Resolution improvement by 3D particle averaging in localization microscopy

Methods and Applications in Fluorescence

Volumn 3, Issue 1, 2015, Pages

  Broeken, Jordi ^a   Johnson, Hannah ^b   Lidke, Diane S ^b   Liu, Sheng ^c   Nieuwenhuizen, Robert P J ^a   Stallinga, Sjoerd ^a   Lidke, Keith A ^c   Rieger, Bernd ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Localization microscopy; Particle averaging; Resolution improvement

Indexed keywords

EID: 84974528132     PISSN: None     EISSN: 20506120     Source Type: Journal    
DOI: 10.1088/2050-6120/3/1/014003     Document Type: Article

References (45)

1. Lidke K A, Rieger B, Jovin T M and Heintzmann R 2005 Superresolution by localization of quantum dots using blinking statistics Opt. Express 13 7052-62
2. Betzig E, Patterson G H, Sougrat R, Lindwasser O W, Olenych S, Bonifacino J S, Davidson M W, Lippincott-Schwartz J and Hess H F 2006 Imaging intracellular fluorescent proteins at nanometer resolution Science 313 1643-5
3. Rust M J, Bates M and Zhuang X W 2006 Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Nat. Methods 3 793-5
4. Hess S T, Girirajan T P K and Mason M D 2006 Ultrahigh resolution imaging by fluorescence photoactivation localization microscopy Biophys. J. 91 4258-72
5. Egner A, Geisler C, von Middendorff C, Bock H, Wenzel D, Medda R andresen M, Stiel A C, Jakobs S, Eggeling C, Schönle A and Hell S W 2007 Fluorescence nanoscopy in whole cells by asynchronous localization of photoswitching emitters Biophys. J. 93 3285-90
6. Heilemann M, van de Linde S, Schüttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P and Sauer M 2008 Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes Angew. Chem. 47 6172-6
7. Klein T, Proppert S and Sauer M 2014 Eight years of singlemolecule localization microscopy Histochem. Cell Biol. 141 561-75
8. Nieuwenhuizen R P J, Lidke K A, Bates M, Leyton Puig D, Grünwald D, Stallinga S and Rieger B 2013 Measuring image resolution in optical nanoscopy Nat. Methods 10 557-62
9. Frank J 2006 3D Electron Microscopy of Macromolecular Assemblies 2nd edn (Oxford: Oxford University Press)
10. Frank J 2009 Single-particle reconstructionof biological macromolecules in electron microscopy-30 years Q. Rev. Biophys. 42 139-58
11. van Heel M, Gowen B, Matadeen R, Orlova E V, Finn R, Pape T, Cohen D, Stark H, Schmidt R, Schatz M and Patwardhan A 2000 Single-particle electron cryo-microscopy: towards atomic resolution Q. Rev. Biophys. 33 307-69
12. Löschberger A, van de Linde S, Dabauvalle M C, Rieger B, Heilemann M, Krohne G and Sauer M 2012 Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution J. Cell Sci. 125 570-5
13. Szymborska A, Marco N, de Daigle A, Cordes V C, Briggs J A G and Elllenberg J 2013 Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging Science 341 655-8
14. Löschberger A, Franke C, Krohne G, van de Linde S and Sauer M 2014 Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution J. Cell Sci.125 570-5
15. van Engelenburg S B, Shtengel G, Sengupta P, Waki K, Jarnik M, Ablan S D, Freed E O, Hess H F and Lippincott-Schwartz J 2014 Distribution of ESCRT machinery at HIV assembly sites reveals virus scaffolding of ESCRT subunits Science 343 653-6
16. Ehmann N et al 2014 Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states Nat. Commun. 5 4650
17. Schmied J J, Raab M, Forthmann C, Pibiri E, Wünsch B, Dammeyer T and Tinnefeld P 2014 DNA origami-based standards for quantitative fluorescence microscopy Nat. Protocols 9 1367-91
18. Vulovic M, Ravelli R B G, van Vliet L J, Koster A J, Lazic I, Lücken U, Rullgårgd H, Öktem O and Rieger B 2013 Image formation modeling in cryo electron microscopy J. Struct. Biol. 183 19-32
19. Ries J, Kaplan C, Platonova E, Eghlidi H and Ewers H 2012 A simple, versatile method for GFP-based super-resolution microscopy via nanobodies Nat. Methods 9 582-7
20. Dempsey G T, Vaughan J C, Chen K H, Bates M and Zhuang X 2011 Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging Nat. Methods 8 1027-31
21. Annibale P, Vanni S, Scarelli M, Rothlisberger U and Radenovic A 2011 Identification of clustering artifacts in photoactivated localization microscopy Nat. Methods 8 527-8
22. Rieger B and Stallinga S 2014 The lateral and axial localization uncertainty in super-resolution light microscopy ChemPhysChem 15 664-70
23. Nieuwenhuizen R P J, Stallinga S and Rieger B 2014 Chapter visualization and resolution in localization microscopy Cell Membrane Nanodomains: from Biochemistry to Nanoscopy (Boca Raton: Taylor and Francis)
24. Liao H Y and Frank J 2010 Definition and estimation of resolution in single-particle reconstructions Structure 18 768-75
25. Kudrayashev M, Castano-Diez D and Stahlberg H 2012 Limiting factors in single particle cryo electron tomography Comput. Struct. Biotechnol. J. 1 e201207002
26. D'Angelo M A and Hetzer M W 2008 Structure, dynamics and function of nuclear pore complexes Trends Cell Biol. 18 456-66
27. Huy Bui K et al 2013 Integrated structural analysis of the human nuclear pore complex scaffold Cell 155 1233-43
28. Smith C S, Joseph N, Rieger B and Lidke K A 2010 Fast, singlemolecule localization that achieves theoretically minimum uncertainty Nat. Methods 7 373-5
29. Liu S, Kromann E B, Krueger W D, Bewersdorf J and Lidke K A 2013 3D single molecule localization using a phase retrieved pupil function Opt. Express 21 29462-87
30. Shtengel G et al 2009 Interferometric fluorescent superresolution microscopy resolves 3D cellular ultrastructure Proc. Natl Acad. Sci. USA 106 3125-30
31. Horn B K P 1987 Closed-form solution of absolute orientation using unit quaternions J. Opt. Soc. Am. A 4 629-42
32. Cha S-H 2007 Comprehensive survey on distance/similarity measures between probability density functions Int. J. Math. Mod. Methods Appl. Sci. 4 300-7
33. Theodoridis S and Koutroumbas K 2009 Pattern Recognition 2nd edn (Amsterdam: Elsevier)
34. Pekalska E and Duin R P W 2005 The Dissimilarity Representation for Pattern Recognition: Foundations and Applications (Singapore: World Scientific)
35. Kuffner J J 2004 Effective sampling and distance metrics for 3d rigid body path planning IEEE Int. Conf. on Robotics and Automation (New Orleans, USA, April 26-1 May 2004) pp 3993-8
36. van Vliet L J and Verbeek P W 1994 Edge localization by MoG filters: multiple-of-Gaussians Pattern Recognit. Lett. 15 485-96
37. Rosenthal P B and Henderson R 2003 Optimal determination of particle orientation, absolute hand and contrast loss in single-particle electron cryomicroscopy J. Mol. Biol. 333 721-45
38. Voortman L M, Vulovic M, Maletta M, Voigt A, Franken E M, Simonetti A, Peter P, van Vliet L J and Rieger B 2014 Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations J. Struct. Biol. 187 103-11
39. Small A R 2009 Theoretical limits on errors and acquisition rates in localizing switchable fluorophores Biophys. J.-Biophys. Lett. 92 L16-8
40. van de Linde S, Wolter S, Heilemann M and Sauer M 2010 The effect of photoswitching kinetics and labeling densities on super-resolution fluorescence imaging J. Biotechnol. 149 260-6
41. Sinko J, Kakonyi R, Rees E, Metcalf D, Knight A E, Kaminski C F, Szabo G and Erdelyi M 2014 TestSTORM: simulator for optimizing sample labeling and image acquisition in localization based super-resolution microscopy Biomed. Opt. Express 5 778-87
42. Scheres S H W and Chen S 2012 Prevention of overfitting in cryo-EM structure determination Nat. Methods 9 853-4
43. Ram S, Ward E S and Ober R J 2006 Beyond Rayleighs criterion: a resolution measure with application to singlemolecule microscopy Proc. Natl Acad. Sci. USA 103 4457-62
44. Briggs J A 2013 Structural biology in situ-the potential of subtomogram averagingCurr. Opin. Struct. Biol. 23 261-7
45. Schur F K M, Hagen W J H, de Marco A and Briggs J A G 2013 Determination of protein structure at 8.5 å resolution using cryo-electron tomography and sub-tomogram averaging J. Struct. Biol. 184 394-400