CellRex

Logo

Welcome to CellRex, a user-friendly full stack application built with Python and Streamlit. This application allows you to upload, download, and manage your research data with ease. CellRex is a platform that establishes a link between biological metadata and experimentally generated files.

Features

CellRex is built as a multipage app with three main pages:

Upload: This page allows you to upload data files by dragging and dropping them into a dedicated upload folder on your filesystem or your NAS and filling out a form with relevant information. The template and check features streamline the upload process, ensuring consistency and accuracy in the information provided.
Search: This page provides a search mask that you can use to specify search criteria and easily find data files.
Dashboard: This page provides insights about your data and helps you manage and organize your data efficiently.

Contributing

We welcome contributions to CellRex! See the repository’s readme.md for instructions on how you can set up the development environment.

Citation

If you find CellRex useful in your research, please cite:

@article{hoelter2025cellrex,
title = {CellRex: Software platform for managing biological cell data},
journal = {SoftwareX},
volume = {31},
pages = {102284},
year = {2025},
issn = {2352-7110},
doi = {https://doi.org/10.1016/j.softx.2025.102284},
url = {https://www.sciencedirect.com/science/article/pii/S2352711025002511},
author = {Jan Hölter and Tim Rickmeyer and Christiane Thielemann},
keywords = {Research data management (RDM), Laboratory information management system (LIMS), Biological cell, Microscopic images, Electrophysiological recordings, Software-as-a-service (SaaS)},
abstract = {This work introduces the software platform CellRex, a research data management system for laboratories capable of storing, searching, and enriching data with biological metadata. CellRex addresses data management challenges by storing data in an ontology-based directory structure within the filesystem, with metadata saved as JSON files and in a document-oriented SQLite database. The framework, deployed as container services in a software-as-a-service model, features a web-based GUI and API for user interaction and machine-readable access, providing functionalities such as duplicate detection, experiment grouping, and templating. CellRex improves research efficiency and facilitates data reuse, providing a targeted solution for laboratories focused on cell analysis research.}
}

CellRex

Features

Contributing

Citation

License