A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography
Abstract
Electron tomography is used in both materials science and structural biology to image features well below the optical resolution limit. Here, we present a new method for high-resolution 3D transmission electron microscopy (TEM) which approximately reconstructs the electrostatic potential of a sample at atomic resolution in all three dimensions. We use phase contrast images captured through-focus and at varying tilt angles, along with an implicit phase retrieval algorithm that accounts for dynamical and strong scattering, providing more accurate results with much lower electron doses than current atomic electron tomography methods. We test our algorithm using simulated images of a synthetic needle geometry dataset composed of an amorphous silicon dioxide shell around a silicon core. By simulating various levels of electron dose, tilt and defocus, missing projections, and regularization methods, we identify a configuration that allows us to accurately determine both atomic positions and species. We also test the ability of our method to recover randomly positioned vacancies in light elements such as silicon, and to accurately reconstruct strongly-scattering elements such as tungsten.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES), Chemical Sciences, Geosciences & Biosciences Division; National Science Foundation (NSF)
- OSTI Identifier:
- 1573259
- Alternate Identifier(s):
- OSTI ID: 1760197
- Grant/Contract Number:
- AC02-05CH11231; DMR1548924
- Resource Type:
- Published Article
- Journal Name:
- Ultramicroscopy
- Additional Journal Information:
- Journal Name: Ultramicroscopy Journal Volume: 208 Journal Issue: C; Journal ID: ISSN 0304-3991
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 42 ENGINEERING; Transmission electron microscopy; phase retrieval; multiple scattering; optimization; atomic electron tomography
Citation Formats
Ren, David, Ophus, Colin, Chen, Michael, and Waller, Laura. A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography. Netherlands: N. p., 2020.
Web. doi:10.1016/j.ultramic.2019.112860.
Ren, David, Ophus, Colin, Chen, Michael, & Waller, Laura. A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography. Netherlands. doi:10.1016/j.ultramic.2019.112860.
Ren, David, Ophus, Colin, Chen, Michael, and Waller, Laura. Wed .
"A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography". Netherlands. doi:10.1016/j.ultramic.2019.112860.
@article{osti_1573259,
title = {A multiple scattering algorithm for three dimensional phase contrast atomic electron tomography},
author = {Ren, David and Ophus, Colin and Chen, Michael and Waller, Laura},
abstractNote = {Electron tomography is used in both materials science and structural biology to image features well below the optical resolution limit. Here, we present a new method for high-resolution 3D transmission electron microscopy (TEM) which approximately reconstructs the electrostatic potential of a sample at atomic resolution in all three dimensions. We use phase contrast images captured through-focus and at varying tilt angles, along with an implicit phase retrieval algorithm that accounts for dynamical and strong scattering, providing more accurate results with much lower electron doses than current atomic electron tomography methods. We test our algorithm using simulated images of a synthetic needle geometry dataset composed of an amorphous silicon dioxide shell around a silicon core. By simulating various levels of electron dose, tilt and defocus, missing projections, and regularization methods, we identify a configuration that allows us to accurately determine both atomic positions and species. We also test the ability of our method to recover randomly positioned vacancies in light elements such as silicon, and to accurately reconstruct strongly-scattering elements such as tungsten.},
doi = {10.1016/j.ultramic.2019.112860},
journal = {Ultramicroscopy},
number = C,
volume = 208,
place = {Netherlands},
year = {2020},
month = {1}
}
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DOI: 10.1016/j.ultramic.2019.112860
DOI: 10.1016/j.ultramic.2019.112860
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