Code Packages

Open source software links

fcsSOFI (in MATLAB): A correlation-based super-resolution imaging analysis method to map and quantify diffusion. (2015 fcsSOFI paper; 2021 GPU GUI manuscript) (GitHub link, please note - requires a NVIDIA graphics card)
Super-Resolution Kinetics (in MATLAB): Produces super-resolution images and temporal statistics for kinetic information for single molecules at interfaces. (paper link) (GitHub link)
STaSI (in MATLAB): A transition point state identification method for any one dimensional vector data, such as single molecule FRET or photobleaching trajectories. (paper link) (GitHub link)
Troika-SPT (in MATLAB): A modular software for single particle tracking. (paper link) (GitHub link)
Diffusion-MLE (in MATLAB): Maximum likelihood estimator to calculate diffusion coefficients from short single-molecule trajectories with photoblinking events (paper link) (GitHub link)

Many of the above codes were developed in collaboration with the Landes Research Group at Rice University and Chen Research Group at Ohio University. While the code listed above is in MATLAB, we also utilize Python (programming language) and ImageJ, MicroManager, Origin (software) in our research. While it is helpful, new lab members are not required/expected to have experience with all or any of these computational tools.