Nano 4(10), 6071–6079. doi:10.1021/nn1011539CrossRefGoogle ScholarPubMed
Catalan, G, Lubk, A, Vlooswijk, AHG, Snoeck, E, Magen, C, Janssens, A, Rispens G, Rijnders G, Blank DH & Noheda, B (2011). Flexoelectric rotation of polarization in ferroelectric thin films. Nat Mater 10(12), 963–967. doi:10.1038/nmat3141CrossRefGoogle ScholarPubMed
Chen, Z, Jiang, Y, Shao, Y-T, Holtz, ME, Odstrčil, M, Guizar-Sicairos, M Hanke I, Ganschow S, Schlom DG & Muller, DA (2021). Electron ptychography achieves atomic-resolution limits set by lattice vibrations. Science 372(6544), 826. doi:10.1126/science.abg2533CrossRefGoogle ScholarPubMed
Choi, KJ, Biegalski, M, Li, YL, Sharan, A, Schubert, J, Uecker, R Reiche P, Chen YB, Pan XQ, Gopalan V, Chen LQ, Schlom DG & Eom CB (2004). Enhancement of ferroelectricity in strained BaTiO3 thin films. Science 306(5698), 1005. doi:10.1126/science.1103218CrossRefGoogle ScholarPubMed
Conroy, M, Moore, K, O'Connell, E, Jones, L, Downing, C, Whatmore, R, Gruverman A, Gregg M & Bangert, U (2020). Probing the dynamics of topologically protected charged ferroelectric domain walls with the electron beam at the atomic scale. Microsc Microanal 1–4. doi:10.1017/S1431927620023594Google Scholar
Das, S, Tang, YL, Hong, Z, Gonçalves, MAP, McCarter, MR, Klewe C, Nguyen KX, Gómez-Ortiz F, Shafer P, Arenholz E, Stoica VA, Hsu SL, Wang B, Ophus C, Liu JF, Nelson CT, Saremi S, Prasad B, Mei AB, Schlom, DG, Íñiguez J, García-Fernández P, Muller DA, Chen LQ, Junquera J, Martin LW & Ramesh R (2019). Observation of room-temperature polar skyrmions. Nature 568(7752), 368–372. doi:10.1038/s41586-019-1092-8CrossRefGoogle ScholarPubMed
de la Peña, F, Prestat, E, Tonaas Fauske, V, Burdet, P, Furnival, T, Jokubauskas, P & Donval, G (2021). Hyperspy/Hyperspy: Release v1.6.2. doi:10.5281/ZENODO.4683076.CrossRefGoogle Scholar
Dowty, E & Clark, JR (1972). Atomic displacements in ferroelectric trigonal and orthorhombic boracite structures. Solid State Commun 10(6), 543–548. doi:10.1016/0038-1098(72)90063-4CrossRefGoogle Scholar
Gonnissen, J, Batuk, D, Nataf, GF, Jones, L, Abakumov, AM, Van Aert, S, Schryvers, D & Salje, Ekh (2016). Direct observation of ferroelectric domain walls in LiNbO3: Wall-meanders, kinks, and local electric charges. Advanced Functional Materials 26(42), 7599–7604. doi:10.1002/adfm.201603489.CrossRefGoogle Scholar
Hadjimichael, M, Li, Y, Zatterin, E, Chahine, GA, Conroy, M, Moore, K, Hlinka, J, Bangert U, Leake S, & Zubko, P (2021). Metal–ferroelectric supercrystals with periodically curved metallic layers. Nat Mater 20(4), 495–502. doi:10.1038/s41563-020-00864-6CrossRefGoogle ScholarPubMed
Haeni, JH, Irvin, P, Chang, W, Uecker, R, Reiche, P, Li, YL, Choudhury S, Tian W, Hawley ME & Craigo, B (2004). Room-temperature ferroelectricity in strained SrTiO3. Nature 430(7001), 758.CrossRefGoogle ScholarPubMed
Hong, Z, Das, S, Nelson, C, Yadav, A, Wu, Y, Junquera, J, Chen LQ, Martin, LM & Ramesh, R (2021). Vortex domain walls in ferroelectrics. Nano Lett 21(8), 3533–3539. doi:10.1021/acs.nanolett.1c00404CrossRefGoogle ScholarPubMed
Hunter, John D (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering 9(3), 90–95. doi: 10.1109/MCSE.2007.55.CrossRefGoogle Scholar
Hÿtch, M, Snoeck, E & Kilaas, R (1998). Quantitative measurement of displacement and strain fields from HREM micrographs. Ultramicroscopy 74, 131. doi:10.1016/S0304-3991(98)00035-7CrossRefGoogle Scholar
Jia, C-L, Mi, S-B, Urban, K, Vrejoiu, I, Alexe, M & Hesse, D (2008). Atomic-scale study of electric dipoles near charged and uncharged domain walls in ferroelectric films. Nat Mater 7(1), 57–61. doi:10.1038/nmat2080CrossRefGoogle ScholarPubMed
Jia, C-L, Urban, KW, Alexe, M, Hesse, D & Vrejoiu, I (2011). Direct observation of continuous electric dipole rotation in flux-closure domains in ferroelectric Pb(Zr,Ti)O3. Science 331(6023), 1420. doi:10.1126/science.1200605CrossRefGoogle Scholar
Ji, D, Cai, S, Paudel, TR, Sun, H, Zhang, C, Han, L, Wei Y, Zang Y, Gu M, Zhang Y, Gao W, Huyan H, Guo W, Wu D, Gu Z, Tsymbal EY, Wang P, Nie Y & Pan, X (2019). Freestanding crystalline oxide perovskites down to the monolayer limit. Nature 570(7759), 87–90. doi:10.1038/s41586-019-1255-7CrossRefGoogle Scholar
Jupyter, BM, Forde, J, Freeman, J, Granger, B, Head, T & Willing, C (2018). Binder 2.0-reproducible, interactive, sharable environments for science at scale. In Paper Presented at the Proceedings of the 17th Python in Science Conference, Akici F, Lippa D, Niederhut D & Pacer M (Eds.).Google Scholar
Kluyver, T, Ragan-Kelley, B, Pérez, F, Granger, BE, Bussonnier, M, Frederic, J & Corlay, S (2016). Jupyter Notebooks — A publishing format for reproducible computational workflows. In Positioning and Power in Academic Publishing: Players, Agents and Agendas, pp. 87–90. IOS Press. doi: 10.3233/978-1-61499-649-1-87.Google Scholar
Lee, D, Xu, H, Dierolf, V, Gopalan, V & Phillpot, SR (2010). Structure and energetics of ferroelectric domain walls in LiNbO3 from atomic-level simulations. Phys Rev B 82(1), 014104. doi:10.1103/PhysRevB.82.014104CrossRefGoogle Scholar
Li, Y, Zatterin, E, Conroy, M, Pylypets, A, Borodavka, F, Björling, A & Zubko, P (2022). Electrostatically driven polarization flop and strain-induced curvature in free-standing ferroelectric superlattices. Adv Mater. 2106826. doi:10.1002/adma.202106826Google ScholarPubMed
Madsen, J & Susi, T (2021). The abTEM code: Transmission electron microscopy from first principles. Open Res Eur 1(24), 24. doi:10.12688/openreseurope.13015.2CrossRefGoogle Scholar
McQuaid, RGP, Campbell, MP, Whatmore, RW, Kumar, A & Gregg, JM (2017). Injection and controlled motion of conducting domain walls in improper ferroelectric Cu-Cl boracite. Nat Commun 8(1), 15105. doi:10.1038/ncomms15105CrossRefGoogle ScholarPubMed
Merkel, D (2014). Docker: Lightweight linux containers for consistent development and deployment. Linux J 2014(239), 2.Google Scholar
Moore, K, Conroy, M & Bangert, U (2020 a). Rapid polarization mapping in ferroelectrics using Fourier masking. J Microsc 279(3), 222–228. doi:10.1111/jmi.12876CrossRefGoogle ScholarPubMed
Moore, K, Conroy, M, O'Connell, EN, Cochard, C, Mackel, J, Harvey, A, Hooper TE, Bell AJ, Gregg JM & Bangert, U (2020 b). Highly charged 180 degree head-to-head domain walls in lead titanate. Commun Phys 3, 231. doi:10.1038/s42005-020-00488-xCrossRefGoogle Scholar
Moore, K, O'Connell, EN, Griffin, SM, Downing, C, Colfer, L, Schmidt, M, Nicolosi V, Bangert U, Keeney L & Conroy, M (2022). Charged domain wall and polar vortex topologies in a room-temperature magnetoelectric multiferroic thin film. ACS Appl Mater Interfaces. doi:10.1021/acsami.1c17383CrossRefGoogle Scholar
Nord, M, Vullum, PE, 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. Adv Struct Chem Imaging 3(1), 9. doi:10.1186/s40679-017-0042-5CrossRefGoogle ScholarPubMed
O'Connell, E, Hennessy, M & Moynihan, E (2021). https://github.com/PinkShnack/TEMUL. doi:10.5281/ZENODO.3832142CrossRefGoogle Scholar
O’Connell, E. N. (2020). Automated Atomic Resolution Open-Source Analysis of Two-Dimensional Entities. Doctoral thesis, University of Limerick, Limerick, Ireland: Available at https://github.com/PinkShnack/PhD_Thesis_EOC. Accessed at 10.03.2022.Google Scholar
Ophus, C (2017). A fast image simulation algorithm for scanning transmission electron microscopy. Adv Struct Chem Imaging 3(1), 1–11. doi:10.1186/s40679-017-0046-1CrossRefGoogle ScholarPubMed
Peng, B, Peng, R-C, Zhang, Y-Q, Dong, G, Zhou, Z, Zhou, Y, Wang, S, Xia Y, Qiu R, Cheng X, Xue F, Hu Z, Ren W, Ye ZG, Chen LQ, Shan Z, Min T & Liu M (2020). Phase transition enhanced superior elasticity in freestanding single-crystalline multiferroic BiFeO3 membranes. Sci Adv 6(34), eaba5847. doi:10.1126/sciadv.aba5847CrossRefGoogle ScholarPubMed
Pryor, A, Ophus, C & Miao, J (2017). A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy. Adv Struct Chem Imaging 3(1), 1–14. doi:10.1186/s40679-017-0048-zCrossRefGoogle ScholarPubMed
Rothmann, MU, Kim, JS, Borchert, J, Lohmann, KB, O'Leary, CM, Sheader, AA, Clark L, Snaith HJ, Johnston MB, Nellist PD & Herz, LM (2020). Atomic-scale microstructure of metal halide perovskite. Science 370(6516), eabb5940. doi:10.1126/science.abb5940CrossRefGoogle ScholarPubMed
Schlom, DG, Chen, L-Q, Eom, C-B, Rabe, KM, Streiffer, SK & Triscone, J-M (2007). Strain tuning of ferroelectric thin films. Annu Rev Mater Res 37(1), 589–626. doi:10.1146/annurev.matsci.37.061206.113016CrossRefGoogle Scholar
Seidel, J, Martin, LW, He, Q, Zhan, Q, Chu, YH, Rother, A, Hawkridge ME, Maksymovych P, Yu P, Gajek P, Balke N, Kalinin SV, Gemming S, Wang F, Catalan G, Scott JF, Spaldin NA, Orenstein J, & Gajek, M (2009). Conduction at domain walls in oxide multiferroics. Nat Mater 8(3), 229. doi:10.1038/nmat2373CrossRefGoogle Scholar
Shao, Y-T, Das, S, Hong, Z, Xu, R, Chandrika, S, Gómez-Ortiz, F, García-Fernández P, Chen LQ, Hwang H, Junquera J, Martin L, Ramamoorthy R & Muller, D (2021). Emergent chirality in a polar meron to skyrmion transition revealed by 4D-STEM. Microsc Microanal 27(S1), 348–350. doi:10.1017/S1431927621001793CrossRefGoogle Scholar
Shirane, G, Axe, JD, Harada, J & Remeika, JP (1970). Soft ferroelectric modes in lead titanate. Phys Rev B 2(1), 155–159. doi:10.1103/PhysRevB.2.155CrossRefGoogle Scholar
Strain++. Available at https://jjppeters.github.io/Strainpp/.Google Scholar
Tang, YL, Zhu, YL, Ma, XL, Borisevich, AY, Morozovska, AN, Eliseev, EA, Wang WY, Wang YJ, Xu YB, Zhang ZD & Pennycook, SJ (2015). Observation of a periodic array of flux-closure quadrants in strained ferroelectric PbTiO3 films. Science 348(6234), 547–551. doi:10.1126/science.1259869CrossRefGoogle Scholar
Van der Walt, S, Schönberger, JL, Nunez-Iglesias, J, Boulogne, F, Warner, JD, Yager, N, Gouillart E & Yu, T (2014). scikit-image: Image processing in python. PeerJ 2, e453.CrossRefGoogle ScholarPubMed
Wang, YJ, Feng, YP, Zhu, YL, Tang, YL, Yang, LX, Zou, MJ, Geng WR, Han MJ, Guo XW, Wu B & Ma, XL (2020). Polar meron lattice in strained oxide ferroelectrics. Nat Mater 19(8), 881–886. doi:10.1038/s41563-020-0694-8CrossRefGoogle ScholarPubMed
Yadav, AK, Nelson, CT, Hsu, SL, Hong, Z, Clarkson, JD, Schlepütz, CM, Damodaran AR, Shafer P, Arenholz E, Dedon LR, Chen D, Vishwanath A, Minor AM, Chen LQ, Scott JF, Martin LW & Ramesh, R (2016). Observation of polar vortices in oxide superlattices. Nature 530(7589), 198–201. doi:10.1038/nature16463CrossRefGoogle ScholarPubMed
Zimmermann, A, Bollmann, W & Schmid, H (1970). Observations of ferroelectric domains in boracites. Phys Status Solidi A 3(3), 707–720. doi:10.1002/pssa.19700030317CrossRefGoogle Scholar
Zubko, P, Wojdeł, JC, Hadjimichael, M, Fernandez-Pena, S, Sené, A, Luk'yanchuk, I, Triscone JM & Íñiguez, J (2016). Negative capacitance in multidomain ferroelectric superlattices. Nature 534(7608), 524–528. doi:10.1038/nature17659CrossRefGoogle ScholarPubMed