Computational methods in super-resolution microscopy

Zhi-ping ZENG; Hao XIE; Long CHEN; Karl ZHANGHAO; Kun ZHAO; Xu-san YANG; Peng XI

doi:10.1631/FITEE.1601628

Your Location：

Home >

Browse articles >

Computational methods in super-resolution microscopy

Special Feature on Computational Photography | Updated：2022-05-19

- Computational methods in super-resolution microscopy
- 超分辨显微成像技术中的计算方法
- Frontiers of Information Technology & Electronic Engineering Vol. 18, Issue 9, Pages: 1222-1235(2017)
- Affiliations：
  
  College of Physics and Information Engineering, Fuzhou University, Fuzhou 350116, China
  Department of Biomedical Engineering, Peking University, Beijing 100871, China
  MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
  Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
  Department of Automation, Tsinghua University, Beijing 100084, China
- Author bio：
  
  Zhi-ping ZENG, E-mail: zhipingzeng@fzu.edu.cn
  Peng XI, E-mail: xipeng@pku.edu.cn
- Funds：
- DOI：10.1631/FITEE.1601628
  CLC： O436
- Received：14 October 2016，
  
  Revised：2017-;9-25，
  
  Published：2017-09
- Accepted：
Scan QR Code
Zhi-ping ZENG, Hao XIE, Long CHEN, et al. Computational methods in super-resolution microscopy[J]. Frontiers of Information Technology & Electronic Engineering, 2017, 18(9): 1222-1235.
DOI：

Zhi-ping ZENG, Hao XIE, Long CHEN, et al. Computational methods in super-resolution microscopy[J]. Frontiers of Information Technology & Electronic Engineering, 2017, 18(9): 1222-1235. DOI： 10.1631/FITEE.1601628.

摘要

超分辨显微成像技术已广泛应用于多个领域。其中，计算方法的优化和提升，对超分辨显微系统成像质量优化至关重要。本文综述了目前主流超分辨显微技术采用的计算方法，包括反卷积显微技术、基于偏振的超分辨显微技术、结构光照明显微技术、图像扫描显微技术、超分辨光学涨落显微成像技术、单分子定位显微技术、贝叶斯分析超分辨显微技术、受激辐射损耗显微技术和移位显微技术。新计算方法的发展将有助于提升超分辨显微的成像效果，使其具备更好的分辨率、更高的精度和更快的图像处理速度。

Abstract

The broad applicability of super-resolution microscopy has been widely demonstrated in various areas and disciplines. The optimization and improvement of algorithms used in super-resolution microscopy are of great importance for achieving optimal quality of super-resolution imaging. In this review

we comprehensively discuss the computational methods in different types of super-resolution microscopy

including deconvolution microscopy

polarization-based super-resolution microscopy

structured illumination microscopy

image scanning microscopy

super-resolution optical fluctuation imaging microscopy

single-molecule localization microscopy

Bayesian super-resolution microscopy

stimulated emission depletion microscopy

and translation microscopy. The development of novel computational methods would greatly benefit super-resolution microscopy and lead to better resolution

improved accuracy

and faster image processing.

关键词

Keywords

references

D.A. Agard , , , Y. Hiraoka , , , J.W. Sedat . . Threedimensional microscopy: image processing for high resolution subcellular imaging . . 33rd Annual Technical Symp. , , 1989 . . 24 - - 30 . . DOI: 10.1117/12.962684 http://doi.org/10.1117/12.962684 . .

D. Axelrod . . Fluorescence polarization microscopy . . Methods Cell Biol. , , 1989 . . 30 333 - - 352 . . DOI: 10.1016/S0091-679X(08)60985-1 http://doi.org/10.1016/S0091-679X(08)60985-1 . .

A. Beck , , , M. Teboulle . . A fast iterative shrinkagethresholding algorithm for linear inverse problems . . SIAM J. Imag. Sci. , , 2009 . . 2 ( ( 1 ): ): 183 - - 202 . . DOI: 10.1137/080716542 http://doi.org/10.1137/080716542 . .

E. Betzig , , , G.H. Patterson , , , R. Sougrat , , , 等 . . Imaging intracellular fluorescent proteins at nanometer resolution . . Science , , 2006 . . 313 ( ( 5793 ): ): 1642 - - 1645 . . DOI: 10.1126/science.1127344 http://doi.org/10.1126/science.1127344 . .

D.S. Biggs . . 3D deconvolution microscopy . . Curr. Protoc. Cytom. , , 2010 . . 52 12.19.1 - - 12.19.20. . . DOI: 10.1002/0471142956.cy1219s52 http://doi.org/10.1002/0471142956.cy1219s52 . .

M. Broxton , , , L. Grosenick , , , S. Yang , , , 等 . . Wave optics theory and 3-D deconvolution for the light field microscope . . Opt. Expr. , , 2013 . . 21 ( ( 21 ): ): 25418 - - 25439 . . DOI: 10.1364/OE.21.025418 http://doi.org/10.1364/OE.21.025418 . .

X. Chen , , , M. Wei , , , M.M. Zheng , , , 等 . . Study of RNA polymerase Ⅱ clustering inside live-cell nuclei using Bayesian nanoscopy . . ACS Nano , , 2016 . . 10 ( ( 2 ): ): 2447 - - 2454 . . DOI: 10.1021/acsnano.5b07257 http://doi.org/10.1021/acsnano.5b07257 . .

S. Cox , , , E. Rosten , , , J. Monypenny , , , 等 . . Bayesian localization microscopy reveals nanoscale podosome dynamics . . Nat. Methods , , 2012 . . 9 ( ( 2 ): ): 195 - - 200 . . DOI: 10.1038/nmeth.1812 http://doi.org/10.1038/nmeth.1812 . .

B.S. DeMay , , , N. Noda , , , A.S. Gladfelter , , , 等 . . Rapid and quantitative imaging of excitation polarized gluorescence reveals ordered septin dynamics in live yeast . . Biophys. J. , , 2011 . . 101 ( ( 4 ): ): 985 - - 994 . . DOI: 10.1016/j.bpj.2011.07.008 http://doi.org/10.1016/j.bpj.2011.07.008 . .

T. Dertinger , , , R. Colyer , , , G. Iyer , , , 等 . . Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI) . . PNAS , , 2009 . . 106 ( ( 52 ): ): 22287 - - 22292 . . DOI: 10.1073/pnas.0907866106 http://doi.org/10.1073/pnas.0907866106 . .

T. Dertinger , , , A. Pallaoro , , , G. Braun , , , 等 . . Advances in superresolution optical fluctuation imaging (SOFI) . . Q. Rev. Biophys. , , 2013 . . 46 ( ( 2 ): ): 210 - - 221 . . DOI: 10.1017/S0033583513000036 http://doi.org/10.1017/S0033583513000036 . .

Y. Ding , , , P. Xi , , , Q. Ren . . Hacking the optical diffraction limit: review on recent developments of fluorescence nanoscopy . . Chin. Sci. Bull. , , 2011 . . 56 ( ( 18 ): ): 1857 - - 1876 . . DOI: 10.1007/s11434-011-4502-3 http://doi.org/10.1007/s11434-011-4502-3 . .

S. Dong , , , J. Liao , , , K. Guo , , , 等 . . Resolution doubling with a reduced number of image acquisitions . . Biomed. Opt. Expr. , , 2015 . . 6 ( ( 8 ): ): 2946 - - 2952 . . DOI: 10.1364/BOE.6.002946 http://doi.org/10.1364/BOE.6.002946 . .

M.M. Falk , , , U. Lauf . . High resolution, fluorescence deconvolution microscopy and tagging with the autofluorescent tracers CFP, GFP, and YFP to study the structural composition of gap junctions in living cells . . Microsc. Res. Techn. , , 2001 . . 52 ( ( 3 ): ): 251 - - 262 . . DOI: 10.1002/(ISSN)1097-0029 http://doi.org/10.1002/(ISSN)1097-0029 . .

J. Gao , , , X. Yang , , , M.N. Djekidel , , , 等 . . Developing bioimaging and quantitative methods to study 3D genome . . Quant. Biol. , , 2016 . . 4 ( ( 2 ): ): 129 - - 147 . . DOI: 10.1007/s40484-016-0065-2 http://doi.org/10.1007/s40484-016-0065-2 . .

S. Geissbuehler , , , N.L. Bocchio , , , C. Dellagiacoma , , , 等 . . Mapping molecular statistics with balanced superresolution optical fluctuation imaging (bSOFI) . . Opt. Nanosc. , , 2012 . . 1 ( ( 1 ): ): 1 - - 7 . . DOI: 10.1186/2192-2853-1-4 http://doi.org/10.1186/2192-2853-1-4 . .

R. Gold . . An Iterative Unfolding Method for Response Matrices . . Argonne National Lab, Lemont, USA , , 1964 . . .

R. C. Gonzalez , , , R. E. Woods . . Digital Image Processing . . Pearson Education, New York, USA , , 2008 . . .

M. Gu , , , X. Li , , , Y. Cao . . Optical storage arrays: a perspective for future big data storage . . Light Sci. Appl. , , 2014 . . 3 ( ( 5 ): ): e177 DOI: 10.1038/lsa.2014.58 http://doi.org/10.1038/lsa.2014.58 . .

M.G. Gustafsson . . Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy . . J. Microsc. , , 2000 . . 198 ( ( 2 ): ): 82 - - 87 . . DOI: 10.1046/j.1365-2818.2000.00710.x http://doi.org/10.1046/j.1365-2818.2000.00710.x . .

M.G. Gustafsson , , , L. Shao , , , P.M. Carlton , , , 等 . . Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination . . Biophys. J. , , 2008 . . 94 ( ( 12 ): ): 4957 - - 4970 . . DOI: 10.1529/biophysj.107.120345 http://doi.org/10.1529/biophysj.107.120345 . .

N. Hafi , , , M. Grunwald , , , L.S. van den Heuvel , , , 等 . . Fluorescence nanoscopy by polarization modulation and polarization angle narrowing . . Nat. Methods , , 2014 . . 11 ( ( 5 ): ): 579 - - 584 . . DOI: 10.1038/nmeth.2919 http://doi.org/10.1038/nmeth.2919 . .

X. Hao , , , C. Kuang , , , Z. Gu , , , 等 . . From microscopy to nanoscopy via visible light . . Light Sci. Appl. , , 2013 . . 2 e108 DOI: 10.1038/lsa.2013.64 http://doi.org/10.1038/lsa.2013.64 . .

S.W. Hell , , , J. Wichmann . . Breaking the diffraction resolution limit by stimulated emission: stimulatedemission-depletion fluorescence microscopy . . Opt. Lett. , , 1994 . . 19 ( ( 11 ): ): 780 - - 782 . . DOI: 10.1364/OL.19.000780 http://doi.org/10.1364/OL.19.000780 . .

S.T. Hess , , , T.P. Girirajan , , , M.D. Mason . . Ultra-high resolution imaging by fluorescence photoactivation localization microscopy . . Biophys. J. , , 2006 . . 91 ( ( 11 ): ): 4258 - - 4272 . . DOI: 10.1529/biophysj.106.091116 http://doi.org/10.1529/biophysj.106.091116 . .

Y.S. Hu , , , X. Nan , , , P. Sengupta , , , 等 . . Accelerating 3B single-molecule super-resolution microscopy with cloud computing . . Nat. Methods , , 2013a . . 10 ( ( 2 ): ): 96 - - 97 . . . .

Y.S. Hu , , , Q. Zhu , , , K. Elkins , , , 等 . . Light-sheet Bayesian microscopy enables deep-cell super-resolution imaging of heterochromatin in live human embryonic stem cells . . Opt. Nanosc. , , 2013b . . 2 ( ( 1 ): ): 7 DOI: 10.1186/2192-2853-2-7 http://doi.org/10.1186/2192-2853-2-7 . .

B. Huang , , , H. Babcock , , , X. Zhuang . . Breaking the diffraction barrier: super-resolution imaging of cells . . Cell , , 2010 . . 143 ( ( 7 ): ): 1047 - - 1058 . . DOI: 10.1016/j.cell.2010.12.002 http://doi.org/10.1016/j.cell.2010.12.002 . .

M. Ingaramo , , , A.G. York , , , P. Wawrzusin , , , 等 . . Twophoton excitation improves multifocal structured illumination microscopy in thick scattering tissue . . PNAS , , 2014 . . 111 ( ( 14 ): ): 5254 - - 5259 . . DOI: 10.1073/pnas.1314447111 http://doi.org/10.1073/pnas.1314447111 . .

P.A. Jansson . . Deconvolution of Images and Spectra . . Courier Corporation, North Chelmsford, USA , , 2014 . . .

T.A. Klar , , , S. Jakobs , , , M. Dyba . . Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission . . PNAS , , 2000 . . 97 ( ( 15 ): ): 8206 DOI: 10.1073/pnas.97.15.8206 http://doi.org/10.1073/pnas.97.15.8206 . .

A. Lal , , , C. Shan , , , P. Xi . . Structured illumination microscopy image reconstruction algorithm . . IEEE J. Sel. Topics Quant. Electron. , , 2016 . . 22 ( ( 4 ): ): 1 - - 14 . . DOI: 10.1109/JSTQE.2016.2521542 http://doi.org/10.1109/JSTQE.2016.2521542 . .

J. Lazar , , , A. Bondar , , , S. Timr , , , 等 . . Two-photon polarization microscopy reveals protein structure and function . . Nat. Methods , , 2011 . . 8 ( ( 8 ): ): 684 - - 690 . . DOI: 10.1038/nmeth.1643 http://doi.org/10.1038/nmeth.1643 . .

D. Li , , , L. Shao , , , B.C. Chen , , , 等 . . Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics . . Science , , 2015 . . 349 ( ( 6251 ): ): aab3500 DOI: 10.1126/science.aab3500 http://doi.org/10.1126/science.aab3500 . .

Y. Liu , , , Y. Ding , , , E. Alonas , , , 等 . . Achieving λ/10 resolution CW STED nanoscopy with a Ti: sapphire oscillator . . PLOS ONE , , 2012 . . 7 ( ( 6 ): ): e40003 DOI: 10.1371/journal.pone.0040003 http://doi.org/10.1371/journal.pone.0040003 . .

J.G. McNally , , , T. Karpova , , , J. Cooper , , , 等 . . Three-dimensional imaging by deconvolution microscopy . . Methods , , 1999 . . 19 ( ( 3 ): ): 373 - - 385 . . DOI: 10.1006/meth.1999.0873 http://doi.org/10.1006/meth.1999.0873 . .

J. Mertz . . Optical sectioning microscopy with planar or structured illumination . . Nat. Methods , , 2011 . . 8 ( ( 10 ): ): 811 - - 819 . . DOI: 10.1038/nmeth.1709 http://doi.org/10.1038/nmeth.1709 . .

C.B. Müller , , , J. Enderlein . . Image scanning microscopy . . Phys. Rev. Lett. , , 2010 . . 104 198101 DOI: 10.1103/PhysRevLett.104.198101 http://doi.org/10.1103/PhysRevLett.104.198101 . .

F. Orieux , , , E. Sepulveda , , , V. Loriette , , , 等 . . Bayesian estimation for optimized structured illumination microscopy . . IEEE Trans. Image Process. , , 2012 . . 21 ( ( 2 ): ): 601 - - 614 . . DOI: 10.1109/TIP.2011.2162741 http://doi.org/10.1109/TIP.2011.2162741 . .

J.B. Pawley . . Handbook of Biological Confocal Microscopy , , : : New York Springer , , 2010 . . DOI: 10.1109/TIP.2011.2162741 http://doi.org/10.1109/TIP.2011.2162741 . .

Z. Qiu , , , R.S. Wilson , , , Y. Liu . . Translation microscopy (TRAM) for super-resolution imaging . . Sci. Rep. , , 2010 . . 6 19993 DOI: 10.1038/srep19993 http://doi.org/10.1038/srep19993 . .

M.A. Rizzo , , , D.W. Piston . . High-contrast imaging of fluorescent protein FRET by fluorescence polarization microscopy . . Biophys. J. , , 2005 . . 88 ( ( 2 ): ): L14 - - L16 . . DOI: 10.1529/biophysj.104.055442 http://doi.org/10.1529/biophysj.104.055442 . .

M.J. Rust , , , M. Bates , , , X. Zhuang . . Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) . . Nat. Methods , , 2006 . . 3 ( ( 10 ): ): 793 - - 796 . . DOI: 10.1038/nmeth929 http://doi.org/10.1038/nmeth929 . .

V. Schoonderwoert , , , R. Dijkstra , , , G. Luckinavicius , , , 等 . . Huygens STED deconvolution increases signal-tonoise and image resolution towards 22 nm . . Microsc. Today , , 2013 . . 21 ( ( 6 ): ): 38 - - 44 . . DOI: 10.1017/S1551929513001089 http://doi.org/10.1017/S1551929513001089 . .

O. Schulz , , , C. Pieper , , , M. Clever , , , 等 . . Resolution doubling in fluorescence microscopy with confocal spinning-disk image scanning microscopy . . PNAS , , 2013 . . 110 ( ( 52 ): ): 21000 - - 21005 . . DOI: 10.1073/pnas.1315858110 http://doi.org/10.1073/pnas.1315858110 . .

C.J. Sheppard , , , S.B. Mehta , , , R. Heintzmann . . Superresolution by image scanning microscopy using pixel reassignment . . Opt. Lett. , , 2013 . . 38 ( ( 15 ): ): 2889 - - 2892 . . DOI: 10.1364/OL.38.002889 http://doi.org/10.1364/OL.38.002889 . .

J. B. Sibarita . . Deconvolution microscopy . . In : Microscopy Techniques. Springer-Verlag, Berlin , , 2005 . . DOI: 10.1364/OL.38.002889 http://doi.org/10.1364/OL.38.002889 . .

A.M. Vrabioiu , , , T.J. Mitchison . . Structural insights into yeast septin organization from polarized fluorescence microscopy . . Nature , , 2006 . . 443 ( ( 7110 ): ): 466 - - 469 . . DOI: 10.1038/nature05109 http://doi.org/10.1038/nature05109 . .

Q. Yang , , , L. Cao , , , H. Zhang , , , 等 . . Method of lateral image reconstruction in structured illumination microscopy with super resolution . . J. Innov. Opt. Health Sci. , , 2015 . . 9 ( ( 3 ): ): 1630002 DOI: 10.1142/S1793545816300020 http://doi.org/10.1142/S1793545816300020 . .

X. Yang , , , H. Xie , , , E. Alonas , , , 等 . . Mirror-enhanced super-resolution microscopy . . Light Sci. Appl. , , 2016a . . 5 ( ( 6 ): ): e16134 DOI: 10.1038/lsa.2016.134 http://doi.org/10.1038/lsa.2016.134 . .

X. Yang , , , K. Zhanghao , , , H. Wang , , , 等 . . Versatile application of fluorescent quantum dot labels in superresolution fluorescence microscopy . . ACS Photon. , , 2016b . . 3 ( ( 9 ): ): 1611 - - 1618 . . DOI: 10.1021/acsphotonics.6b00178 http://doi.org/10.1021/acsphotonics.6b00178 . .

J. Yassif . . Quantitative Imaging in Cell Biology . . Academic Press, Cambridge, USA , , 2012 . . DOI: 10.1021/acsphotonics.6b00178 http://doi.org/10.1021/acsphotonics.6b00178 . .

W. Yu , , , Z. Ji , , , D. Dong , , , 等 . . Super-resolution deep imaging with hollow Bessel beam STED microscopy . . Laser Photon. Rev. , , 2016 . . 10 ( ( 1 ): ): 147 - - 152 . . DOI: 10.1002/lpor.201500151 http://doi.org/10.1002/lpor.201500151 . .

Z. Zeng , , , X. Chen , , , H. Wang , , , 等 . . Fast superresolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging . . Sci. Rep. , , 2015 . . 5 8359 DOI: 10.1038/srep08359 http://doi.org/10.1038/srep08359 . .

X. Zhang , , , X. Chen , , , Z. Zeng , , , 等 . . Development of a reversibly switchable fluorescent protein for superresolution optical fluctuation imaging (SOFI) . . ACS Nano , , 2015 . . 9 ( ( 3 ): ): 2659 - - 2667 . . DOI: 10.1021/nn5064387 http://doi.org/10.1021/nn5064387 . .

K. Zhanghao , , , L. Chen , , , M.Y. Wang , , , 等 . . Superresolution dipole orientation mapping via polarization demodulation . . Light Sci. Appl. , , 2016 . . 5 ( ( 10 ): ): e16166 DOI: 10.1038/lsa.2016.166 http://doi.org/10.1038/lsa.2016.166 . .

X. Zhou , , , M. Lei , , , D. Dan , , , 等 . . Image recombination transform algorithm for superresolution structured illumination microscopy . . J. Biomed. Opt. , , 2016 . . 21 ( ( 9 ): ): 96009 DOI: 10.1117/1.JBO.21.9.096009 http://doi.org/10.1117/1.JBO.21.9.096009 . .

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

No data

Related Author

No data

Related Institution

No data

Chat

Address：Zhejiang University Press, 148 Tianmushan Road, Hangzhou, China Postal code：310028
Tel：+86-571-88273162 Email：fitee@zju.edu.cn
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰