rapidSTORM

Summary

The rapidSTORM project is an open source evaluation tool that provides fast and highly configurable data processing for single-molecule localization microscopy such as dSTORM. It provides both two-dimensional and three-dimensional, multi-color data analysis as well as a wide range of filtering and image generation capabilities. The general operation of rapidSTORM is described in this article.

rapidSTORM is currently available in two versions: rapidSTORM 2 is the current stable branch, where only outstanding bugs are fixed, while rapidSTORM 3 is the unstable development branch with an improved user interface and simplified technical deployment.

rapidSTORM features

Basic rapidSTORM features
Feature rapidSTORM 1 rapidSTORM 2/3
Graphical user interface x x
Command line interface x x
Easy scriptability and testability through simparm framework x x
Reading Andor SIF files x x
Reading and writing TIFF files x x
Direct connection to Andor cameras x x
Pseudorandom input data simulation with true Besselian PSFs x x
Input simulation for 3D PSFs   x
Least-squares fitting x x
Data analysis in seconds x x
Modular, easily extensible architecture x x
rapidSTORM processing features
Feature rapidSTORM 1 rapidSTORM 2/3
Least-squares fitting x x
MLE fitting   x
2D processing with known PSF x x
2D fitting with per-spot PSF width x x
Estimation of PSF from input data x x
Estimation of 3D PSF from input data x x
3D using astigmatism   x
3D using biplane   x
Multi-color and multi-plane support   x
Two-kernel analysis for multi-spot events x x
rapidSTORM result analysis features
Feature rapidSTORM 1 rapidSTORM 2/3
Online result view during analysis x x
High & adaptable image contrast through WHN x x
Time-resolved images x x
Can create time-lapse movies x x
Free selection of coordinate and hue axes in image generation   x
Online filtering of results during analysis x x
Advanced result filtering using arithmetic expressions   x
Easy linear drift correction x x
Joining multiple time-consecutive localizations by Kalman tracking x x

Download and installation

We offer the rapidSTORM software in three formats: source code, Win32 binaries and GNU/Linux deb packages (e.g. for Debian and Ubuntu). You can obtain the current source as gzip-compressed tar archives from our software repository, as well as a setup installing thecompiled software under Microsoft Windows.

Debian and Ubuntu packages for rapidSTORM 2 are available using the following sources lines. Debian versions prior to wheezy (currently testing) and Ubuntu versions prior to precise (12.04) can unfortunately not be supported. The packages rapidstorm (main program), rapidstorm-doc (documentation) and rapidstorm-dev-doc (Doxygen programmer's documentation) are offered. 

deb https://idefix.biozentrum.uni-wuerzburg.de/debian wheezy main contrib non-free
deb-src https://idefix.biozentrum.uni-wuerzburg.de/debian wheezy main contrib non-free
deb https://idefix.biozentrum.uni-wuerzburg.de/ubuntu precise main universe
deb-src https://idefix.biozentrum.uni-wuerzburg.de/ubuntu precise main universe

The Debian/Ubuntu packages for rapidSTORM 1 are available from: 

deb https://idefix.biozentrum.uni-wuerzburg.de/debian squeeze main contrib non-free
deb-src https://idefix.biozentrum.uni-wuerzburg.de/debian squeeze main contrib non-free

It might be necessary to install the apt-transport-https package to enable downloads from https sources, and to install the super-resolution-de-keyring package to enable authentication.

Documentation and support

The rapidSTORM manual is available online in HTML format or PDF format.

We are grateful for any comments and bug reports on the rapidSTORM software and strive for active development of the software. Please report your bugs and comments to the bug tracking system. The rapidSTORM framework is also highly extensible and an excellent starting position for developing and testing new algorithms for super-resolution microscopy; please contact Steve Wolter if you are interested in such collaboration.