Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Levin, Barnaby D. A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M. C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

doi:10.1038/sdata.2016.41

Title: Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Abstract

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co₂ P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Authors:

Levin, Barnaby D. A. ^[1]; Padgett, Elliot ^[1]; Chen, Chien-Chun ^[2]; Scott, M. C. ^[3]; Xu, Rui ^[4]; Theis, Wolfgang ^[5]; Jiang, Yi ^[6]; Yang, Yongsoo ^[4]; Ophus, Colin ^[7]; Zhang, Haitao ^[8]; Ha, Don-Hyung ^[8]; Wang, Deli ^[9]; Yu, Yingchao ^[10]; Abruña, Hector D. ^[10]; Robinson, Richard D. ^[8];

^[7]; Kourkoutis, Lena F. ^[11]; Miao, Jianwei ^[4];

^[11]; Hovden, Robert ^[1]

Cornell Univ., Ithaca, NY (United States). School of Applied and Engineering Physics
Univ. of California, Los Angeles, CA (United States). Dept. of Physics and Astronomy, California NanoSystems Inst.; National Sun Yat-SEn Univ., Kaohsiung (Taiwan). Dept. of Physics
Univ. of California, Los Angeles, CA (United States). Dept. of Physics and Astronomy, California NanoSystems Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy
Univ. of California, Los Angeles, CA (United States). Dept. of Physics and Astronomy, California NanoSystems Inst.
Univ. of Birmingham (United Kingdom). Nanoscale Physics Research Lab.
Cornell Univ., Ithaca, NY (United States). Dept. of Physics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Center for Electron Microscopy
Cornell Univ., Ithaca, NY (United States). Dept. of Materials Science and Engineering
Cornell Univ., Ithaca, NY (United States). Dept. of Chemistry and Chemical Biology; Huazhong Univ. of Science and Technology, Wuhan (China). School of Chemistry and Chemical Engineering
Cornell Univ., Ithaca, NY (United States). Dept. of Chemistry and Chemical Biology
Cornell Univ., Ithaca, NY (United States). School of Applied and Engineering Physics, Kavli Inst. for Nanoscale Science

Publication Date:: Tue Jun 07 00:00:00 EDT 2016

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1379388

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Scientific Data

Additional Journal Information:: Journal Volume: 3; Journal ID: ISSN 2052-4463

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

Subject:: 36 MATERIALS SCIENCE; fuel cells; nanoparticles; transmission electron microscopy

Citation Formats


                    Levin, Barnaby D. A., Padgett, Elliot, Chen, Chien-Chun, Scott, M. C., Xu, Rui, Theis, Wolfgang, Jiang, Yi, Yang, Yongsoo, Ophus, Colin, Zhang, Haitao, Ha, Don-Hyung, Wang, Deli, Yu, Yingchao, Abruña, Hector D., Robinson, Richard D., Ercius, Peter, Kourkoutis, Lena F., Miao, Jianwei, Muller, David A., and Hovden, Robert. Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.  United States: N. p., 2016. 
Web.  doi:10.1038/sdata.2016.41.

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                    Levin, Barnaby D. A., Padgett, Elliot, Chen, Chien-Chun, Scott, M. C., Xu, Rui, Theis, Wolfgang, Jiang, Yi, Yang, Yongsoo, Ophus, Colin, Zhang, Haitao, Ha, Don-Hyung, Wang, Deli, Yu, Yingchao, Abruña, Hector D., Robinson, Richard D., Ercius, Peter, Kourkoutis, Lena F., Miao, Jianwei, Muller, David A., & Hovden, Robert. Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.  United States.  https://doi.org/10.1038/sdata.2016.41

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                    Levin, Barnaby D. A., Padgett, Elliot, Chen, Chien-Chun, Scott, M. C., Xu, Rui, Theis, Wolfgang, Jiang, Yi, Yang, Yongsoo, Ophus, Colin, Zhang, Haitao, Ha, Don-Hyung, Wang, Deli, Yu, Yingchao, Abruña, Hector D., Robinson, Richard D., Ercius, Peter, Kourkoutis, Lena F., Miao, Jianwei, Muller, David A., and Hovden, Robert. Tue .  
"Nanomaterial datasets to advance tomography in scanning transmission electron microscopy".  United States.  https://doi.org/10.1038/sdata.2016.41.  https://www.osti.gov/servlets/purl/1379388.

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@article{osti_1379388,

  title        = {Nanomaterial datasets to advance tomography in scanning transmission electron microscopy},

  author       = {Levin, Barnaby D. A. and Padgett, Elliot and Chen, Chien-Chun and Scott, M. C. and Xu, Rui and Theis, Wolfgang and Jiang, Yi and Yang, Yongsoo and Ophus, Colin and Zhang, Haitao and Ha, Don-Hyung and Wang, Deli and Yu, Yingchao and Abruña, Hector D. and Robinson, Richard D. and Ercius, Peter and Kourkoutis, Lena F. and Miao, Jianwei and Muller, David A. and Hovden, Robert},

  abstractNote = {Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co 2 P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.},

  doi          = {10.1038/sdata.2016.41},

  journal      = {Scientific Data},

  number       = ,

  volume       = 3,

  place        = {United States},

  year         = {Tue Jun 07 00:00:00 EDT 2016},

  month        = {Tue Jun 07 00:00:00 EDT 2016}

}

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Figure 1: Illustration of electron tomography data acquisition and reconstruction process. Series of 2D images acquired of object of unknown 3D structure at different viewing angles. Images shown are from tiltser_Co2P.tif. 2D images combined into image stack ordered by viewing angle i.e., a tilt series. Tilt series is aligned, andmore »

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Works referenced in this record:

Three-dimensional coordinates of individual atoms in materials revealed by electron tomography
journal, September 2015

Xu, Rui; Chen, Chien-Chun; Wu, Li
Nature Materials, Vol. 14, Issue 11
DOI: 10.1038/nmat4426

Electron tomography at 2.4-ångström resolution
journal, March 2012

Scott, M. C.; Chen, Chien-Chun; Mecklenburg, Matthew
Nature, Vol. 483, Issue 7390
DOI: 10.1038/nature10934

Electron tomography and holography in materials science
journal, April 2009

Midgley, Paul A.; Dunin-Borkowski, Rafal E.
Nature Materials, Vol. 8, Issue 4
DOI: 10.1038/nmat2406

A method for monitoring the collapse of plastic sections as a function of electron dose
journal, January 1988

Luther, P. K.; Lawrence, M. C.; Crowther, R. A.
Ultramicroscopy, Vol. 24, Issue 1
DOI: 10.1016/0304-3991(88)90322-1

Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers
journal, January 2005

Lanzavecchia, S.; Cantele, F.; Bellon, P. L.
Journal of Structural Biology, Vol. 149, Issue 1
DOI: 10.1016/j.jsb.2004.09.004

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research
journal, June 2015

Ercius, Peter; Alaidi, Osama; Rames, Matthew J.
Advanced Materials, Vol. 27, Issue 38
DOI: 10.1002/adma.201501015

Reconstruction of Three Dimensional Structures from Electron Micrographs
journal, January 1968

De Rosier, D. J.; Klug, A.
Nature, Vol. 217, Issue 5124
DOI: 10.1038/217130a0

Fast Fourier method for the accurate rotation of sampled images
journal, June 1997

Larkin, Kieran G.; Oldfield, Michael A.; Klemm, Hanno
Optics Communications, Vol. 139, Issue 1-3
DOI: 10.1016/S0030-4018(97)00097-7

Controlled Synthesis of Uniform Cobalt Phosphide Hyperbranched Nanocrystals Using Tri- n -octylphosphine Oxide as a Phosphorus Source
journal, January 2011

Zhang, Haitao; Ha, Don-Hyung; Hovden, Robert
Nano Letters, Vol. 11, Issue 1
DOI: 10.1021/nl103400a

Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution
journal, March 2013

Chen, Chien-Chun; Zhu, Chun; White, Edward R.
Nature, Vol. 496, Issue 7443
DOI: 10.1038/nature12009

Three-Dimensional Morphology of Iron Oxide Nanoparticles with Reactive Concave Surfaces. A Compressed Sensing-Electron Tomography (CS-ET) Approach
journal, November 2011

Saghi, Zineb; Holland, Daniel J.; Leary, Rowan
Nano Letters, Vol. 11, Issue 11
DOI: 10.1021/nl202253a

Phase evolution for conversion reaction electrodes in lithium-ion batteries
journal, February 2014

Lin, Feng; Nordlund, Dennis; Weng, Tsu-Chien
Nature Communications, Vol. 5, Issue 1
DOI: 10.1038/ncomms4358

Visibility of Single Atoms
journal, June 1970

Crewe, A. V.; Wall, J.; Langmore, J.
Science, Vol. 168, Issue 3937
DOI: 10.1126/science.168.3937.1338

Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series
journal, February 2014

Dahmen, Tim; Baudoin, Jean-Pierre; Lupini, Andrew R.
Microscopy and Microanalysis, Vol. 20, Issue 2
DOI: 10.1017/S1431927614000075

Characterization of multi-scale microstructural features in Opalinus Clay
journal, April 2013

Keller, Lukas M.; Schuetz, Philipp; Erni, Rolf
Microporous and Mesoporous Materials, Vol. 170
DOI: 10.1016/j.micromeso.2012.11.029

Transmission electron microtomography without the “missing wedge” for quantitative structural analysis
journal, January 2007

Kawase, Noboru; Kato, Mitsuro; Nishioka, Hideo
Ultramicroscopy, Vol. 107, Issue 1
DOI: 10.1016/j.ultramic.2006.04.007

Data Processing for Atomic Resolution Electron Energy Loss Spectroscopy
journal, June 2012

Cueva, Paul; Hovden, Robert; Mundy, Julia A.
Microscopy and Microanalysis, Vol. 18, Issue 4
DOI: 10.1017/S1431927612000244

Formation Mechanism of LiFePO4 Sticks Grown by a Microwave-Assisted Liquid-Phase Process
journal, April 2012

Carriazo, Daniel; Rossell, Marta D.; Zeng, Guobo
Small, Vol. 8, Issue 14
DOI: 10.1002/smll.201102515

The Reconstruction of a Three-Dimensional Structure from Projections and its Application to Electron Microscopy
journal, June 1970

Crowther, R. A.; DeRosier, D. J.; Klug, A.
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 317, Issue 1530
DOI: 10.1098/rspa.1970.0119

Three-dimensional STEM for observing nanostructures
journal, May 2001

Koguchi, M.; Kakibayashi, H.; Tsuneta, R.
Microscopy, Vol. 50, Issue 3
DOI: 10.1093/jmicro/50.3.235

Tuning Oxygen Reduction Reaction Activity via Controllable Dealloying A Model Study of Ordered Cu₃Pt/C Intermetallic Nanocatalysts
journal, September 2012

Wang, Deli; Yu, Yingchao; Xin, Huolin L.
Nano Letters, Vol. 12, Issue 10, p. 5230-5238
DOI: 10.1021/nl302404g

Electron tomography of embedded semiconductor quantum dot
journal, January 2008

Inoue, Tomoya; Kita, Takashi; Wada, Osamu
Applied Physics Letters, Vol. 92, Issue 3
DOI: 10.1063/1.2837453