After discussing where to find the source code implementation of the most important effects with James, need to go through all of these and fully understand how the implementation is expected to affect the simulated images.

These investigations are done regarding Parakeet with commit hash:
17a0c864f6cfd84b5fd56b60fa446f7b021d338c

The main issues/topics include:

• Generation of the simulated Gaussian random field (GRF) ice model
• Beam damage model and implementation
• CTF simulation
• MTF generation and e-/A^2/second dependence in implementation (also relation to DQE)
• inelastic scattering models
• dose fractionation and beam induced motion
• relation of the above to power spectra in synthetic data

Which are all added as issues linked to this milestone.