mousetumortrack 0.0.1

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 mouselungseg
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 BSD-3 license.

Related projects

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