Systematic assessment of freely-diffusing single-molecule fluorescence detection using Brownian motion simulations - Jupyter notebooks that document the photon timestamp simulations as well as their analysis by FRETbursts

The Jupyter notebooks here document all of the 3D diffusion simulations, timestamping simulations, and the analysis of the simulation results. The notebook named 'PyBroMo - 1-. Simulate 3D trajectories - single core - different 3D diffusion simulation conditions', is used to produce the photon HDF5 files that hold the 3D diffusion trajectories of all simulated molecules. The timestamping is performed on the resulting photon HDF5 file that holds the 3D diffusion trajectories. It is documented in the beginning of all notebooks here with a name starting with the string 'PyBroMo_sim_'. Then, after photon timestamps are allocated, the resulting photonHDF5 files, are analyzed for single-molecule photon bursts using FRETbursts