Skip to main content

2019 | OriginalPaper | Buchkapitel

DM-SIRT: A Distributed Method for Multi-tilt Reconstruction in Electron Tomography

verfasst von : Zihao Wang, Jingrong Zhang, Xintong Liu, Zhiyong Liu, Xiaohua Wan, Fa Zhang

Erschienen in: Bioinformatics Research and Applications

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

The ‘missing wedge’ of single tilt in electron tomography introduces severely artifacts into the reconstructed results. To reduce the ‘missing wedge’ effect, a widely used method is ‘multi-tilt reconstruction’, which collects projections using multiple different axes. However, as the number of tilt series increases, its computing and memory costs also rises. While the demand to speed up its reconstruction procedure grows, the huge memory requirement from the 3D structure and strong data dependencies from projections heavily limit its parallelization. In our work, we present a new fully distributed multi-tilt reconstruction framework named DM-SIRT. To improve the parallelism of the reconstruction process and reduce the memory requirements of each process, we formulate the multi-tilt reconstruction as a consensus optimization problem and design a distributed multi-tilt SIRT algorithm. To improve the reconstruction resolution, we applied a multi-agent consensus equilibrium (MACE) with a new data division strategy. Experiments show that along with the visually and quantitatively improvement in resolution, DM-SIRT can acquire a 5.4x speedup ratio compared to the raw multi-tilt reconstruction version. It also has 87% decrease of memory overhead and 8 times more scalable than the raw reconstruction version.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Literatur
1.
Zurück zum Zitat Lučić, V., Rigort, A., Baumeister, W.: Cryo-electron tomography: the challenge of doing structural biology in situ. J. Cell Biol. 202(3), 407–419 (2013)CrossRef Lučić, V., Rigort, A., Baumeister, W.: Cryo-electron tomography: the challenge of doing structural biology in situ. J. Cell Biol. 202(3), 407–419 (2013)CrossRef
2.
Zurück zum Zitat Grotjahn, D.A., Chowdhury, S., Xu, Y., McKenney, R.J., Schroer, T.A., Lander, G.C.: Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility. Nat. Struct. Mol. Biol. 25(3), 203 (2018)CrossRef Grotjahn, D.A., Chowdhury, S., Xu, Y., McKenney, R.J., Schroer, T.A., Lander, G.C.: Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility. Nat. Struct. Mol. Biol. 25(3), 203 (2018)CrossRef
3.
Zurück zum Zitat Batenburg, K.J., et al.: 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy 109(6), 730–740 (2009)CrossRef Batenburg, K.J., et al.: 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy 109(6), 730–740 (2009)CrossRef
4.
Zurück zum Zitat Deng, Y., Chen, Y., Zhang, Y., Wang, S., Zhang, F., Sun, F.: ICON: 3D reconstruction with “missing-information” restoration in biological electron tomography. J. Struct. Biol. 195(1), 100–112 (2016)CrossRef Deng, Y., Chen, Y., Zhang, Y., Wang, S., Zhang, F., Sun, F.: ICON: 3D reconstruction with “missing-information” restoration in biological electron tomography. J. Struct. Biol. 195(1), 100–112 (2016)CrossRef
5.
Zurück zum Zitat Yan, R., Venkatakrishnan, S.V., Liu, J., Bouman, C.A., Jiang, W.: MBIR: a cryo-electron tomography 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. bioRxiv (2018). 355529 Yan, R., Venkatakrishnan, S.V., Liu, J., Bouman, C.A., Jiang, W.: MBIR: a cryo-electron tomography 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information. bioRxiv (2018). 355529
6.
Zurück zum Zitat Penczek, P., Marko, M., Buttle, K., Frank, J.: Double-tilt electron tomography. Ultramicroscopy 60(3), 393–410 (1995)CrossRef Penczek, P., Marko, M., Buttle, K., Frank, J.: Double-tilt electron tomography. Ultramicroscopy 60(3), 393–410 (1995)CrossRef
7.
Zurück zum Zitat Phan, S., et al.: 3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography. Adv. Struct. Chem. Imaging 2(1), 8 (2017)CrossRef Phan, S., et al.: 3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography. Adv. Struct. Chem. Imaging 2(1), 8 (2017)CrossRef
8.
Zurück zum Zitat Kremer, J.R., Mastronarde, D.N., McIntosh, J.R.: Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116(1), 71–76 (1996)CrossRef Kremer, J.R., Mastronarde, D.N., McIntosh, J.R.: Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116(1), 71–76 (1996)CrossRef
9.
Zurück zum Zitat Lawrence, A., Bouwer, J.C., Perkins, G., Ellisman, M.H.: Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J. Struct. Biol. 154(2), 144–167 (2006)CrossRef Lawrence, A., Bouwer, J.C., Perkins, G., Ellisman, M.H.: Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J. Struct. Biol. 154(2), 144–167 (2006)CrossRef
10.
Zurück zum Zitat Han, R., et al.: Autom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinformatics 35(2), 319–328 (2018)CrossRef Han, R., et al.: Autom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinformatics 35(2), 319–328 (2018)CrossRef
12.
Zurück zum Zitat Buzzard, G.T., Chan, S.H., Sreehari, S., Bouman, C.A.: Plug-and-Play unplugged: optimization-free reconstruction using consensus equilibrium. SIAM J. Imaging Sci. 11(3), 2001–2020 (2018)MathSciNetCrossRef Buzzard, G.T., Chan, S.H., Sreehari, S., Bouman, C.A.: Plug-and-Play unplugged: optimization-free reconstruction using consensus equilibrium. SIAM J. Imaging Sci. 11(3), 2001–2020 (2018)MathSciNetCrossRef
13.
Zurück zum Zitat Arslan, I., Tong, J.R., Midgley, P.A.: Reducing the missing wedge: high-resolution dual axis tomography of inorganic materials. Ultramicroscopy 106(11–12), 994–1000 (2006)CrossRef Arslan, I., Tong, J.R., Midgley, P.A.: Reducing the missing wedge: high-resolution dual axis tomography of inorganic materials. Ultramicroscopy 106(11–12), 994–1000 (2006)CrossRef
14.
Zurück zum Zitat Gilbert, P.: Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 36(1), 105–117 (1972)CrossRef Gilbert, P.: Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 36(1), 105–117 (1972)CrossRef
15.
Zurück zum Zitat Haberfehlner, G., Serra, R., Cooper, D., Barraud, S., Bleuet, P.: 3D spatial resolution improvement by dual-axis electron tomography: application to tri-gate transistors. Ultramicroscopy 136, 144–153 (2014)CrossRef Haberfehlner, G., Serra, R., Cooper, D., Barraud, S., Bleuet, P.: 3D spatial resolution improvement by dual-axis electron tomography: application to tri-gate transistors. Ultramicroscopy 136, 144–153 (2014)CrossRef
16.
Zurück zum Zitat Boyd, S., Parikh, N., Chu, E., Peleato, B., Eckstein, J., et al.: Distributed optimization and statistical learning via the alternating direction method of multipliers. Found. Trends® Mach. Learn. 3(1), 1–122 (2011)MATH Boyd, S., Parikh, N., Chu, E., Peleato, B., Eckstein, J., et al.: Distributed optimization and statistical learning via the alternating direction method of multipliers. Found. Trends® Mach. Learn. 3(1), 1–122 (2011)MATH
17.
Zurück zum Zitat Gregor, J., Benson, T.: Computational analysis and improvement of SIRT. IEEE Trans. Med. Imaging 27(7), 918–924 (2008)CrossRef Gregor, J., Benson, T.: Computational analysis and improvement of SIRT. IEEE Trans. Med. Imaging 27(7), 918–924 (2008)CrossRef
18.
Zurück zum Zitat Sorzano, C., et al.: A survey of the use of iterative reconstruction algorithms in electron microscopy. BioMed Research International (2017) Sorzano, C., et al.: A survey of the use of iterative reconstruction algorithms in electron microscopy. BioMed Research International (2017)
20.
Zurück zum Zitat Van der Sluis, A., van der Vorst, H.A.: SIRT-and CG-type methods for the iterative solution of sparse linear least-squares problems. Linear Algebr. Appl. 130, 257–303 (1990)MathSciNetMATHCrossRef Van der Sluis, A., van der Vorst, H.A.: SIRT-and CG-type methods for the iterative solution of sparse linear least-squares problems. Linear Algebr. Appl. 130, 257–303 (1990)MathSciNetMATHCrossRef
Metadaten
Titel
DM-SIRT: A Distributed Method for Multi-tilt Reconstruction in Electron Tomography
verfasst von
Zihao Wang
Jingrong Zhang
Xintong Liu
Zhiyong Liu
Xiaohua Wan
Fa Zhang
Copyright-Jahr
2019
DOI
https://doi.org/10.1007/978-3-030-20242-2_19