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Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging
Open accessAbstract
One approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. Essential to this technique is the choice of fluorescent probes; the properties of the probes, including photons per switching event, on-off duty cycle, photostability and number of switching cycles, largely dictate the quality of super-resolution images. Although many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. Here we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. This analysis provides guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low–cross-talk, four-color super-resolution imaging.
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Hell, S. W. (2007) · Science · doi:10.1126/science.1137395 · Cited by 2,967
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“(Selected data for certain dyes specifically for the related technique of STORM were given in a recent study [17]).”
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Metadata
- Authors
- Dempsey, G. T., Vaughan, J. C., Chen, K. H., Bates, M., & Zhuang, X.
- Venue
- Nature Methods
- Published
- 2011-11-06
- Volume
- 8
- Issue
- 12
- Pages
- 1027-1036
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2133161896
- Cited by
- 1,369
- References
- 2
- FWCI
- 34.36
- Type
- journal article
- Language
- en
- Open access
- green
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