Molecule Simulation

Dr. M. Hamilton created this repository. The provided script simulates the behavior of molecules across a specified number of frames. Originally designed for simulating Stochastic Optical Reconstruction Microscopy (STORM) imaging data, it can also be applied to other systems such as Live Imaging and single-molecule FRET. The molecules are initially assigned a random state: 0 (off), 1 (on), or -1 (bleached). They exhibit blinking behavior, transitioning between these states based on a calculated transition matrix within a Markov Chain.

The script was created using Python 3.9 and to run it, install the anaconda environment provided here (called menv.yml).

The resulting TIFF file has been updated as an example. For convenience, the file has been zipped to upload on GitHub.