mousetumortrack 0.0.3

Tracking tumor nodules in mice CT scans.

💫 Tumor nodules tracking in mice CT scans

We provide a Python package for tracking tumor nodules in mice CT scans. The project is based on Trackpy and Laptrack (algorithms from both libraries are implemented). It also provides a registration utility to align CT scans before tracking objects based on segmentation masks of the lungs cavity produced by the mouselungseg model.

[Installation] [Usage]

This project is part of a collaboration between the EPFL Center for Imaging and the De Palma Lab.

Installation

We recommend performing the installation in a clean Python environment. Install our package from PyPi:

pip install mousetumortrack

or from the repository:

pip install git+https://github.com/EPFL-Center-for-Imaging/mousetumortrack.git

or clone the repository and install with:

git clone git+https://github.com/EPFL-Center-for-Imaging/mousetumortrack.git
cd mousetumortrack
pip install -e .

Usage

Track tumor nodules from a labelled 3D timesereies array:

from mousetumortrack import run_tracking

# labels_timeseries is a 4D array of shape (TZYX)
linkage_df, grouped_df, labels_timeseries_tracked = run_tracking(labels_timeseries)

For more details, see example.py.

Issues

If you encounter any problems, please file an issue along with a detailed description.

License

This project is licensed under the AGPL-3 license.

This project depends on the ultralytics package which is licensed under AGPL-3.

Related projects

• Mouse Tumor Net | Detect tumor nodules in mice CT scans.
• Mouse Lungs Seg | Detect the lungs cavity in mice CT scans.

Acknowledgements

Special thanks go to Sandra Gebraiel for her contribution to the ideation and exploration of the data and for developing the preliminary code that laid the foundations for this project during the course of her lab immersion in Summer 2024.