GitHub - Code & Hardware Packages

We believe in open science. Our group makes code, hardware, and data available at GitHub @KisleyLabAtCWRU

• Tensile Expansion Microscopy (TExM) (CAD files and video): Hardware and assembly instructions for tensile expansion microscopy iris stretcher. An assembly video is also provided on YouTube.
   

• fcsSOFI (in MATLAB; Python also available upon request): 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 mostly in MATLAB, we also use 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.