This code was used in part for generating the figures presented in Low-dose cryo electron ptychography via non-convex Bayesian optimization.
It is a modified version of InSilicoTEM v0.93. The authors did not specify a license in their release, so I cannot include a license either.
Changes:
- custom pdb reader
- writes arrays that are needed for ptychography simulation into hdf5 files
- K2 mtf und dqe added
Please cite the article
@article{VULOVIC201319,
title = "Image formation modeling in cryo-electron microscopy",
journal = "Journal of Structural Biology",
volume = "183",
number = "1",
pages = "19 - 32",
year = "2013",
note = "",
issn = "1047-8477",
doi = "http://dx.doi.org/10.1016/j.jsb.2013.05.008",
url = "http://www.sciencedirect.com/science/article/pii/S1047847713001226",
author = "Miloš Vulović and Raimond B.G. Ravelli and Lucas J. van Vliet and Abraham J. Koster and Ivan Lazić and Uwe Lücken and Hans Rullgård and Ozan Öktem and Bernd Rieger",
}
if you use this code. If you use one of the new file starting with InSilicTEM_1ryp*, InSilicTEM_4hhb*, or InSilicTEM_4V5F*, please also consider citing
@article{pelz_low-dose_2017,
langid = {english},
title = {Low-Dose Cryo Electron Ptychography via Non-Convex {{Bayesian}} Optimization},
volume = {7},
issn = {2045-2322},
doi = {10.1038/s41598-017-07488-y},
number = {1},
journaltitle = {Scientific Reports},
date = {2017-08-29},
pages = {9883}
}