A hydrophilic gel matrix for single-molecule super-resolution microscopy

Optical Nanoscopy

Volumn 2, Issue 1, 2013, Pages 1-8

  Zessin, Patrick J M ^a   Krüger, Carmen L ^a   Malkusch, Sebastian ^a   Endesfelder, Ulrike ^a   Heilemann, Mike ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

Drift correction; Registration; Single molecule localization microscopy; Super resolution microscopy

Indexed keywords

FLUOROPHORES; HYDROPHILICITY; MOLECULES; OPTICAL RESOLVING POWER;

DATA INTERPRETATION; DRIFT CORRECTION; MICROSCOPIC TECHNIQUES; MULTI-CHANNEL REGISTRATIONS; REGISTRATION; SINGLE-MOLECULE LOCALIZATIONS; SUPER RESOLUTION IMAGING; SUPER-RESOLUTION MICROSCOPY;

MATRIX ALGEBRA;

EID: 84891385250     PISSN: None     EISSN: 21922853     Source Type: Journal    
DOI: 10.1186/2192-2853-2-4     Document Type: Article

References (45)

1. Adler J, Pagakis SN (2003) Reducing image distortions due to temperaturerelated microscope stage drift. J Microsc 210:131-137
2. Augst AD, Kong HJ, Mooney DJ (2006) Alginate hydrogels as biomaterials. Macromol Biosci 6:623-633
3. Bell E, Ivarsson B, Merrill C (1979) Production of a tissue-like structure by contraction of collagen lattices by human fibroblasts of different proliferative potential in vitro. Proc Natl Acad Sci USA 76:1274-1278
4. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642-1645
5. Blomback B, Bark N (2004) Fibrinopeptides and fibrin gel structure. Biophys Chem 112:147-151
6. Carter AR, King GM, Ulrich TA, Halsey W, Alchenberger D, Perkins TT (2007) Stabilization of an optical microscope to 0.1 nm in three dimensions. Appl Opt 46:421-427
7. Churchman LS, Okten Z, Rock RS, Dawson JF, Spudich JA (2005) Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc Natl Acad Sci USA 102:1419-1423
8. Delano WL (2004) Use of PYMOL as a communcations tool for molecular science. Abstr Pap Am Chem Soc 228:U313-U314
9. Endesfelder U, Malkusch S, Flottmann B, Mondry J, Liguzinski P, Verveer PJ, Heilemann M (2011) Chemically induced photoswitching of fluorescent probes-a general concept for super-resolution microscopy. Molecules 16:3106-3118
10. Endesfelder U, Finan K, Holden SJ, Cook PR, Kapanidis AN, Heilemann M (2013) Multiscale Spatial Organization of RNA Polymerase in Escherichia coli. Biophys J 105:172-181
11. Fitzpatrick JM, West JB (2001) The distribution of target registration error in rigidbody point-based registration. IEEE Trans Med Imaging 20:917-927
12. Folling J, Bossi M, Bock H, Medda R, Wurm CA, Hein B, Jakobs S, Eggeling C, Hell SW (2008) Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat Methods 5:943-945
13. Galbraith CG, Galbraith JA (2011) Super-resolution microscopy at a glance. J Cell Sci 124:1607-1611
14. Gao L, Shao L, Higgins CD, Poulton JS, Peifer M, Davidson MW, Wu X, Goldstein B, Betzig E (2012) Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens. Cell 151:1370-1385
15. Heilemann M (2010) Fluorescence microscopy beyond the diffraction limit. J Biotechnol 149:243-251
16. Heilemann M, van de Linde S, Schuttpelz M, Kasper R, Seefeldt B, Mukherjee A, Tinnefeld P, Sauer M (2008) Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. Angew Chem Int Ed Engl 47:6172-6176
17. Hell SW (2009) Microscopy and its focal switch. Nat Methods 6:24-32
18. Hess ST, Girirajan TP, Mason MD (2006) Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 91:4258-4272
19. Huang B, Wang W, Bates M, Zhuang X (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319:810-813
20. Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EH (2008) Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322:1065-1069
21. Kleinman HK, Martin GR (2005) Matrigel: basement membrane matrix with biological activity. Semin Cancer Biol 15:378-386
22. Lee J, Cuddihy MJ, Kotov NA (2008) Three-dimensional cell culture matrices: state of the art. Tissue Eng Part B Rev 14:61-86
23. Malkusch S, Endesfelder U, Mondry J, Gelleri M, Verveer PJ, Heilemann M (2012) Coordinate-based colocalization analysis of single-molecule localization microscopy data. Histochem Cell Biol 137:1-10
24. Maurer Cr JR, Fitzpatrick JM, Wang MY, Galloway RLJR, Maciunas RJ, Allen GS (1997) Registration of head volume images using implantable fiducial markers. IEEE Trans Med Imaging 16:447-462
25. Mcgorthy R, Kamiyama D, Huang B (2013) Active microscope stabilization in three dimensions using image correlation. Optical Nanoscopy 2:2-3
26. Mennella V, Keszthelyi B, Mcdonald KL, Chhun B, Kan F, Rogers GC, Huang B, Agard DA (2012) Subdiffraction-resolution fluorescence microscopy reveals a domain of the centrosome critical for pericentriolar material organization. Nat Cell Biol 14:1159-1168
27. Mlodzianoski MJ, Schreiner JM, Callahan SP, Smolkova K, Dlaskova A, Santorova J, Jezek P, Bewersdorf J (2011) Sample drift correction in 3D fluorescence photoactivation localization microscopy. Opt Express 19:15009-15019
28. Nakayasu H, Berezney R (1989) Mapping replicational sites in the eucaryotic cell nucleus. J Cell Biol 108:1-11
29. Oheim M, Schapper F (2005) Non-linear evanescent-field imaging. J Phys D-Appl Phys 38:R185-R197
30. Pertsinidis A, Zhang Y, Chu S (2010) Subnanometre single-molecule localization, registration and distance measurements. Nature 466:647-651
31. Peterson P (2009) F2PY: a tool for connection Fortran and Python programs. J Comput Sci Eng 4:296-305
32. Planchon TA, Gao L, Milkie DE, Davidson MW, Galbraith JA, Galbraith CG, Betzig E (2011) Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination. Nat Methods 8:417-423
33. Qu D, Wang G, Wang Z, Zhou L, Chi W, Cong S, Ren X, Liang P, Zhang B (2011) 5-Ethynyl-2′-deoxycytidine as a new agent for DNA labeling: detection of proliferating cells. Anal Biochem 417:112-121
34. Quan T, Li P, Long F, Zeng S, Luo Q, Hedde PN, Nienhaus GU, Huang ZL (2010) Ultra-fast, high-precision image analysis for localization-based super resolution microscopy. Opt Express 18:11867-11876
35. Ripley BD (1977) Modeling Spatial Patterns. J R Stat Soc Ser B-Methodological 39:172-212
36. Rohrbach A (2000) Observing secretory granules with a multiangle evanescent wave microscope. Biophys J 78:2641-2654
37. Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793-795
38. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biologicalimage analysis. Nat Methods 9:676-682
39. Shtengel G, Galbraith JA, Galbraith CG, Lippincott-Schwartz J, Gillette JM, Manley S, Sougrat R, Waterman CM, Kanchanawong P, Davidson MW, Fetter RD, Hess HF (2009) Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure. Proc Natl Acad Sci USA 106:3125-3130
40. Tokunaga M, Imamoto N, Sakata-Sogawa K (2008) Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods 5:159-161
41. van de Linde S, Loschberger A, Klein T, Heidbreder M, Wolter S, Heilemann M, Sauer M (2011) Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat Protoc 6:991-1009
42. Van T, Hoff M, De Sars V, Oheim M (2008) A programmable light engine for quantitative single molecule TIRF and HILO imaging. Opt Express 16:18495-18504
43. Wolter S, Schüttpelz M, Tscherepanow M, Van de Linde S, Heilemann M, Sauer M (2010) Real-time computation of subdiffraction-resolution fluorescence images. J Microsc 237:12-22
44. Xu K, Babcock HP, Zhuang X (2012) Dual-objective STORM reveals threedimensional filament organization in the actin cytoskeleton. Nat Methods 9:185-188
45. Zessin PJ, Finan K, Heilemann M (2012) Super-resolution fluorescence imaging of chromosomal DNA. J Struct Biol 177:344-348