CT covid segmentation

Segmentation of CT scans with use of Pytorch Lightning and segmentation models pytorch.

Install

Install this directory with pip install -e ..

Prepare Data

Create folder input in this directory. Download https://www.kaggle.com/datasets/andrewmvd/covid19-ct-scans or similar dataset and unzip it into input as covid19-ct-scans (so input/covid19-ct-scans/metadata.csv is relative path to medata).

Run python ./scripts/prepare_pngs.py to preprocess dataset into 256*256 images.

Train

Run python ./scripts/train.py to start training with basic configuration. There are placeholder, that reduces size of dataset to 100 pngs and training goes for 1 epoch.

Result of training can be viewed in ./notebooks/visualization.ipynb (requires jupyter notebook, pip install notebook ipywidgets)

Example

Uninstalling

Uninstall this directory by pip uninstall ct_covid_segmentation as you done with it