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README.md

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+Processing Codes for 4D-BioSTEM Project in LBEM
+======
+
+This repository presents the codes used in the 4D-BioSTEM project. Details of the individual projects and publications are found in their corresponding notebooks.
+
+## Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution
+
+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.
+
+### Prerequisites
+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](https://github.com/py4dstem/py4DSTEM).
+
+### Data Access
+The example 4D-STEM dataset for this notebook can be accessed at [Dataset link](<DatasetLink>). 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.
+
+### Citation
+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](https://doi.org/10.1101/2024.02.12.579607)
+
+### Contact
+For support, please contact Henning Stahlberg at [email protected] or Berk Kucukoglu at [email protected]