vishalkumar-1997/Data-Analysis-Scripts: Data Analysis Scripts for Cryo-EM Radiation Damage Studies
Year: 2026
Type: software
Abstract: Initial public release of the analysis pipeline developed for our study on radiation damage in cryogenic electron microscopy under pulsed and continuous electron beam illumination. What's included This repository provides the Jupyter notebook–based analysis scripts used to process and analyze three benchmark cryo-EM specimens: Paraffin 2D crystals Tobacco mosaic virus (TMV) in vitreous ice Bacteriorhodopsin (purple membrane) 2D crystals The scripts cover reproducible workflows for quantifying critical electron dose (N_e) from the decay of computed diffraction intensities, along with data preprocessing, normalization, and visualization routines for publication-quality figures. Associated data and publication Raw data: available in the BioImage Archive at S-BIAD2466 (DOI: 10.6019/S-BIAD2466) Preprint: bioRxiv 2025.07.29.667395 Features Per-sample analysis notebooks for paraffin, TMV, and bacteriorhodopsin datasets Diffraction-intensity decay tracking and critical dose estimation Statistical comparison between pulsed (RF-modulated) and continuous illumination modes Plotting utilities for box plots, FSC curves, and dose-dependent intensity profiles Requirements Python 3.x with Jupyter Standard scientific stack: numpy, matplotlib, scipy mrcfile for MRC image handling Citation If you use this code or the associated dataset, please cite both the BioImage Archive entry and the bioRxiv manuscript. License GPL-3.0
Authors: vishalkumar-1997, Henning Stahlberg
Institution: École Polytechnique Fédérale de Lausanne
Language: English
Subfield: Structural Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7155401653