DOI: 10.1093/bioinformatics/btu202. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

10.1093/bioinformatics/btu202

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Summary: ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. ThunderSTORM offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. ThunderSTORM also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using Monte Carlo simulations. Availability and implementation: ThunderSTORM and the online documentation are both freely accessible at https://code.google.com/p/thunder-storm/ Contact: guy.hagen@lf1.cuni.cz Supplementary information: Supplementary Data are available at Bioinformatics online.

Bibliography

OvesnÃ½, M., KÅÃÅ¾ek, P., Borkovec, J., Å vindrych, Z., & Hagen, G. M. (2014). ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics, 30(16), 2389â2390.

Authors 5

Martin Ovesný (first)
Pavel Křížek (additional)
Josef Borkovec (additional)
Zdeněk Švindrych (additional)
Guy M. Hagen (additional)

References 12 Referenced 1,402

10.1126/science.1127344 / Science / Imaging intracellular fluorescent proteins at nanometer resolution by Betzig (2006)
10.1126/science.1153529 / Science / Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy by Huang (2008)
10.1364/BOE.2.001377 / Biomed. Opt. Express / Simultaneous multiple-emitter fitting for single molecule super-resolution imaging by Huang (2011)
10.1364/OE.20.002081 / Opt. Express / Wavelet analysis for single molecule localization microscopy by Izeddin (2012)
10.1364/OE.19.003226 / Opt. Express / Minimizing detection errors in single molecule localization microscopy by Křížek (2011)
10.1364/OE.19.015009 / Opt. Express / Sample drift correction in 3D fluorescence photoactivation localization microscopy by Mlodzianoski (2011)
10.1038/nmeth.1447 / Nat. Methods / Optimized localization analysis for single-molecule tracking and super-resolution microscopy by Mortensen (2010)
10.1038/nmeth.2071 / Nat. Methods / Rapid, accurate particle tracking by calculation of radial symmetry centers by Parthasarathy (2012)
10.1117/1.3505017 / J. Biomed. Opt. / Localization capability and limitation of electron-multiplying charge-coupled, scientific complementary metal-oxide semiconductor, and charge-coupled devices for superresolution imaging by Quan (2010)
10.1038/nmeth929 / Nat. Methods / Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) by Rust (2006)
10.1214/aos/1176349654 / Ann. Stat. / Averaged shifted histograms: effective nonparametric density estimators in several dimensions by Scott (1985)
10.1016/S0006-3495(02)75618-X / Biophys. J. / Precise nanometer localization analysis for individual fluorescent probes by Thompson (2002)

Dates

Type	When
Created	11 years, 3 months ago (April 26, 2014, 12:03 a.m.)
Deposited	2 years, 6 months ago (Jan. 27, 2023, 7:11 a.m.)
Indexed	19 hours, 34 minutes ago (Aug. 21, 2025, 12:53 p.m.)
Issued	11 years, 3 months ago (May 15, 2014)
Published	11 years, 3 months ago (May 15, 2014)
Published Online	11 years, 3 months ago (May 15, 2014)
Published Print	11 years ago (Aug. 15, 2014)

Funders 0

None

BibTeX

@article{Ovesn__2014, title={ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging}, volume={30}, ISSN={1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/btu202}, DOI={10.1093/bioinformatics/btu202}, number={16}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Ovesný, Martin and Křížek, Pavel and Borkovec, Josef and Švindrych, Zdeněk and Hagen, Guy M.}, year={2014}, month=may, pages={2389–2390} }

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