Reproducible Research Platform Microscopy and FACS Data Player Bundle

RRP Microscopy and FACS data interaction Reproducible Research Platform project for microscopy and FACS data interaction. Overview This RRP project repository demonstrates how to work with microscopy or FACS data mounted from the research data management system (RDMS) openBIS ELN-LIMS. Micrsocpy and FACS data are managed in the RDMS and annotated with respective metadata. Using their permID the data is directly available in the RRP project for Visualization or analysis and can be integrated in reproducible workflows. The main outcome of this example is: Visualization of Microscopy and FACS data in RRP. Features Integration with RRP and openBIS ELN--LIMS: Mounts data (microscopy, FACS) from the research data management system openBIS in RRP for direct use. Reproducible workflow: Notebook documents interaction with data. Visualization: Generates visualizations of the data sets. Installation Prerequisites Local Docker installation. Steps Download and extract the .zip file Run the play script for your operating system Linux / macOS: play Windows: play.bat or play.ps1 Usage In RRP open and run the Jupyter notebook visualize_data.ipynb Workflow Overview Visualization: View mounted FACS and microscopy data. Directory Structure ├── .binder/ # Environment specifications, Python version, packages (fcsparser) etc. ├── .rrp/ # Specification of required data from RDMS openBIS ELN-LIMS (Microscopy, FACS data) ├── LICENSE # License ├── README.md # This file └── visualize_data.ipynb # Notebook demonstrating mounted data. Contributing We welcome contributions to improve this repository! Please follow these steps: Fork the repository. Create a new branch for your feature or bug fix. Submit a pull request with a clear description of your changes. Authors and acknowledgment Andreas P. Cuny, ETH Zurich initial implementation License This project is licensed under the Apache 2.0 License. See LICENSE file for details. Copyright © 2020-2025 ETH Zurich, Andreas P. Cuny, D-BSSE, CSB Group