Automatic lung tumor segmentation

This repository offers a proof of concept release of an automatic lung tumor segmentation method given a CT scan. Pre-trained weights are available for anyone to use. The repository structure is inspired by Johannes Hofmanninger's lungmask repo, and part of the preprocessing pipeline is based on his lungmask release.

Dependencies

In addition to the python packages specified in requirements.txt, PyTorch and Hofmanninger's lungmask must be installed.

Installation


pip install git+https://github.com/VemundFredriksen/LungTumorMask

Usage

When the package is installed through pip, simply specify the input and output filenames.

# Format
lungtumormask input_file output_file

# Example
lungtumormask patient_01.nii.gz mask_01.nii.gz

Limitations

This repository is a proof of concept. It is not intended to be used in clinical or commercial use. However, it might be interesting for research, play a role as a baseline, or even aid semi-supervised lung tumor segmentation.