Smart align -- A new tool for robust non-rigid registration of scanning microscope data
Abstract
Many microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities andmore »
- Authors:
-
- Univ. of Oxford, Oxford (United Kingdom)
- Univ. of Oxford, Oxford (United Kingdom); Daresbury Lab., Warrington (United Kingdom)
- Yale Univ., New Haven, CT (United States)
- Univ. of Antwerp, Antwerp (Belgium)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1214821
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Advanced Structural and Chemical Imaging
- Additional Journal Information:
- Journal Volume: 1; Journal Issue: 1; Journal ID: ISSN 2198-0926
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; 47 OTHER INSTRUMENTATION; image registration; non-rigid registration; quantitative ADF; strain mapping; principle component analysis; scanning tunnelling microscopy (STM)
Citation Formats
Jones, Lewys, Yang, Hao, Pennycook, Timothy J., Marshall, Matthew S. J., Van Aert, Sandra, Browning, Nigel D., Castell, Martin R., and Nellist, Peter D. Smart align -- A new tool for robust non-rigid registration of scanning microscope data. United States: N. p., 2015.
Web. doi:10.1186/s40679-015-0008-4.
Jones, Lewys, Yang, Hao, Pennycook, Timothy J., Marshall, Matthew S. J., Van Aert, Sandra, Browning, Nigel D., Castell, Martin R., & Nellist, Peter D. Smart align -- A new tool for robust non-rigid registration of scanning microscope data. United States. https://doi.org/10.1186/s40679-015-0008-4
Jones, Lewys, Yang, Hao, Pennycook, Timothy J., Marshall, Matthew S. J., Van Aert, Sandra, Browning, Nigel D., Castell, Martin R., and Nellist, Peter D. Fri .
"Smart align -- A new tool for robust non-rigid registration of scanning microscope data". United States. https://doi.org/10.1186/s40679-015-0008-4. https://www.osti.gov/servlets/purl/1214821.
@article{osti_1214821,
title = {Smart align -- A new tool for robust non-rigid registration of scanning microscope data},
author = {Jones, Lewys and Yang, Hao and Pennycook, Timothy J. and Marshall, Matthew S. J. and Van Aert, Sandra and Browning, Nigel D. and Castell, Martin R. and Nellist, Peter D.},
abstractNote = {Many microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities and positions is evaluated.},
doi = {10.1186/s40679-015-0008-4},
journal = {Advanced Structural and Chemical Imaging},
number = 1,
volume = 1,
place = {United States},
year = {Fri Jul 10 00:00:00 EDT 2015},
month = {Fri Jul 10 00:00:00 EDT 2015}
}
Works referenced in this record:
Correcting scanning instabilities from images of periodic structures
journal, July 2012
- Braidy, Nadi; Le Bouar, Yann; Lazar, Sorin
- Ultramicroscopy, Vol. 118
Revolving scanning transmission electron microscopy: Correcting sample drift distortion without prior knowledge
journal, March 2014
- Sang, Xiahan; LeBeau, James M.
- Ultramicroscopy, Vol. 138
Self-manifestation and universal correction of image distortion in scanning tunneling microscopy with spiral scan
journal, July 2010
- Wang, Junting; Wang, Jihui; Hou, Yubin
- Review of Scientific Instruments, Vol. 81, Issue 7
Principal component analysis
journal, August 1987
- Wold, Svante; Esbensen, Kim; Geladi, Paul
- Chemometrics and Intelligent Laboratory Systems, Vol. 2, Issue 1-3
Optimized imaging using non-rigid registration
journal, March 2014
- Berkels, Benjamin; Binev, Peter; Blom, Douglas A.
- Ultramicroscopy, Vol. 138
Non rigid geometric distortions correction - Application to atmospheric turbulence stabilization
journal, August 2012
- Mao, Yu; Gilles, Jérôme
- Inverse Problems and Imaging, Vol. 6, Issue 3
Testing the accuracy of the two-dimensional object model in HAADF STEM
journal, August 2014
- Jones, Lewys; Nellist, Peter D.
- Micron, Vol. 63
Experimental quantification of annular dark-field images in scanning transmission electron microscopy
journal, November 2008
- LeBeau, James M.; Stemmer, Susanne
- Ultramicroscopy, Vol. 108, Issue 12
Identifying and Correcting Scan Noise and Drift in the Scanning Transmission Electron Microscope
journal, May 2013
- Jones, Lewys; Nellist, Peter D.
- Microscopy and Microanalysis, Vol. 19, Issue 4
Ad Hoc Auto-Tuning of Aberrations Using High-Resolution STEM Images by Autocorrelation Function
journal, July 2012
- Sawada, Hidetaka; Watanabe, Masashi; Chiyo, Izuru
- Microscopy and Microanalysis, Vol. 18, Issue 4
An approach to the systematic distortion correction in aberration-corrected HAADF images
journal, January 2006
- Sanchez, A. M.; Galindo, P. L.; Kret, S.
- Journal of Microscopy, Vol. 221, Issue 1
Error Sources in Atomic Force Microscopy for Dimensional Measurements: Taxonomy and Modeling
journal, May 2010
- Marinello, F.; Carmignato, S.; Voltan, A.
- Journal of Manufacturing Science and Engineering, Vol. 132, Issue 3
AFM image reconstruction for deformation measurements by digital image correlation
journal, January 2006
- Sun, Yaofeng; Pang, John H. L.
- Nanotechnology, Vol. 17, Issue 4
Correlation functions revisited
journal, October 1992
- van Heel, Marin; Schatz, Michael; Orlova, Elena
- Ultramicroscopy, Vol. 46, Issue 1-4
Lattice and strain analysis of atomic resolution Z-contrast images based on template matching
journal, January 2014
- Zuo, Jian-Min; Shah, Amish B.; Kim, Honggyu
- Ultramicroscopy, Vol. 136
Thermal drift study on different commercial scanning probe microscopes during the initial warming-up phase
journal, August 2011
- Marinello, F.; Balcon, M.; Schiavuta, P.
- Measurement Science and Technology, Vol. 22, Issue 9
Vertical and lateral drift corrections of scanning probe microscopy images
journal, May 2010
- Rahe, P.; Bechstein, R.; Kühnle, A.
- Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, Vol. 28, Issue 3
Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting
journal, April 2015
- De Backer, A.; Martinez, G. T.; MacArthur, K. E.
- Ultramicroscopy, Vol. 151
Atomic scale dynamics of a solid state chemical reaction directly determined by annular dark-field electron microscopy
journal, December 2014
- Pennycook, Timothy J.; Jones, Lewys; Pettersson, Henrik
- Scientific Reports, Vol. 4, Issue 1
Atom Column Indexing: Atomic Resolution Image Analysis Through a Matrix Representation
journal, November 2014
- Sang, Xiahan; Oni, Adedapo A.; LeBeau, James M.
- Microscopy and Microanalysis, Vol. 20, Issue 6
Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts
journal, June 2014
- Yankovich, Andrew B.; Berkels, Benjamin; Dahmen, W.
- Nature Communications, Vol. 5, Issue 1
Probe integrated scattering cross sections in the analysis of atomic resolution HAADF STEM images
journal, October 2013
- E., H.; MacArthur, K. E.; Pennycook, T. J.
- Ultramicroscopy, Vol. 133
Local crystal structure analysis with several picometer precision using scanning transmission electron microscopy
journal, June 2010
- Kimoto, Koji; Asaka, Toru; Yu, Xiuzhen
- Ultramicroscopy, Vol. 110, Issue 7
Strain fields around dislocation arrays in a Σ9 silicon bicrystal measured by scanning transmission electron microscopy
journal, April 2013
- Couillard, Martin; Radtke, Guillaume; Botton, Gianluigi A.
- Philosophical Magazine, Vol. 93, Issue 10-12
Three-dimensional atomic imaging of crystalline nanoparticles
journal, February 2011
- Van Aert, Sandra; Batenburg, Kees J.; Rossell, Marta D.
- Nature, Vol. 470, Issue 7334
IMAGE-WARP: A real-space restoration method for high-resolution STEM images using quantitative HRTEM analysis
journal, July 2005
- Rečnik, Aleksander; Möbus, Günter; Šturm, Sašo
- Ultramicroscopy, Vol. 103, Issue 4
Atom counting in HAADF STEM using a statistical model-based approach: Methodology, possibilities, and inherent limitations
journal, November 2013
- De Backer, A.; Martinez, G. T.; Rosenauer, A.
- Ultramicroscopy, Vol. 134
Surface and Defect Structure of Oxide Nanowires on
journal, August 2011
- Marshall, Matthew S. J.; Becerra-Toledo, Andres E.; Marks, Laurence D.
- Physical Review Letters, Vol. 107, Issue 8
A method for the alignment of heterogeneous macromolecules from electron microscopy
journal, April 2009
- Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.
- Journal of Structural Biology, Vol. 166, Issue 1
Image registration methods: a survey
journal, October 2003
- Zitová, Barbara; Flusser, Jan
- Image and Vision Computing, Vol. 21, Issue 11
A fast and fully automatic registration approach based on point features for multi-source remote-sensing images
journal, July 2008
- Yu, Le; Zhang, Dengrong; Holden, Eun-Jung
- Computers & Geosciences, Vol. 34, Issue 7
Validation of an accelerated ‘demons’ algorithm for deformable image registration in radiation therapy
journal, June 2005
- Wang, He; Dong, Lei; O'Daniel, Jennifer
- Physics in Medicine and Biology, Vol. 50, Issue 12
Rapid Estimation of Catalyst Nanoparticle Morphology and Atomic-Coordination by High-Resolution Z-Contrast Electron Microscopy
journal, October 2014
- Jones, Lewys; MacArthur, Katherine E.; Fauske, Vidar T.
- Nano Letters, Vol. 14, Issue 11
Voltage-Dependent STM Images of Covalently Bound Molecules on Si(100)
journal, October 1998
- Padowitz, David F.; Hamers, Robert J.
- The Journal of Physical Chemistry B, Vol. 102, Issue 43
MRI modalitiy transformation in demon registration
conference, June 2009
- Kroon, Dirk-Jan; Slump, Cornelis H.
- 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI)
Standardless Atom Counting in Scanning Transmission Electron Microscopy
journal, November 2010
- LeBeau, James M.; Findlay, Scott D.; Allen, Leslie J.
- Nano Letters, Vol. 10, Issue 11
Procedure to count atoms with trustworthy single-atom sensitivity
journal, February 2013
- Van Aert, S.; De Backer, A.; Martinez, G. T.
- Physical Review B, Vol. 87, Issue 6
Principal Component Analysis
book, January 2016
- Vidal, René; Ma, Yi; Sastry, S. Shankar
- Interdisciplinary Applied Mathematics
Optimized imaging using non-rigid registration
text, January 2014
- Berkels, Benjamin; Binev, Peter; Blom, Douglas A.
- arXiv
Principal component analysis
journal, August 1987
- Wold, Svante; Esbensen, Kim; Geladi, Paul
- Chemometrics and Intelligent Laboratory Systems, Vol. 2, Issue 1-3
IMAGE-WARP: A real-space restoration method for high-resolution STEM images using quantitative HRTEM analysis
journal, July 2005
- Rečnik, Aleksander; Möbus, Günter; Šturm, Sašo
- Ultramicroscopy, Vol. 103, Issue 4
Correcting scanning instabilities from images of periodic structures
journal, July 2012
- Braidy, Nadi; Le Bouar, Yann; Lazar, Sorin
- Ultramicroscopy, Vol. 118
A cross-measurement procedure (CMP) for near noise-free imaging in scanning microscopes
journal, February 1999
- Anguiano, Eloy; Aguilar, Miguel
- Ultramicroscopy, Vol. 76, Issue 1-2
Voltage-Dependent STM Images of Covalently Bound Molecules on Si(100)
journal, October 1998
- Padowitz, David F.; Hamers, Robert J.
- The Journal of Physical Chemistry B, Vol. 102, Issue 43
Error Sources in Atomic Force Microscopy for Dimensional Measurements: Taxonomy and Modeling
journal, May 2010
- Marinello, F.; Carmignato, S.; Voltan, A.
- Journal of Manufacturing Science and Engineering, Vol. 132, Issue 3
Vertical and lateral drift corrections of scanning probe microscopy images
journal, May 2010
- Rahe, P.; Bechstein, R.; Kühnle, A.
- Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, Vol. 28, Issue 3
Works referencing / citing this record:
Managing dose-, damage- and data-rates in multi-frame spectrum-imaging
journal, January 2018
- Jones, Lewys; Varambhia, Aakash; Beanland, Richard
- Microscopy, Vol. 67, Issue suppl_1
Direct Observation of Ferroelectric Domain Walls in LiNbO 3 : Wall-Meanders, Kinks, and Local Electric Charges
journal, September 2016
- Gonnissen, Julie; Batuk, Dmitry; Nataf, Guillaume F.
- Advanced Functional Materials, Vol. 26, Issue 42
Large Electric‐Field‐Induced Strain Close to the Surface in Barium Titanate Studied by Atomic‐Scale In Situ Electron Microscopy
journal, November 2019
- Sato, Yukio; Miyauchi, Ryuki; Aoki, Mai
- physica status solidi (RRL) – Rapid Research Letters, Vol. 14, Issue 1
Measurement of Barium Ion Displacement Near Surface in a Barium Titanate Nanoparticle by Scanning Transmission Electron Microscopy
journal, March 2018
- Aoki, Mai; Sato, Yukio; Teranishi, Ryo
- Applied Microscopy, Vol. 48, Issue 1
The ultrathin limit of improper ferroelectricity
journal, December 2019
- Nordlander, J.; Campanini, M.; Rossell, M. D.
- Nature Communications, Vol. 10, Issue 1
Enhancing the thermoelectric power factor of Sr 0.9 Nd 0.1 TiO 3 through control of the nanostructure and microstructure
journal, January 2018
- Ekren, Dursun; Azough, Feridoon; Gholinia, Ali
- Journal of Materials Chemistry A, Vol. 6, Issue 48
Influence of the support on stabilizing local defects in strained monolayer oxide films
journal, January 2019
- Wang, Shuqiu; Hu, Xiao; Goniakowski, Jacek
- Nanoscale, Vol. 11, Issue 5
Electron microscopy with high accuracy and precision at atomic resolution: In-situ observation of a dielectric crystal under electric field
journal, August 2017
- Sato, Yukio; Gondo, Takashi; Miyazaki, Hiroya
- Applied Physics Letters, Vol. 111, Issue 6
Universal geometric frustration in pyrochlores
journal, July 2018
- Trump, B. A.; Koohpayeh, S. M.; Livi, K. J. T.
- Nature Communications, Vol. 9, Issue 1
Structural and compositional study of precipitates in under-aged Cu-added Al-Mg-Si alloy
journal, November 2018
- Maeda, Takuya; Kaneko, Kenji; Namba, Takuya
- Scientific Reports, Vol. 8, Issue 1
Chemical and electronic structure analysis of a SrTiO3 (001)/p-Ge (001) hydrogen evolution photocathode
journal, March 2018
- Stoerzinger, Kelsey A.; Du, Yingge; Spurgeon, Steven R.
- MRS Communications, Vol. 8, Issue 02
ADF-STEM Imaging of Nascent Phases and Extended Disorder Within the Mo–V–Nb–Te–O Catalyst System
journal, August 2016
- Vogt, T.; Blom, D. A.; Jones, L.
- Topics in Catalysis, Vol. 59, Issue 17-18
Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting
journal, February 2017
- Nord, Magnus; Vullum, Per Erik; MacLaren, Ian
- Advanced Structural and Chemical Imaging, Vol. 3, Issue 1
Quantifying a Heterogeneous Ru Catalyst on Carbon Black Using ADF STEM
journal, June 2016
- Varambhia, Aakash M.; Jones, Lewys; De Backer, Annick
- Particle & Particle Systems Characterization, Vol. 33, Issue 7
Ge/SiGe parabolic quantum wells
journal, July 2019
- Ballabio, Andrea; Frigerio, Jacopo; Firoozabadi, Saleh
- Journal of Physics D: Applied Physics, Vol. 52, Issue 41
Control of Knock-On Damage for 3D Atomic Scale Quantification of Nanostructures: Making Every Electron Count in Scanning Transmission Electron Microscopy
journal, February 2019
- Van Aert, Sandra; De Backer, Annick; Jones, Lewys
- Physical Review Letters, Vol. 122, Issue 6
Recent breakthroughs in scanning transmission electron microscopy of small species
journal, January 2018
- van den Bos, Karel Hendrik Wouter; Altantzis, Thomas; De Backer, Annick
- Advances in Physics: X, Vol. 3, Issue 1
Prospect for detecting magnetism of a single impurity atom using electron magnetic chiral dichroism
journal, September 2019
- Negi, Devendra; Zeiger, Paul M.; Jones, Lewys
- Physical Review B, Vol. 100, Issue 10
Self‐Assembly of Atomically Thin Chiral Copper Heterostructures Templated by Black Phosphorus
journal, July 2019
- Nerl, Hannah C.; Pokle, Anuj; Jones, Lewys
- Advanced Functional Materials, Vol. 29, Issue 37
In situ observations of the reversible vacancy ordering process in van der Waals-bonded Ge–Sb–Te thin films and GeTe–Sb 2 Te 3 superlattices
journal, January 2019
- Lotnyk, Andriy; Dankwort, Torben; Hilmi, Isom
- Nanoscale, Vol. 11, Issue 22
Interfacial sharpness and intermixing in a Ge-SiGe multiple quantum well structure
journal, January 2018
- Bashir, A.; Gallacher, K.; Millar, R. W.
- Journal of Applied Physics, Vol. 123, Issue 3
Maghemite-like regions at the crossing of two antiphase boundaries in doped BiFeO 3
journal, May 2015
- Salih, J. M.; Wang, L. Q.; Ramasse, Q. M.
- Materials Science and Technology
HAADF-STEM Image Resolution Enhancement Using High-Quality Image Reconstruction Techniques: Case of the Fe 3 O 4 (111) Surface
journal, August 2019
- Bárcena-González, G.; Guerrero-Lebrero, M. P.; Guerrero, E.
- Microscopy and Microanalysis, Vol. 25, Issue 6
Nano-scale characterisation of sheared β” precipitates in a deformed Al-Mg-Si alloy
journal, November 2019
- Christiansen, Emil; Marioara, Calin Daniel; Holmedal, Bjørn
- Scientific Reports, Vol. 9, Issue 1
Characterisation of structural similarities of precipitates in Mg–Zn and Al–Zn–Mg alloys systems
journal, July 2019
- Bendo, Artenis; Maeda, Tomoyoshi; Matsuda, Kenji
- Philosophical Magazine, Vol. 99, Issue 21
Multislice image simulations of sheared needle‐like precipitates in an Al‐Mg‐Si alloy
journal, May 2020
- Christiansen, E.; Ringdalen, I. G.; BjØRge, R.
- Journal of Microscopy
Scanning Transmission Electron Microscopy
book, January 2019
- Nellist, Peter D.
- Springer Handbook of Microscopy, 49–99
Nature of the “Z”-phase in layered Na-ion battery cathodes
journal, January 2019
- Somerville, James W.; Sobkowiak, Adam; Tapia-Ruiz, Nuria
- Energy & Environmental Science, Vol. 12, Issue 7
Three-dimensional atomic models from a single projection using Z-contrast imaging: verification by electron tomography and opportunities
journal, January 2017
- De Backer, A.; Jones, L.; Lobato, I.
- Nanoscale, Vol. 9, Issue 25
Azetidinium as cation in lead mixed halide perovskite nanocrystals of optoelectronic quality
journal, February 2020
- Kesava, Sameer Vajjala; Hassan, Yasser; Privitera, Alberto
- AIP Advances, Vol. 10, Issue 2
Large Electric‐Field‐Induced Strain Close to the Surface in Barium Titanate Studied by Atomic‐Scale In Situ Electron Microscopy
journal, November 2019
- Sato, Yukio; Miyauchi, Ryuki; Aoki, Mai
- physica status solidi (RRL) – Rapid Research Letters, Vol. 14, Issue 1
Maghemite-like regions at the crossing of two antiphase boundaries in doped BiFeO 3
text, January 2015
- Salih, J. M.; Wang, L. Q.; Ramasse, Q. M.
- RWTH Aachen University
The ultrathin limit of improper ferroelectricity
text, January 2019
- Johanna, Nordlander,; Marco, Campanini,; Dacil, Rossell, Marta
- ETH Zurich
Scanning Transmission Electron Microscopy
book, January 2007
- Nellist, Peter D.
- Science of Microscopy
Universal geometric frustration in pyrochlores
journal, July 2018
- Trump, B. A.; Koohpayeh, S. M.; Livi, K. J. T.
- Nature Communications, Vol. 9, Issue 1
Structural and compositional study of precipitates in under-aged Cu-added Al-Mg-Si alloy
journal, November 2018
- Maeda, Takuya; Kaneko, Kenji; Namba, Takuya
- Scientific Reports, Vol. 8, Issue 1
Nano-scale characterisation of sheared β” precipitates in a deformed Al-Mg-Si alloy
journal, November 2019
- Christiansen, Emil; Marioara, Calin Daniel; Holmedal, Bjørn
- Scientific Reports, Vol. 9, Issue 1
Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting
journal, February 2017
- Nord, Magnus; Vullum, Per Erik; MacLaren, Ian
- Advanced Structural and Chemical Imaging, Vol. 3, Issue 1
The ultrathin limit of improper ferroelectricity
text, January 2019
- Johanna, Nordlander,; Marco, Campanini,; Dacil, Rossell, Marta
- ETH Zurich