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

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Journal Article · Tue Jun 07 00:00:00 EDT 2016 · Scientific Data

DOI:https://doi.org/10.1038/sdata.2016.41· OSTI ID:1379388

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

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.

View Accepted Manuscript (DOE)

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

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379388

Journal Information:: Scientific Data, Journal Name: Scientific Data Vol. 3; ISSN 2052-4463

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (44)

Electron Tomography: Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research (Adv. Mater. 38/2015) Ercius, Peter; Alaidi, Osama; Rames, Matthew J. Advanced Materials, Vol. 27, Issue 38 https://doi.org/10.1002/adma.201570253	journal	October 2015
Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy Guckenberger, R. Ultramicroscopy, Vol. 9, Issue 1-2 https://doi.org/10.1016/0304-3991(82)90239-x	journal	January 1982
Resolution and optimum conditions for dark-field STEM and CTEM imaging Hammel, M.; Rose, H. Ultramicroscopy, Vol. 49, Issue 1-4 https://doi.org/10.1016/0304-3991(93)90214-i	journal	February 1993
3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Midgley, P. A.; Weyland, M. Ultramicroscopy, Vol. 96, Issue 3-4 https://doi.org/10.1016/s0304-3991(03)00105-0	journal	September 2003
Multicomponent Nanomaterials with Complex Networked Architectures from Orthogonal Degradation and Binary Metal Backfilling in ABC Triblock Terpolymers Cowman, Christina D.; Padgett, Elliot; Tan, Kwan Wee Journal of the American Chemical Society, Vol. 137, Issue 18 https://doi.org/10.1021/jacs.5b01915	journal	April 2015
Three-dimensional metrology and fractal analysis of dendritic nanostructures Saghi, Zineb; Xu, Xiaojing; Möbus, Günter Physical Review B, Vol. 78, Issue 20 https://doi.org/10.1103/physrevb.78.205428	journal	November 2008
Nanomaterial datasets to advance tomography in scanning transmission electron microscopy [Supplemental Data] Abruña, Héctor; Muller, David; Xu, Rui figshare-Supplementary information for journal article at DOI: 10.1038/sdata.2016.41, 12 files https://doi.org/10.6084/m9.figshare.c.2185342	dataset	June 2016
Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research Ercius, Peter; Alaidi, Osama; Rames, Matthew J. Advanced Materials, Vol. 27, Issue 38 https://doi.org/10.1002/adma.201501015	journal	June 2015
Formation Mechanism of LiFePO4 Sticks Grown by a Microwave-Assisted Liquid-Phase Process Carriazo, Daniel; Rossell, Marta D.; Zeng, Guobo Small, Vol. 8, Issue 14 https://doi.org/10.1002/smll.201102515	journal	April 2012
Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy Guckenberger, R. Ultramicroscopy, Vol. 9, Issue 1-2 https://doi.org/10.1016/0304-3991(82)90239-X	journal	January 1982
A method for monitoring the collapse of plastic sections as a function of electron dose Luther, P. K.; Lawrence, M. C.; Crowther, R. A. Ultramicroscopy, Vol. 24, Issue 1 https://doi.org/10.1016/0304-3991(88)90322-1	journal	January 1988
Resolution and optimum conditions for dark-field STEM and CTEM imaging Hammel, M.; Rose, H. Ultramicroscopy, Vol. 49, Issue 1-4 https://doi.org/10.1016/0304-3991(93)90214-I	journal	February 1993
Double-tilt electron tomography Penczek, Pawel; Marko, Michael; Buttle, Karolyn Ultramicroscopy, Vol. 60, Issue 3 https://doi.org/10.1016/0304-3991(95)00078-X	journal	October 1995
Fast Fourier method for the accurate rotation of sampled images Larkin, Kieran G.; Oldfield, Michael A.; Klemm, Hanno Optics Communications, Vol. 139, Issue 1-3 https://doi.org/10.1016/S0030-4018(97)00097-7	journal	June 1997
3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Midgley, P. A.; Weyland, M. Ultramicroscopy, Vol. 96, Issue 3-4 https://doi.org/10.1016/S0304-3991(03)00105-0	journal	September 2003
Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers Lanzavecchia, S.; Cantele, F.; Bellon, P. L. Journal of Structural Biology, Vol. 149, Issue 1 https://doi.org/10.1016/j.jsb.2004.09.004	journal	January 2005
Characterization of multi-scale microstructural features in Opalinus Clay Keller, Lukas M.; Schuetz, Philipp; Erni, Rolf Microporous and Mesoporous Materials, Vol. 170 https://doi.org/10.1016/j.micromeso.2012.11.029	journal	April 2013
Transmission electron microtomography without the “missing wedge” for quantitative structural analysis Kawase, Noboru; Kato, Mitsuro; Nishioka, Hideo Ultramicroscopy, Vol. 107, Issue 1 https://doi.org/10.1016/j.ultramic.2006.04.007	journal	January 2007
Breaking the Crowther limit: Combining depth-sectioning and tilt tomography for high-resolution, wide-field 3D reconstructions Hovden, Robert; Ercius, Peter; Jiang, Yi Ultramicroscopy, Vol. 140 https://doi.org/10.1016/j.ultramic.2014.01.013	journal	May 2014
Extended Depth of Field for High-Resolution Scanning Transmission Electron Microscopy Hovden, Robert; Xin, Huolin L.; Muller, David A. Microscopy and Microanalysis, Vol. 17, Issue 1 https://doi.org/10.1017/S1431927610094171	journal	December 2010
Data Processing for Atomic Resolution Electron Energy Loss Spectroscopy Cueva, Paul; Hovden, Robert; Mundy, Julia A. Microscopy and Microanalysis, Vol. 18, Issue 4 https://doi.org/10.1017/S1431927612000244	journal	June 2012
Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series Dahmen, Tim; Baudoin, Jean-Pierre; Lupini, Andrew R. Microscopy and Microanalysis, Vol. 20, Issue 2 https://doi.org/10.1017/S1431927614000075	journal	February 2014
Periodic Artifact Reduction in Fourier Transforms of Full Field Atomic Resolution Images Hovden, Robert; Jiang, Yi; Xin, Huolin L. Microscopy and Microanalysis, Vol. 21, Issue 2 https://doi.org/10.1017/S1431927614014639	journal	January 2015
Repeatable and Transferable Processing for Electron Tomography: An Open Platform for Visualization and Reconstruction of 3D Materials Hovden, Robert; Hanwell, Marcus D.; Ayachit, Utkarsh Microscopy and Microanalysis, Vol. 21, Issue S3 https://doi.org/10.1017/S1431927615012817	journal	August 2015
Interplay of Three-Dimensional Morphologies and Photocarrier Dynamics of Polymer/TiO ₂ Bulk Heterojunction Solar Cells Li, Shao-Sian; Chang, Ching-Pin; Lin, Chih-Cheng Journal of the American Chemical Society, Vol. 133, Issue 30 https://doi.org/10.1021/ja203151z	journal	August 2011
Electron Tomography of Nanoparticle Catalysts on Porous Supports: A New Technique Based on Rutherford Scattering Weyland, Matthew; Midgley, Paul A.; Thomas, John Meurig The Journal of Physical Chemistry B, Vol. 105, Issue 33 https://doi.org/10.1021/jp011566s	journal	August 2001
Controlled Synthesis of Uniform Cobalt Phosphide Hyperbranched Nanocrystals Using Tri- n -octylphosphine Oxide as a Phosphorus Source Zhang, Haitao; Ha, Don-Hyung; Hovden, Robert Nano Letters, Vol. 11, Issue 1 https://doi.org/10.1021/nl103400a	journal	January 2011
Three-Dimensional Morphology of Iron Oxide Nanoparticles with Reactive Concave Surfaces. A Compressed Sensing-Electron Tomography (CS-ET) Approach Saghi, Zineb; Holland, Daniel J.; Leary, Rowan Nano Letters, Vol. 11, Issue 11 https://doi.org/10.1021/nl202253a	journal	November 2011
Tuning Oxygen Reduction Reaction Activity via Controllable Dealloying A Model Study of Ordered Cu₃Pt/C Intermetallic Nanocatalysts Wang, Deli; Yu, Yingchao; Xin, Huolin L. Nano Letters, Vol. 12, Issue 10, p. 5230-5238 https://doi.org/10.1021/nl302404g	journal	September 2012
Reconstruction of Three Dimensional Structures from Electron Micrographs De Rosier, D. J.; Klug, A. Nature, Vol. 217, Issue 5124 https://doi.org/10.1038/217130a0	journal	January 1968
Three-dimensional atomic imaging of crystalline nanoparticles Van Aert, Sandra; Batenburg, Kees J.; Rossell, Marta D. Nature, Vol. 470, Issue 7334 https://doi.org/10.1038/nature09741	journal	February 2011
Electron tomography at 2.4-ångström resolution Scott, M. C.; Chen, Chien-Chun; Mecklenburg, Matthew Nature, Vol. 483, Issue 7390 https://doi.org/10.1038/nature10934	journal	March 2012
Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution Chen, Chien-Chun; Zhu, Chun; White, Edward R. Nature, Vol. 496, Issue 7443 https://doi.org/10.1038/nature12009	journal	March 2013
Phase evolution for conversion reaction electrodes in lithium-ion batteries Lin, Feng; Nordlund, Dennis; Weng, Tsu-Chien Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4358	journal	February 2014
Electron tomography and holography in materials science Midgley, Paul A.; Dunin-Borkowski, Rafal E. Nature Materials, Vol. 8, Issue 4 https://doi.org/10.1038/nmat2406	journal	April 2009
Three-dimensional coordinates of individual atoms in materials revealed by electron tomography Xu, Rui; Chen, Chien-Chun; Wu, Li Nature Materials, Vol. 14, Issue 11 https://doi.org/10.1038/nmat4426	journal	September 2015
Electron tomography of embedded semiconductor quantum dot Inoue, Tomoya; Kita, Takashi; Wada, Osamu Applied Physics Letters, Vol. 92, Issue 3 https://doi.org/10.1063/1.2837453	journal	January 2008
Three-dimensional STEM for observing nanostructures Koguchi, M.; Kakibayashi, H.; Tsuneta, R. Microscopy, Vol. 50, Issue 3 https://doi.org/10.1093/jmicro/50.3.235	journal	May 2001
The Reconstruction of a Three-Dimensional Structure from Projections and its Application to Electron Microscopy Crowther, R. A.; DeRosier, D. J.; Klug, A. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 317, Issue 1530 https://doi.org/10.1098/rspa.1970.0119	journal	June 1970
Equally sloped tomography with oversampling reconstruction Miao, Jianwei; Förster, Friedrich; Levi, Ofer Physical Review B, Vol. 72, Issue 5 https://doi.org/10.1103/PhysRevB.72.052103	journal	August 2005
Three-dimensional metrology and fractal analysis of dendritic nanostructures Saghi, Zineb; Xu, Xiaojing; Möbus, Günter Physical Review B, Vol. 78, Issue 20 https://doi.org/10.1103/PhysRevB.78.205428	journal	November 2008
Visualizing the 3D Internal Structure of Calcite Single Crystals Grown in Agarose Hydrogels Li, Hanying; Xin, Huolin L.; Muller, David A. Science, Vol. 326, Issue 5957 https://doi.org/10.1126/science.1178583	journal	November 2009
Visibility of Single Atoms Crewe, A. V.; Wall, J.; Langmore, J. Science, Vol. 168, Issue 3937 https://doi.org/10.1126/science.168.3937.1338	journal	June 1970
Nanomaterial datasets to advance tomography in scanning transmission electron microscopy [Supplemental Data] Abruña, Héctor; Muller, David A.; Xu, Rui figshare-Supplementary information for journal article at DOI: 10.1038/sdata.2016.41, 12 files https://doi.org/10.6084/m9.figshare.c.2185342.v1	collection	June 2016

Cited By (11)

Controlled Synthesis of Uniform Cobalt Phosphide Hyperbranched Nanocrystals Using Tri- n -octylphosphine Oxide as a Phosphorus Source Zhang, Haitao; Ha, Don-Hyung; Hovden, Robert Nano Letters, Vol. 11, Issue 1 https://doi.org/10.1021/nl103400a	journal	January 2011
Visualization of the effect of additives on the nanostructures of individual bio-inspired calcite crystals Ihli, Johannes; Clark, Jesse N.; Kanwal, Nasima Chemical Science, Vol. 10, Issue 4 https://doi.org/10.1039/c8sc03733g	journal	January 2019
Multimodal x-ray and electron microscopy of the Allende meteorite Lo, Yuan Hung; Liao, Chen-Ting; Zhou, Jihan Science Advances, Vol. 5, Issue 9 https://doi.org/10.1126/sciadv.aax3009	journal	September 2019
Multiscale higher-order TV operators for L1 regularization Sanders, Toby; Platte, Rodrigo B. Advanced Structural and Chemical Imaging, Vol. 4, Issue 1 https://doi.org/10.1186/s40679-018-0061-x	journal	October 2018
Approaches to Exploring Spatio-Temporal Surface Dynamics in Nanoparticles with In Situ Transmission Electron Microscopy Lawrence, Ethan L.; Levin, Barnaby D. A.; Miller, Benjamin K. Microscopy and Microanalysis, Vol. 26, Issue 1 https://doi.org/10.1017/s1431927619015228	journal	December 2019
Tutorial on the Visualization of Volumetric Data Using tomviz Levin, Barnaby D. A.; Jiang, Yi; Padgett, Elliot Microscopy Today, Vol. 26, Issue 1 https://doi.org/10.1017/s1551929517001213	journal	January 2018
Quantitative characterization of high temperature oxidation using electron tomography and energy-dispersive X-ray spectroscopy Zhou, Jihan; Taylor, Matthew; Melinte, Georgian A. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-28348-3	journal	July 2018
Towards a classification strategy for complex nanostructures Castagnola, V.; Cookman, J.; de Araújo, J. M. Nanoscale Horizons, Vol. 2, Issue 4 https://doi.org/10.1039/c6nh00219f	journal	January 2017
A quantitative methodology for the study of particle–electrode impacts Little, Christopher A.; Xie, Ruochen; Batchelor-McAuley, Christopher Physical Chemistry Chemical Physics, Vol. 20, Issue 19 https://doi.org/10.1039/c8cp01561a	journal	January 2018
Exploring the Capability of HAADF-STEM Techniques to Characterize Graphene Distribution in Nanocomposites by Simulations Baladés, N.; Sales, D. L.; Herrera, M. Journal of Nanomaterials, Vol. 2018 https://doi.org/10.1155/2018/4906746	journal	December 2018
Electron tomography for functional nanomaterials Hovden, Robert; Muller, David A. MRS Bulletin, Vol. 45, Issue 4 https://doi.org/10.1557/mrs.2020.87	journal	April 2020

Figures / Tables (6)

Similar Records

Nanoscale TEM tomography of metal oxide photocatalyst systems.

Conference · Sun Aug 01 00:00:00 EDT 2004 · OSTI ID:959241

A Simple Preparation Method for Full-Range Electron Tomography of Nanoparticles and Fine Powders

Journal Article · Thu Nov 30 23:00:00 EST 2017 · Microscopy and Microanalysis · OSTI ID:1538941

Related Subjects

36 MATERIALS SCIENCE
fuel cells
nanoparticles
transmission electron microscopy

3D reconstruction of platinum nanoparticles on carbon nanofibre using electron tomography Hovden, Robert; Padgett, Elliot; Muller, David A. https://doi.org/10.6084/M9.FIGSHARE.C.2185342_D3 The current record is supplemented by this dataset	dataset	January 2016
Electron tomography series of platinum nanoparticle at atomic resolution Chen, Chien-Chun; Scott, Mary Cooper; Miao, John https://doi.org/10.6084/M9.FIGSHARE.C.2185342_D7 The current record is supplemented by this dataset	dataset	January 2016
Preprocessed electron tomography series of tungsten at atomic resolution Xu, Rui; Ercius, Peter; Yang, Yongsoo https://doi.org/10.6084/M9.FIGSHARE.C.2185342_D9 The current record is supplemented by this dataset	dataset	January 2016
Nanomaterial datasets to advance tomography in scanning transmission electron microscopy [Supplemental Data] Abruña, Héctor; Muller, David; Xu, Rui https://doi.org/10.6084/m9.figshare.c.2185342 The current record is supplemented by this dataset	dataset	June 2016
Nanomaterial datasets to advance tomography in scanning transmission electron microscopy [Supplemental Data] Abruña, Héctor; Muller, David A.; Xu, Rui https://doi.org/10.6084/m9.figshare.c.2185342.v1 The current record is supplemented by this collection	collection	June 2016
Nanomaterial datasets to advance tomography in scanning transmission electron microscopy [Supplemental Data] Abruña, Héctor; Muller, David A.; Xu, Rui https://doi.org/10.6084/m9.figshare.c.2185342.v2 The current record is supplemented by this collection	collection	June 2016
Electron tomography of hyperbranched Co2P nanoparticle Robinson, Richard; Zhang, Haitao; Hovden, Robert https://doi.org/10.6084/m9.figshare.c.2185342_d1 The current record is supplemented by this dataset	dataset	January 2016
Electron tomography of hyperbranched Co2P nanoparticle Robinson, Richard; Zhang, Haitao; Hovden, Robert https://doi.org/10.6084/m9.figshare.c.2185342_d1.v2 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of Pt-Cu nanocatalysts using electron tomography Wang, Deli; Jiang, Yi; Ercius, Peter https://doi.org/10.6084/m9.figshare.c.2185342_d14 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of hyperbranched Co2P nanoparticle using electron tomography Robinson, Richard; Hovden, Robert; Kourkoutis, Lena Fitting https://doi.org/10.6084/m9.figshare.c.2185342_d2 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of hyperbranched Co2P nanoparticle using electron tomography Robinson, Richard; Hovden, Robert; Kourkoutis, Lena Fitting https://doi.org/10.6084/m9.figshare.c.2185342_d2.v2 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of platinum nanoparticles on carbon nanofibre using electron tomography Hovden, Robert; Padgett, Elliot; Muller, David A. https://doi.org/10.6084/m9.figshare.c.2185342_d3.v3 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of platinum nanoparticles on carbon nanofibre using electron tomography Chen, Chien-Chun; Scott, Mary Cooper; Miao, John https://doi.org/10.6084/m9.figshare.c.2185342_d6 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of platinum nanoparticles on carbon nanofibre using electron tomography Chen, Chien-Chun; Scott, Mary Cooper; Miao, John https://doi.org/10.6084/m9.figshare.c.2185342_d6.v2 The current record is supplemented by this dataset	dataset	January 2016
Electron tomography series of platinum nanoparticle at atomic resolution Chen, Chien-Chun; Scott, Mary Cooper; Miao, John https://doi.org/10.6084/m9.figshare.c.2185342_d7.v2 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of tungsten at atomic resolution using electron tomography Xu, Rui; Ercius, Peter; Yang, Yongsoo https://doi.org/10.6084/m9.figshare.c.2185342_d8 The current record is supplemented by this dataset	dataset	January 2016
3D reconstruction of tungsten at atomic resolution using electron tomography Xu, Rui; Ercius, Peter; Yang, Yongsoo https://doi.org/10.6084/m9.figshare.c.2185342_d8.v2 The current record is supplemented by this dataset	dataset	January 2016

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Citation Formats

References (44)

Cited By (11)

Linked Research (17)

Figures / Tables (6)

Similar Records

Related Subjects