This repository presents the codes used in the 4D-BioSTEM project. Details of the individual projects and publications are found in their corresponding notebooks.
This repository contains the Phi92_Notebook.ipynb, which is designed to perform the data analysis as described in our recent publication "Low-Dose Cryo-Electron Ptychography of Proteins at Sub-Nanometer Resolution." The notebook includes detailed steps for the ptychographic reconstruction and analysis of the 4D-STEM data of the Phi92 bacteriophage.
Ensure you have the following installed:
- Python 3.8+
- Jupyter Notebook or JupyterLab
- Required Python libraries:
numpy,scipy,matplotlib,py4DSTEM
py4DSTEM is an open-source software, and installation details can be found on its GitHub page.
The example 4D-STEM dataset for this notebook can be accessed at Dataset link. Additional datasets of Apoferritin, Phi92 bacteriophage, and Tobacco Mosaic Virus are available in the Electron Microscopy Public Image Archive (EMPIAR) with the accession code EMPIAR-XXX.
If you use this code in your research, please cite our paper:
Küçükoğlu, B., Mohammed, I., Guerrero-Ferreira, R. C., et al. (2024). Low-Dose Cryo-Electron Ptychography of Proteins at Sub-Nanometer Resolution. bioRxiv. DOI link
For support, please contact Henning Stahlberg at [email protected] or Berk Kucukoglu at [email protected]