SMLM Acquisition Simulation Software

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Toolkit for simulating non-stationary fluorescence photodynamics and real-time control systems for single molecule localization microscopy (SMLM).

Documentation

http://sass.readthedocs.io/en/latest/

Usage

API Notice

The API for SASS is still under development and may change until major version 1.0.0. Any methods or classes that are marked as deprecated will be removed by this release.

Installation

Download the latest .jar from releases.

As standalone application

• Executing the .jar file by double-clicking launches a BeanShell console. Example scripts can be found in /scripts/ folder.
• Running SASS from command line: java -jar <SASS-jar-name> --help brings up available options, such as executing a script, or an interactive session within the terminal.

As FIJI plugin

Placing the .jar file in FIJI/plugins/ folder (file MUST have an underscore in the name, e.g. SASS_v0.0.2.jar) enables FIJI integration:

• Plugins -> SASS -> GUI launches an interactive simulator (not all options are available through the GUI).
• Plugins -> SASS -> Command Prompt launches BeanShell console. Generated images can be analyzed immediately with FIJI.

Where to find help

• How to use SASS: https://gitter.im/smlm-acquisition-simulation-software/Lobby
• Bug reports: https://github.com/LEB-EPFL/SASS/issues
• Feature requests: https://github.com/LEB-EPFL/SASS/issues
• Developer questions: https://gitter.im/smlm-acquisition-simulation-software/Lobby

Acknowledgements

SASS uses adapted code and algorithms from the following projects:

• SOFItool by Arik Girsault and Tomas Lukes (GPL)
• ALICA by Marcel Stefko (GPL)
• MicroscPSF-ImageJ by Jizhou Li (MIT)
• OpenSimplexNoise by Kurt Spencer (Unlicense/Public Domain)