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Title: Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection

Abstract

As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [3];  [1];  [2];  [5];  [5];  [5];  [1];  [4];  [3];  [3];  [6]
+ Show Author Affiliations
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
  2. Northwestern Univ., Evanston, IL (United States). Dept. of Physics and Astronomy
  3. Northwestern Univ., Evanston, IL (United States). Dept. of Electrical Engineering and Computer Science
  4. Northwestern Univ., Evanston, IL (United States). Dept. of Materials Science and Engineering
  5. Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)
  6. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Northwestern Univ., Evanston, IL (United States). Dept. of Physics and Astronomy; Northwestern Univ., Evanston, IL (United States). Chemistry of Life Processes Inst.
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States); Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Org.:
Northwestern University; National Science Foundation (NSF); National Institutes of Health (NIH); Northwestern University, International Institute for Nanotechnology (IIN); W.M. Keck Foundation; USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1393872
Alternate Identifier(s):
OSTI ID: 1413918
Report Number(s):
BNL-114399-2017-JA
Journal ID: ISSN 2045-2322; 134341
Grant/Contract Number:  
AC02-06CH11357; SC0012704
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
47 OTHER INSTRUMENTATION; Three-dimensional microscopy; Tomographic image processing; X-ray microscopy; 97 MATHEMATICS AND COMPUTING

Citation Formats

Gürsoy, Doğa, Hong, Young P., He, Kuan, Hujsak, Karl, Yoo, Seunghwan, Chen, Si, Li, Yue, Ge, Mingyuan, Miller, Lisa M., Chu, Yong S., De Andrade, Vincent, He, Kai, Cossairt, Oliver, Katsaggelos, Aggelos K., and Jacobsen, Chris. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. United States: N. p., 2017. Web. doi:10.1038/s41598-017-12141-9.
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Gürsoy, Doğa, Hong, Young P., He, Kuan, Hujsak, Karl, Yoo, Seunghwan, Chen, Si, Li, Yue, Ge, Mingyuan, Miller, Lisa M., Chu, Yong S., De Andrade, Vincent, He, Kai, Cossairt, Oliver, Katsaggelos, Aggelos K., & Jacobsen, Chris. Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection. United States. https://doi.org/10.1038/s41598-017-12141-9
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Gürsoy, Doğa, Hong, Young P., He, Kuan, Hujsak, Karl, Yoo, Seunghwan, Chen, Si, Li, Yue, Ge, Mingyuan, Miller, Lisa M., Chu, Yong S., De Andrade, Vincent, He, Kai, Cossairt, Oliver, Katsaggelos, Aggelos K., and Jacobsen, Chris. Mon . "Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection". United States. https://doi.org/10.1038/s41598-017-12141-9. https://www.osti.gov/servlets/purl/1393872.
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@article{osti_1393872,
title = {Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection},
author = {Gürsoy, Doğa and Hong, Young P. and He, Kuan and Hujsak, Karl and Yoo, Seunghwan and Chen, Si and Li, Yue and Ge, Mingyuan and Miller, Lisa M. and Chu, Yong S. and De Andrade, Vincent and He, Kai and Cossairt, Oliver and Katsaggelos, Aggelos K. and Jacobsen, Chris},
abstractNote = {As x-ray and electron tomography is pushed further into the nanoscale, the limitations of rotation stages become more apparent, leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality three-dimensional images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. With simulated data where we know the alignment error of each projection image, our approach shows a residual alignment error that is a factor of a thousand smaller, and it reaches the same error level in the reconstructed image in less than half the number of iterations. We then show its application to experimental data in x-ray and electron nanotomography.},
doi = {10.1038/s41598-017-12141-9},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Mon Sep 18 00:00:00 EDT 2017},
month = {Mon Sep 18 00:00:00 EDT 2017}
}
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https://doi.org/10.1038/s41598-017-12141-9
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    Ab initio nonrigid X-ray nanotomography.
    journalarticle, January 2019

    • Odstrcil, Michal; Holler, Mirko; Raabe, Jörg
    • Springer Science and Business Media LLC
    • DOI: 10.17863/cam.43115

    Ab initio nonrigid X-ray nanotomography
    text, January 2019

    • Odstrcil, Michal; Holler, Mirko; Raabe, Jörg
    • Deutsches Elektronen-Synchrotron, DESY, Hamburg
    • DOI: 10.3204/pubdb-2020-00848
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