Reproducible Research Platform TracX Bundle

RRP TRACX

Reproducible Research Platform project, including TracX.

Overview

This RRP project repository demonstrates how to use TracX, a cell-tracking library for MATLAB, on RRP.

The main outcome of this example is:

Example of using a MATLAB-based tool, TracX.

This repository utilizes TracX [1], Detailed explanations of these tools can be found in the respective publications.

Features

Integration with RRP and openBIS ELN--LIMS: Mounts data (image data) from the research data management system openBIS in RRP for direct use.

MATLAB: Keeping user habits, allowing to work with the MATLAB IDE.

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

Note

Use at least 8 GB of RAM before starting the RRP Project.

Usage

In RRP start the MATLAB environment.

Workflow Overview

Start MATLAB. In the Launcher, click on Open MATLAB. When you start MATLAB the first time you need to enter your License information.

Tracking: In MATLAB run the tracking script: run_tracx_example.

Note

MATLAB requires the matlab-proxy-app; It should start automatically in the background. In case you need to manually start it open a Terminal and type matlab-proxy-app. Then you can open MATLAB. Important is, that the environment variable MWI_BASE_URL is set correctly. When running an RRP project online, the variable should be set as follows MWI_BASE_URL="/servers/<id>/matlab", with the being the current RRP project id. When run locally, it should be set to MWI_BASE_URL="/matlab". To check if the process is already running type pgrep -fl matlab-proxy-app. To kill the process type pkill matlab-proxy-app.

Directory Structure

├── tracx # The TracX toolbox/library
├── tracx_demo_data # Demo data of TracX. Note the
├── .binder/ # Environment specifications, Python version, packages (MATLAB) etc.
├── .rrp/ # Specification of required data from RDMS openBIS ELN-LIMS (e.g. image data)
├── LICENSE # License
├── run_tracx_example.m # Demo script for Tracking
└── README.md # This file

Notes

The TracX library was added to this RRP repository with the following commands:

git submodule add https://gitlab.com/csb.ethz/tracx.git
git submodule add https://gitlab.com/csb.ethz/tracx_demo_data.git
git submodule update --init --recursive
git add .gitmodules tracx tracx_demo_data
git commit -m "add tracx submodule and tracx demo data"
git push

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

References

1: Cuny, A. P., Ponti, A., Kündig, T., Rudolf, F. & Stelling, J. Cell region fingerprints enable highly precise single-cell tracking and lineage reconstruction. Nat. Methods 2021.10.26.465883 (2022) doi:https://doi.org/10.1038/s41592-022-01603-2.