Single-molecule FRET analysis

This repository contains a Python package and several Jupyter notebooks to analyze single molecule FRET data. The procedure is discribed in our article published in the Journal of Visualized Experiments. The supplemental information contains screen shots with step-by-step instructions. Note that over time, some function names may have changed slightly, but with the current notebooks from this repository it should still be easily possible to follow the manual.

If you use this software in a project resulting in a scientific publication, please cite the software.

Suggested workflow:

• Install the uv Python package manager. Linux users can use their distribution's package management system to install uv.

• Create a new folder.

• Download Jupyter notebooks for the analysis into the folder.

• Navigate into the folder it using a command line prompt.

• Initialize uv in this folder by executing

  uv init --bare
  

• Install the FRET analysis python package, either from PyPI,

  uv add fret-analysis
  

  or from Github,

  uv add git+https://github.com/schuetzgroup/fret-analysis.git
  

• Start Jupyter Lab,

  uv run --with jupyter jupyter lab
  

• Open 01. Tracking notebook. Run each cell and adjust file paths and parameters as needed.

• When finished, do the same using the 02. Filter notebook.

• Summary plots can be created with the 03. Plots notebook.