Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging
Abstract
Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. As a result, the use of sparse line-hopping scan tomore »
- Authors:
-
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Duke Univ., Durham, NC (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Washington, Seattle, WA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1332608
- Alternate Identifier(s):
- OSTI ID: 1329496
- Report Number(s):
- PNNL-SA-120342
Journal ID: ISSN 0003-6951; 49204; KP1704020
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Applied Physics Letters
- Additional Journal Information:
- Journal Volume: 109; Journal Issue: 16; Journal ID: ISSN 0003-6951
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; 47 OTHER INSTRUMENTATION; Environmental Molecular Sciences Laboratory
Citation Formats
Kovarik, Libor, Stevens, Andrew J., Liyu, Andrey V., and Browning, Nigel D. Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging. United States: N. p., 2016.
Web. doi:10.1063/1.4965720.
Kovarik, Libor, Stevens, Andrew J., Liyu, Andrey V., & Browning, Nigel D. Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging. United States. https://doi.org/10.1063/1.4965720
Kovarik, Libor, Stevens, Andrew J., Liyu, Andrey V., and Browning, Nigel D. Mon .
"Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging". United States. https://doi.org/10.1063/1.4965720. https://www.osti.gov/servlets/purl/1332608.
@article{osti_1332608,
title = {Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging},
author = {Kovarik, Libor and Stevens, Andrew J. and Liyu, Andrey V. and Browning, Nigel D.},
abstractNote = {Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. As a result, the use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.},
doi = {10.1063/1.4965720},
journal = {Applied Physics Letters},
number = 16,
volume = 109,
place = {United States},
year = {Mon Oct 17 00:00:00 EDT 2016},
month = {Mon Oct 17 00:00:00 EDT 2016}
}
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Works referenced in this record:
The potential for Bayesian compressive sensing to significantly reduce electron dose in high-resolution STEM images
journal, October 2013
- Stevens, Andrew; Yang, Hao; Carin, Lawrence
- Microscopy, Vol. 63, Issue 1
Optimized imaging using non-rigid registration
text, January 2014
- Berkels, Benjamin; Binev, Peter; Blom, Douglas A.
- arXiv
Compressed Sensing MRI
journal, March 2008
- Lustig, M.; Donoho, D. L.; Santos, J. M.
- IEEE Signal Processing Magazine, Vol. 25, Issue 2
Segregation of Mn 2+ Dopants as Interstitials in SrTiO 3 Grain Boundaries
journal, October 2013
- Yang, Hao; Kotula, Paul G.; Sato, Yukio
- Materials Research Letters, Vol. 2, Issue 1
Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging
journal, January 2012
- Humphry, M. J.; Kraus, B.; Hurst, A. C.
- Nature Communications, Vol. 3, Issue 1
Optimized imaging using non-rigid registration
journal, March 2014
- Berkels, Benjamin; Binev, Peter; Blom, Douglas A.
- Ultramicroscopy, Vol. 138
Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
journal, May 2013
- Li, Xueming; Mooney, Paul; Zheng, Shawn
- Nature Methods, Vol. 10, Issue 6
Compressed sensing
journal, April 2006
- Donoho, D. L.
- IEEE Transactions on Information Theory, Vol. 52, Issue 4
ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography
journal, July 2016
- Deng, Yuchen; Chen, Yu; Zhang, Yan
- Journal of Structural Biology, Vol. 195, Issue 1
Electron beam damage in oxides: a review
journal, December 2015
- Jiang, Nan
- Reports on Progress in Physics, Vol. 79, Issue 1
Electron microscopy image enhanced
journal, April 1998
- Haider, Maximilian; Uhlemann, Stephan; Schwan, Eugen
- Nature, Vol. 392, Issue 6678
Sparse imaging for fast electron microscopy
conference, February 2013
- Anderson, Hyrum S.; Ilic-Helms, Jovana; Rohrer, Brandon
- IS&T/SPIE Electronic Imaging, SPIE Proceedings
The structural study of membrane proteins by electron crystallography
journal, January 1998
- Fujiyoshi, Y.
- Advances in Biophysics, Vol. 35
Opportunities and challenges in liquid cell electron microscopy
journal, December 2015
- Ross, F. M.
- Science, Vol. 350, Issue 6267
Reduced-dose and high-speed acquisition strategies for multi-dimensional electron microscopy
journal, May 2015
- Saghi, Zineb; Benning, Martin; Leary, Rowan
- Advanced Structural and Chemical Imaging, Vol. 1, Issue 1
Applying compressive sensing to TEM video: a substantial frame rate increase on any camera
journal, August 2015
- Stevens, Andrew; Kovarik, Libor; Abellan, Patricia
- Advanced Structural and Chemical Imaging, Vol. 1, Issue 10
Atomic-Resolution STEM Imaging of Graphene at Low Voltage of 30 kV with Resolution Enhancement by Using Large Convergence Angle
journal, April 2015
- Sawada, H.; Sasaki, T.; Hosokawa, F.
- Physical Review Letters, Vol. 114, Issue 16
Development of a fast electromagnetic beam blanker for compressed sensing in scanning transmission electron microscopy
journal, February 2016
- Béché, A.; Goris, B.; Freitag, B.
- Applied Physics Letters, Vol. 108, Issue 9
Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy
journal, December 2014
- McMullan, G.; Faruqi, A. R.; Clare, D.
- Ultramicroscopy, Vol. 147
Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information
journal, February 2006
- Candes, E.J.; Romberg, J.; Tao, T.
- IEEE Transactions on Information Theory, Vol. 52, Issue 2, p. 489-509
Controlled Growth of Nanoparticles from Solution with In Situ Liquid Transmission Electron Microscopy
journal, July 2011
- Evans, James E.; Jungjohann, Katherine L.; Browning, Nigel D.
- Nano Letters, Vol. 11, Issue 7
Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry
journal, February 2016
- Ophus, Colin; Ciston, Jim; Pierce, Jordan
- Nature Communications, Vol. 7, Issue 1
Robust Uncertainty Principles: Exact Signal Reconstruction from Highly Incomplete Frequency Information
preprint, January 2004
- Candes, Emmanuel; Romberg, Justin; Tao, Terence
- arXiv
Radiation damage in the TEM and SEM
journal, August 2004
- Egerton, R. F.; Li, P.; Malac, M.
- Micron, Vol. 35, Issue 6
XEDS STEM tomography for 3D chemical characterization of nanoscale particles
journal, August 2013
- Genc, Arda; Kovarik, Libor; Gu, Meng
- Ultramicroscopy, Vol. 131
Low-dose aberration corrected cryo-electron microscopy of organic specimens
journal, November 2008
- Evans, James E.; Hetherington, Crispin; Kirkland, Angus
- Ultramicroscopy, Vol. 108, Issue 12
The structural study of membrane proteins by electron crystallography
journal, January 1998
- Fujiyoshi, Y.
- Advances in Biophysics, Vol. 35
Low-dose high-resolution electron microscopy of zeolite materials with a slow-scan CCD camera
journal, March 1993
- Pan, M.; Crozier, P. A.
- Ultramicroscopy, Vol. 48, Issue 3
Nonparametric Bayesian Dictionary Learning for Analysis of Noisy and Incomplete Images
journal, January 2012
- Zhou, Mingyuan; Chen, Haojun; Paisley, John
- IEEE Transactions on Image Processing, Vol. 21, Issue 1, p. 130-144
Quantifying the Advantages of Compressive Sensing and Sparse Reconstruction for Scanning Transmission Electron Microscopy
journal, July 2016
- Reed, Bryan W.; Park, Sang Tae; Masiel, Daniel J.
- Microscopy and Microanalysis, Vol. 22, Issue S3
TEM preparation methods and influence of radiation damage on the beam sensitive CaCO3 shell of Emiliania huxleyi
journal, July 2014
- Hoffmann, Ramona; Wochnik, Angela S.; Betzler, Sophia B.
- Micron, Vol. 62
Compressed sensing electron tomography
journal, August 2013
- Leary, Rowan; Saghi, Zineb; Midgley, Paul A.
- Ultramicroscopy, Vol. 131
Sub-ångstrom resolution using aberration corrected electron optics
journal, August 2002
- Batson, P. E.; Dellby, N.; Krivanek, O. L.
- Nature, Vol. 418, Issue 6898
Modeling Nanoscale Imaging in Electron Microscopy
book, January 2012
- Vogt, Thomas; Dahmen, Wolfgang; Binev, Peter
- Nanostructure Science and Technology
Works referencing / citing this record:
Emerging Electron Microscopy Techniques for Probing Functional Interfaces in Energy Materials
journal, October 2019
- Zachman, Michael J.; Hachtel, Jordan A.; Idrobo, Juan Carlos
- Angewandte Chemie, Vol. 132, Issue 4
Liquid cell transmission electron microscopy and its applications
journal, January 2020
- Pu, Shengda; Gong, Chen; Robertson, Alex W.
- Royal Society Open Science, Vol. 7, Issue 1
Materials Structure, Properties and Dynamics through Scanning Transmission Electron Microscopy
text, January 2019
- Pennycook, Stephen J.; Li, Changjian; Li, Mengsha
- arXiv
Automating material image analysis for material discovery
journal, April 2019
- Park, Chiwoo; Ding, Yu
- MRS Communications, Vol. 9, Issue 02
Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback
journal, April 2018
- Jesse, Stephen; Hudak, Bethany M.; Zarkadoula, Eva
- Nanotechnology, Vol. 29, Issue 25
Materials Structure, Properties and Dynamics through Scanning Transmission Electron Microscopy
text, January 2019
- Pennycook, Stephen J.; Li, Changjian; Li, Mengsha
- arXiv
Quantitative Mapping of Nanoscale Chemical Dynamics in Sub-Sampled Operando (S)TEM Images using Spatio-Temporal Analytics
journal, May 2018
- Stanfill, Bryan A.; Reehl, Sarah M.; Johnson, Margaret C.
- ChemCatChem, Vol. 10, Issue 14
Material structure, properties, and dynamics through scanning transmission electron microscopy
journal, April 2018
- Pennycook, Stephen J.; Li, Changjian; Li, Mengsha
- Journal of Analytical Science and Technology, Vol. 9, Issue 1
Emerging Electron Microscopy Techniques for Probing Functional Interfaces in Energy Materials
journal, January 2020
- Zachman, Michael J.; Hachtel, Jordan A.; Idrobo, Juan Carlos
- Angewandte Chemie International Edition, Vol. 59, Issue 4
Acquisition of STEM Images by Adaptive Compressive Sensing
journal, July 2017
- Xie, Weiyi; Feng, Qianli; Srinivasan, Ramprakash
- Microscopy and Microanalysis, Vol. 23, Issue S1
A sub-sampled approach to extremely low-dose STEM
journal, January 2018
- Stevens, A.; Luzi, L.; Yang, H.
- Applied Physics Letters, Vol. 112, Issue 4
Liquid cell transmission electron microscopy and its applications
journal, January 2020
- Pu, Shengda; Gong, Chen; Robertson, Alex W.
- Royal Society Open Science, Vol. 7, Issue 1
Controlling the spatio-temporal dose distribution during STEM imaging by subsampled acquisition: In-situ observations of kinetic processes in liquids
journal, August 2019
- Mehdi, B. L.; Stevens, A.; Kovarik, L.
- Applied Physics Letters, Vol. 115, Issue 6
Event detection for undersampled electron microscopy experiments: A control chart case study
journal, November 2019
- Reehl, Sarah; Stanfill, Bryan; Johnson, Margaret
- Quality Engineering, Vol. 32, Issue 2