Serial Electron Diffraction Data Processing

Notebooks and scripts for serial electron diffraction analysis using diffractem (https://github.com/robertbuecker/diffractem) and CrystFEL (https://www.desy.de/~twhite/crystfel/), version 1.0 or higher.

Get the required raw data from MPDL EDMOND at https://dx.doi.org/10.17617/3.53.

The example Jupyter notebooks include:

• preprocessing.ipynb - Sorting, movie summation, data viewing, center and peak finding, image artifact correction, background subtraction, creation of intermediate files for indexing.
• peak_processing.ipynb - Refinement of experiment geometry and crystal unit cell using the found positions of Bragg peaks.
• indexing.ipynb - Crystal orientation finding (indexing), using CrystFELs indexamajig tool, some data mangling, and Bragg spot integration (again using indexamajig)
• dose_fractionation.ipynb - Preprocessing and integration of dose-fractionation movies, using the obtained indexing results.
• merging.ipynbg - Merging of Bragg spot observations from all indexed crystals using CrystFELs partialator, including pre- and post-processing of data, and validation. Also creates nice figures for validation.
• merging_fractionated.ipynb - Another merging script, this time looking at dose fractionated results/radiation damage. Its result may guide the way to optimize which dose fractionation to use in the end.