(PALM). Proc Natl Acad Sci U S A
109:17436–17441
12. Fricke F, Beaudouin J, Eils R et al (2015) One,
two or three? Probing the stoichiometry of
membrane proteins by single-molecule localization microscopy. Sci Rep 5:14072
13. Cooper M, Ebner A, Briggs M et al (2004)
Cy3B™: improving the performance of cyanine dyes. J Fluoresc 14:145–150
14. Olivier N, Keller D, Rajan VS et al (2013)
Simple buffers for 3D STORM microscopy.
Biomed Opt Express 4:885–899
15. Nahidiazar L, Agronskaia AV, Broertjes J et al
(2016) Optimizing imaging conditions for
demanding multi-color super resolution localization microscopy. PLoS One 11:e0158884
16. Adler H, Spady G (1997) The use of microbial
membranes to achieve anaerobiosis. J Rapid
Methods Autom Microbiol 5:1–12
17. Tokunaga M, Imamoto N, Sakata-Sogawa K
(2008) Highly inclined thin illumination
enables clear single-molecule imaging in cells.
Nat Methods 5:159–161
18. Staudt T, Lang MC, Medda R et al (2007)
2,2
0 -thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy. Microsc Res Tech 70:1–9
19. Thompson RE, Larson DR, Webb WW (2002)
Precise nanometer localization analysis for individual fluorescent probes. Biophys J
82:2775–2783
20. Holden SJ, Uphoff S, Kapanidis AN (2011)
DAOSTORM: an algorithm for high- density
super-resolution microscopy. Nat Methods
8:279–280
21. Abraham AV, Ram S, Chao J et al (2009)
Quantitative study of single molecule location
estimation
techniques.
Opt
Express
17:23352–23373
22. Quan T, Zhu H, Liu X et al (2011) Highdensity localization of active molecules using
structured sparse model and Bayesian information criterion. Opt Express 19:16963–16974
23. Ovesny ´ M, Kr ˇı ´z ˇek P, Borkovec J et al (2014)
ThunderSTORM: a comprehensive ImageJ
plug-in for PALM and STORM data analysis
and super-resolution imaging. Bioinformatics
30:2389–2390
24. Rouault H (2013) Brecs: reconstruction of
dense localization microscopy datasets
https://github.com/hrouault/Brecs
25. Ko ¨the U, Herrmannsdo ¨rfer F, Kats I et al
(2014) SimpleSTORM: a fast, self-calibrating
reconstruction algorithm for localization
microscopy.
Histochem
Cell
Biol
141:613–627
26. Sage D, Kirshner H, Pengo T et al (2015)
Quantitative evaluation of software packages
for single-molecule localization microscopy.
Nat Methods 12:717–724
27. Baddeley D, Cannell MB, Soeller C (2010)
Visualization of localization microscopy data.
Microsc Microanal 16:64–72
28. Glushonkov O, Re ´al E, Boutant E et al (2018)
Optimized protocol for combined PALMdSTORM imaging. Sci Rep 8:8749
29. Andronov L, Lutz Y, Vonesch J-L et al (2016)
SharpViSu: integrated analysis and segmentation of super-resolution microscopy data. Bioinformatics 32:2239–2241
30. Erdelyi M, Rees E, Metcalf D et al (2013)
Correcting chromatic offset in multicolor
super-resolution localization microscopy. Opt
Express 21:10978–10988
31. Annibale P, Vanni S, Scarselli M et al (2011)
Quantitative photo activated localization
microscopy: unraveling the effects of Photoblinking. PLoS One 6:e22678
32. Ripley BD (1976) The second-order analysis of
stationary point processes. J Appl Probab
13:255–266
33. Nicovich PR, Owen DM, Gaus K (2017) Turning single-molecule localization microscopy
into a quantitative bioanalytical tool. Nat Protoc 12:453–460
34. Ester M, Kriegel H-P, Sander J, Xu X (1996) A
density-based algorithm for discovering clusters in large spatial databases with noise.
KDD-96 Proceedings 226–231 (http://www.
aaai.org)
35. Voronoi G (1908) Nouvelles applications des
parame `tres continus a ` la the ´orie des formes
quadratiques. J Reine Angew Math
1908:97–102
36. Levet F, Hosy E, Kechkar A et al (2015)
SR-Tesseler: a method to segment and quantify
localization-based super-resolution microscopy
data. Nat Methods 12:1065–1071
37. Andronov L, Michalon J, Ouararhni K et al
(2018) 3DClusterViSu: 3D clustering analysis
of super-resolution microscopy data by 3D
Voronoi tessellations. Bioinformatics 34
(17):3004–3012
38. Beheiry ME, Dahan M (2013) ViSP: representing single-particle localizations in three dimensions. Nat Methods 10:689–690
39. Malkusch S, Heilemann M (2016) Extracting
quantitative information from single-molecule
super-resolution imaging data with LAMA—
LocAlization microscopy analyzer. Sci Rep
6:34486
Practical Aspects of Super-Resolution Imaging and Segmentation of. . .
285
109:17436–17441
12. Fricke F, Beaudouin J, Eils R et al (2015) One,
two or three? Probing the stoichiometry of
membrane proteins by single-molecule localization microscopy. Sci Rep 5:14072
13. Cooper M, Ebner A, Briggs M et al (2004)
Cy3B™: improving the performance of cyanine dyes. J Fluoresc 14:145–150
14. Olivier N, Keller D, Rajan VS et al (2013)
Simple buffers for 3D STORM microscopy.
Biomed Opt Express 4:885–899
15. Nahidiazar L, Agronskaia AV, Broertjes J et al
(2016) Optimizing imaging conditions for
demanding multi-color super resolution localization microscopy. PLoS One 11:e0158884
16. Adler H, Spady G (1997) The use of microbial
membranes to achieve anaerobiosis. J Rapid
Methods Autom Microbiol 5:1–12
17. Tokunaga M, Imamoto N, Sakata-Sogawa K
(2008) Highly inclined thin illumination
enables clear single-molecule imaging in cells.
Nat Methods 5:159–161
18. Staudt T, Lang MC, Medda R et al (2007)
2,2
0 -thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy. Microsc Res Tech 70:1–9
19. Thompson RE, Larson DR, Webb WW (2002)
Precise nanometer localization analysis for individual fluorescent probes. Biophys J
82:2775–2783
20. Holden SJ, Uphoff S, Kapanidis AN (2011)
DAOSTORM: an algorithm for high- density
super-resolution microscopy. Nat Methods
8:279–280
21. Abraham AV, Ram S, Chao J et al (2009)
Quantitative study of single molecule location
estimation
techniques.
Opt
Express
17:23352–23373
22. Quan T, Zhu H, Liu X et al (2011) Highdensity localization of active molecules using
structured sparse model and Bayesian information criterion. Opt Express 19:16963–16974
23. Ovesny ´ M, Kr ˇı ´z ˇek P, Borkovec J et al (2014)
ThunderSTORM: a comprehensive ImageJ
plug-in for PALM and STORM data analysis
and super-resolution imaging. Bioinformatics
30:2389–2390
24. Rouault H (2013) Brecs: reconstruction of
dense localization microscopy datasets
https://github.com/hrouault/Brecs
25. Ko ¨the U, Herrmannsdo ¨rfer F, Kats I et al
(2014) SimpleSTORM: a fast, self-calibrating
reconstruction algorithm for localization
microscopy.
Histochem
Cell
Biol
141:613–627
26. Sage D, Kirshner H, Pengo T et al (2015)
Quantitative evaluation of software packages
for single-molecule localization microscopy.
Nat Methods 12:717–724
27. Baddeley D, Cannell MB, Soeller C (2010)
Visualization of localization microscopy data.
Microsc Microanal 16:64–72
28. Glushonkov O, Re ´al E, Boutant E et al (2018)
Optimized protocol for combined PALMdSTORM imaging. Sci Rep 8:8749
29. Andronov L, Lutz Y, Vonesch J-L et al (2016)
SharpViSu: integrated analysis and segmentation of super-resolution microscopy data. Bioinformatics 32:2239–2241
30. Erdelyi M, Rees E, Metcalf D et al (2013)
Correcting chromatic offset in multicolor
super-resolution localization microscopy. Opt
Express 21:10978–10988
31. Annibale P, Vanni S, Scarselli M et al (2011)
Quantitative photo activated localization
microscopy: unraveling the effects of Photoblinking. PLoS One 6:e22678
32. Ripley BD (1976) The second-order analysis of
stationary point processes. J Appl Probab
13:255–266
33. Nicovich PR, Owen DM, Gaus K (2017) Turning single-molecule localization microscopy
into a quantitative bioanalytical tool. Nat Protoc 12:453–460
34. Ester M, Kriegel H-P, Sander J, Xu X (1996) A
density-based algorithm for discovering clusters in large spatial databases with noise.
KDD-96 Proceedings 226–231 (http://www.
aaai.org)
35. Voronoi G (1908) Nouvelles applications des
parame `tres continus a ` la the ´orie des formes
quadratiques. J Reine Angew Math
1908:97–102
36. Levet F, Hosy E, Kechkar A et al (2015)
SR-Tesseler: a method to segment and quantify
localization-based super-resolution microscopy
data. Nat Methods 12:1065–1071
37. Andronov L, Michalon J, Ouararhni K et al
(2018) 3DClusterViSu: 3D clustering analysis
of super-resolution microscopy data by 3D
Voronoi tessellations. Bioinformatics 34
(17):3004–3012
38. Beheiry ME, Dahan M (2013) ViSP: representing single-particle localizations in three dimensions. Nat Methods 10:689–690
39. Malkusch S, Heilemann M (2016) Extracting
quantitative information from single-molecule
super-resolution imaging data with LAMA—
LocAlization microscopy analyzer. Sci Rep
6:34486
Practical Aspects of Super-Resolution Imaging and Segmentation of. . .
285