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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]
  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 Lab. (ANL), Argonne, IL (United States); Brookhaven National Lab. (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) (SC-22)
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.
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. doi:10.1038/s41598-017-12141-9.
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. doi:10.1038/s41598-017-12141-9. https://www.osti.gov/servlets/purl/1393872.
@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 = {2017},
month = {9}
}

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Works referenced in this record:

Missing wedge computed tomography by iterative algorithm DIRECTT: MISSING WEDGE COMPUTED TOMOGRAPHY BY ITERATIVE ALGORITHM DIRECTT
journal, January 2016

  • Kupsch, Andreas; Lange, Axel; Hentschel, Manfred P.
  • Journal of Microscopy, Vol. 261, Issue 1
  • DOI: 10.1111/jmi.12313

Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography
journal, June 2006

  • Ercius, Peter; Weyland, Matthew; Muller, David A.
  • Applied Physics Letters, Vol. 88, Issue 24
  • DOI: 10.1063/1.2213185

XDesign : an open-source software package for designing X-ray imaging phantoms and experiments
journal, February 2017


Efficient subpixel image registration algorithms
journal, January 2008

  • Guizar-Sicairos, Manuel; Thurman, Samuel T.; Fienup, James R.
  • Optics Letters, Vol. 33, Issue 2
  • DOI: 10.1364/OL.33.000156

Multiphase Method for Automatic Alignment of Transmission Electron Microscope Images Using Markers
journal, January 2001

  • Brandt, Sami; Heikkonen, Jukka; Engelhardt, Peter
  • Journal of Structural Biology, Vol. 133, Issue 1
  • DOI: 10.1006/jsbi.2001.4343

Z-contrast stem for materials science
journal, June 1989


Transform-based backprojection for volume reconstruction of large format electron microscope tilt series
journal, May 2006

  • Lawrence, Albert; Bouwer, James C.; Perkins, Guy
  • Journal of Structural Biology, Vol. 154, Issue 2
  • DOI: 10.1016/j.jsb.2005.12.012

A novel fully automatic scheme for fiducial marker-based alignment in electron tomography
journal, December 2015


Marker-free image registration of electron tomography tilt-series
journal, April 2009

  • Sorzano, Carlos Oscar Sanchez; Messaoudi, Cédric; Eibauer, Matthias
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-124

Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography
journal, February 2006


Computed tomography of cryogenic biological specimens based on X-ray microscopic images
journal, August 2000


Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series
journal, April 2010

  • Castaño-Díez, Daniel; Scheffer, Margot; Al-Amoudi, Ashraf
  • Journal of Structural Biology, Vol. 170, Issue 1
  • DOI: 10.1016/j.jsb.2010.01.014

Pushing the limits: an instrument for hard X-ray imaging below 20 nm
journal, January 2015


MAPS : A set of software tools for analysis and visualization of 3D X-ray fluorescence data sets
journal, March 2003


Multi-resolution radiograph alignment for motion correction in x-ray micro-tomography
conference, October 2016

  • Latham, Shane J.; Kingston, Andrew M.; Recur, Benoit
  • SPIE Optical Engineering + Applications, SPIE Proceedings
  • DOI: 10.1117/12.2238259

Joint 3D alignment-reconstruction multi-scale approach for cryo electron tomography
conference, April 2016

  • Rojbani, Hmida; Baudrier, Etienne; Naegel, Benoit
  • 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI 2016), 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI)
  • DOI: 10.1109/isbi.2016.7493460

Reliable method for calculating the center of rotation in parallel-beam tomography
journal, January 2014

  • Vo, Nghia T.; Drakopoulos, Michael; Atwood, Robert C.
  • Optics Express, Vol. 22, Issue 16
  • DOI: 10.1364/OE.22.019078

Maximum Likelihood Reconstruction for Emission Tomography
journal, October 1982


Enhancing grain boundary ionic conductivity in mixed ionic–electronic conductors
journal, April 2015

  • Lin, Ye; Fang, Shumin; Su, Dong
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms7824

An automatic method of detecting and tracking fiducial markers for alignment in electron tomography
journal, November 2010

  • Cao, M.; Takaoka, A.; Zhang, H. -B.
  • Journal of Electron Microscopy, Vol. 60, Issue 1
  • DOI: 10.1093/jmicro/dfq076

A Fast Sinc Function Gridding Algorithm for Fourier Inversion in Computer Tomography
journal, December 1985


Nanoscale 3D imaging at the Advanced Photon Source
journal, May 2016


A marker-free alignment method for electron tomography
journal, June 1995


The Bionanoprobe: hard X-ray fluorescence nanoprobe with cryogenic capabilities
journal, December 2013


An instrument for 3D x-ray nano-imaging
journal, July 2012

  • Holler, M.; Raabe, J.; Diaz, A.
  • Review of Scientific Instruments, Vol. 83, Issue 7
  • DOI: 10.1063/1.4737624

TomoPy: a framework for the analysis of synchrotron tomographic data
journal, August 2014

  • Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui
  • Journal of Synchrotron Radiation, Vol. 21, Issue 5
  • DOI: 10.1107/S1600577514013939

Automatic object and image alignment using Fourier Descriptors
journal, September 2008


A marker-free automatic alignment method based on scale-invariant features
journal, April 2014


scikit-image: image processing in Python
journal, January 2014

  • van der Walt, Stéfan; Schönberger, Johannes L.; Nunez-Iglesias, Juan
  • PeerJ, Vol. 2
  • DOI: 10.7717/peerj.453

Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography
journal, December 1970


Towards automatic electron tomography II. Implementation of autofocus and low-dose procedures
journal, February 1993


Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm
journal, January 2005

  • Yang, Chao; Ng, Esmond G.; Penczek, Pawel A.
  • Journal of Structural Biology, Vol. 149, Issue 1
  • DOI: 10.1016/j.jsb.2004.08.010

Runout error correction in tomographic reconstruction by intensity summation method
journal, July 2016


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

X-ray Tomography Generates 3-D Reconstructions of the Yeast, Saccharomyces cerevisiae , at 60-nm Resolution
journal, March 2004

  • Larabell, Carolyn A.; Le Gros, Mark A.
  • Molecular Biology of the Cell, Vol. 15, Issue 3
  • DOI: 10.1091/mbc.E03-07-0522

Automated markerless full field hard x-ray microscopic tomography at sub-50 nm 3-dimension spatial resolution
journal, April 2012

  • Wang, Jun; Karen Chen, Yu-chen; Yuan, Qingxi
  • Applied Physics Letters, Vol. 100, Issue 14
  • DOI: 10.1063/1.3701579

TXM-Wizard : a program for advanced data collection and evaluation in full-field transmission X-ray microscopy
journal, January 2012

  • Liu, Yijin; Meirer, Florian; Williams, Phillip A.
  • Journal of Synchrotron Radiation, Vol. 19, Issue 2
  • DOI: 10.1107/S0909049511049144

Alignment of electron tomographic series by correlation without the use of gold particles
journal, April 1996


Automatic Alignment of Transmission Electron Microscope Tilt Series without Fiducial Markers
journal, December 2001

  • Brandt, Sami; Heikkonen, Jukka; Engelhardt, Peter
  • Journal of Structural Biology, Vol. 136, Issue 3
  • DOI: 10.1006/jsbi.2001.4443

Iterative methods for the three-dimensional reconstruction of an object from projections
journal, July 1972


Phase tomography from x-ray coherent diffractive imaging projections
journal, January 2011

  • Guizar-Sicairos, Manuel; Diaz, Ana; Holler, Mirko
  • Optics Express, Vol. 19, Issue 22
  • DOI: 10.1364/OE.19.021345

Software image alignment for X-ray microtomography with submicrometre resolution using a SEM-based X-ray microscope
journal, December 2007


Compensation of mechanical inaccuracies in micro-CT and nano-CT
conference, September 2008

  • Sasov, Alexander; Liu, Xuan; Salmon, Phil L.
  • Optical Engineering + Applications, SPIE Proceedings
  • DOI: 10.1117/12.793212

Ptychographic X-ray computed tomography at the nanoscale
journal, September 2010

  • Dierolf, Martin; Menzel, Andreas; Thibault, Pierre
  • Nature, Vol. 467, Issue 7314
  • DOI: 10.1038/nature09419

Non-linear Bundle Adjustment for Electron Tomography
conference, March 2009

  • Phan, Sébastien; Bouwer, James; Lanman, Jason
  • 2009 WRI World Congress on Computer Science and Information Engineering
  • DOI: 10.1109/CSIE.2009.864

Techniques for calibrating spindles with nanometer error motion
journal, January 2005


Alignment of tomographic projections using an incomplete set of fiducial markers
journal, January 1991


Three-dimensional reconstruction of imperfect two-dimensional crystals
journal, January 1984


Refinement procedure for the image alignment in high-resolution electron tomography
journal, August 2011


Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography
journal, January 1999


Fiducial-less alignment of cryo-sections
journal, September 2007

  • Castaño-Díez, Daniel; Al-Amoudi, Ashraf; Glynn, Anne-Marie
  • Journal of Structural Biology, Vol. 159, Issue 3
  • DOI: 10.1016/j.jsb.2007.04.014

Quantitative interior x-ray nanotomography by a hybrid imaging technique
journal, January 2015


Automatic alignment and reconstruction of images for soft X-ray tomography
journal, February 2012

  • Parkinson, Dilworth Y.; Knoechel, Christian; Yang, Chao
  • Journal of Structural Biology, Vol. 177, Issue 2
  • DOI: 10.1016/j.jsb.2011.11.027

Markov random field based automatic image alignment for electron tomography
journal, March 2008

  • Amat, Fernando; Moussavi, Farshid; Comolli, Luis R.
  • Journal of Structural Biology, Vol. 161, Issue 3
  • DOI: 10.1016/j.jsb.2007.07.007

Automatic coarse-alignment for TEM tilt series of rod-shaped specimens collected with a full angular range
journal, July 2010


Automated determination of the center of rotation in tomography data
journal, January 2006

  • Donath, Tilman; Beckmann, Felix; Schreyer, Andreas
  • Journal of the Optical Society of America A, Vol. 23, Issue 5
  • DOI: 10.1364/JOSAA.23.001048

Electron microscope tomography: transcription in three dimensions
journal, April 1983


Zur elektronenmikroskopisch dreidimensionalen Rekonstruktion eines Objektes
journal, December 1974


Practical pseudo-3D registration for large tomographic images
conference, September 2014

  • Liu, Xuan; Laperre, Kjell; Sasov, Alexander
  • SPIE Optical Engineering + Applications, SPIE Proceedings
  • DOI: 10.1117/12.2061618

Maximum Likelihood from Incomplete Data Via the EM Algorithm
journal, September 1977

  • Dempster, A. P.; Laird, N. M.; Rubin, D. B.
  • Journal of the Royal Statistical Society: Series B (Methodological), Vol. 39, Issue 1
  • DOI: 10.1111/j.2517-6161.1977.tb01600.x

    Works referencing / citing this record:

    Multimodal x-ray nanotomography
    journal, April 2020