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ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

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## Links
  * [Cover page](http://zitmen.github.io/thunderstorm/)
  * [Documentation wiki](https://github.com/zitmen/thunderstorm/wiki)
  * My Ph.D. thesis [Computational methods in single molecule localization microscopy](https://www.researchgate.net/publication/311426573_Computational_methods_in_single_molecule_localization_microscopy) now available.
  * [Discussion group](http://groups.google.com/group/thunderstorm-users), [![Join the chat at https://gitter.im/thunder-storm/Lobby](https://badges.gitter.im/thunder-storm/Lobby.svg)](https://gitter.im/thunder-storm/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
  * [Issues](https://github.com/zitmen/thunderstorm/issues), [![Stories in Ready](https://badge.waffle.io/zitmen/thunderstorm.svg?label=ready&title=Ready)](http://waffle.io/zitmen/thunderstorm)
  * [Releases](https://github.com/zitmen/thunderstorm/releases), [![Build Status](https://travis-ci.org/zitmen/thunderstorm.svg?branch=master)](https://travis-ci.org/zitmen/thunderstorm)

## About ThunderSTORM
ThunderSTORM is an open-source, interactive, and modular plug-in for [ImageJ](http://rsb.info.nih.gov/ij/) 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](http://imagej.nih.gov/ij/index.html) and download the latest version of [ThunderSTORM](https://github.com/zitmen/thunderstorm/releases/latest). For installation, copy the downloaded file into ImageJ's plugin subdirectory and run ImageJ. See the [Installation guide](https://github.com/zitmen/thunderstorm/wiki/Installation) for more information. To get started using ThunderSTORM, see the [Tutorials](https://github.com/zitmen/thunderstorm/wiki/Tutorials). Example data are provided [here](https://github.com/zitmen/thunderstorm/releases/download/v1.0/example_data.zip).

## How to cite ThunderSTORM
If you use ThunderSTORM to process your data, please, cite our [paper](http://dx.doi.org/10.1093/bioinformatics/btu202):
  * 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.

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