Toolkit for simulating non-stationary fluorescence photodynamics and real-time control systems for super-resolution microscopy.
http://sass.readthedocs.io/en/latest/
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.
- Download the latest .jar from releases.
- Download the latest .jar from ALICA_ACPack.
- If using SASS as a ImageJ/Fiji plugin, place the SASS jar in
<IMAGEJ_ROOT>/pluginsand 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.
- 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> --helpbrings up available options, such as executing a script, or an interactive session within the terminal.
- 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 -> Simulationlaunches an interactive simulator (not all options are available through the GUI).Plugins -> SASS -> Command Promptlaunches BeanShell console. Generated images can be analyzed immediately with Fiji.
- How to use SASS: https://gitter.im/leb_epfl/SASS
- Bug reports: https://github.com/LEB-EPFL/SASS/issues
- Feature requests: https://github.com/LEB-EPFL/SASS/issues
- Developer questions: https://gitter.im/leb_epfl/SASS
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)
In addition, SASS relies on these projects to provide core functionality.
...and the many, many people behind all the software that we rely on.