simS2E: Start-to-end simulation for single particle coherent diffractive imaging


simS2E [Yoon et al 2016] is a software suite for simulation of single particle imaging experiments using x-ray free electron laser radiation. It bundles designated codes for the simulation of the generation of the XFEL pulse, propagation through the x-ray optics, photon matter interaction, diffraction from the sample, detection in a x-ray 2D detector, and tools for reconstruction of the electron density from the simulated diffraction patterns. Its modular structure allows to exchange the default modules by other tools. simS2E is platform independent as it uses the Docker virtualisation technology. Simulation parameters are controlled through a central project configuration deck (ascii file.)


Documentation for simS2E together with a small tutorial can be found at

Description of data formats

FEL Source

Wave propagation

Photon matter interaction

Coherent diffraction



Source code and Installation

simS2E is on github. Instructions how to clone the repository are provided in the documentation.