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Toolkit for simulating real-time control systems for super-resolution microscopy.

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Super-resolution Acquisition Simulation Software

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Toolkit for simulating non-stationary fluorescence photodynamics and real-time control systems for super-resolution microscopy.

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

  1. Download the latest .jar from releases.
  2. Download the latest .jar from ALICA_ACPack.
  3. If using SASS as a ImageJ/Fiji plugin, place the SASS jar in <IMAGEJ_ROOT>/plugins and the ALICA_ACPack jar in <IMAGEJ_ROOT>/jars. Otherwise, place both jars in the same folder of your choosing.

Note: The SASS .jar file that is found in the releases is an uber-jar, i.e. it contains all the dependencies that are necessary to run.

As a standalone application

  • Executing the .jar file by double-clicking on it 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

  • If launching Fiji from the command line, launch it from within the Fiji directory so that the ALICA_ACPack.jar is properly found.
  • Plugins -> SASS -> Simulation 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

Acknowledgements

SASS uses adapted code and algorithms from the following projects:

In addition, SASS relies on these projects to provide core functionality.

...and the many, many people behind all the software that we rely on.