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.

News, updates and discussion

You can track announcements, news and new releases for rapidSTORM by subscribing to the Opens external link in new windowrapidstorm-announce mailing list. This list is very low volume (typically less than one mail per month) and read-only. Your questions, feedback, and discussions about rapidSTORM are very welcome on the Opens external link in new windowrapidstorm-discuss list.

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 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. To install rapidSTORM, edit the file /etc/apt/sources.list.d/rapidstorm.list to reference our repository.

For Debian Wheezy or later, use:

 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

For Ubuntu Precise (12.04) or later, use:

 deb https://idefix.biozentrum.uni-wuerzburg.de/ubuntu precise main universe
deb-src https://idefix.biozentrum.uni-wuerzburg.de/ubuntu precise main universe

For Ubuntu Saucy (13.10) or later, use:

 deb https://idefix.biozentrum.uni-wuerzburg.de/ubuntu saucy main universe
deb-src https://idefix.biozentrum.uni-wuerzburg.de/ubuntu saucy main universe

For Debian Squeeze, only rapidSTORM 1 is available. Use:

 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

Install the package apt-transport-https to enable downloads from https sources, then run apt-get update and install the super-resolution-de-keyring package to enable package authentication. Afterwards, you can install rapidSTORM with apt-get install rapidstorm. Commands for easier reference:

sudo apt-get install apt-transport-https
sudo apt-get update
sudo apt-get install super-resolution-de-keyring
sudo apt-get update
sudo apt-get install rapidstorm

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.