ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
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Documentation of changes in ThunderSTORM with Phasor added.docx

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About ThunderSTORM

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 PALM and STORM. Our philosophy in developing ThunderSTORM has been to offer an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data.

Getting started

Install ImageJ and download the latest version of ThunderSTORM. For installation, copy the downloaded file into ImageJ's plugin subdirectory and run ImageJ. See the Installation guide for more information. To get started using ThunderSTORM, see the Tutorials. Example data are provided here.

How to cite ThunderSTORM

If you use ThunderSTORM to process your data, please, cite our paper:

  • M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, G. M. Hagen. ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30(16):2389-2390, 2014.

If you use the phasor sub-pixel estimator, please cite this paper in addition (

  • K.J.A. Martens, A.N. Bader, S. Baas, B. Rieger, J. Hohlbein. Phasor based single-molecule localization microscopy in 3D (pSMLM-3D): an algorithm for MHz localization rates using standard CPUs bioRxiv, 2017.