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} }