diff --git a/README.md b/README.md index 0e9c8b9..690b78b 100644 --- a/README.md +++ b/README.md @@ -1,27 +1,27 @@ -# Playing with SimpleITK +# Playing with SimpleITK and nnU-Net [![Build status][build-image]][build] [![Code coverage][codecov-image]][codecov] [![Code Quality][codacy-image]][codacy] -This repository contains Python code to play with [SimpleITK](https://github.com/SimpleITK/SimpleITK). +This repository contains Python code to play with [SimpleITK](https://github.com/SimpleITK/SimpleITK) and [nnU-Net](https://github.com/MIC-DKFZ/nnUNet). ## Requirements -- Install version 3.7 of [Python 3.X](https://www.python.org/downloads/), +- Install [Python 3.X](https://www.python.org/downloads/), - Install the required packages: ```bash pip install -r requirements.txt ``` -NB: As of November 2019, the PyPI package of SimpleITK does not work with Python 3.8. - ## Data - Download data from the [Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://chaos.grand-challenge.org/Combined_Healthy_Abdominal_Organ_Segmentation/) (CHAOS) challenge, - Extract the archive to `data/`. +Alternatively, data can be found in [**Releases**](https://github.com/woctezuma/playing-with-simpleitk/releases) on Github. + ## Usage ### Prepare data @@ -35,8 +35,6 @@ python convert_to_nii.py ### Train nnU-Net -- Connect to a session of [Google Colaboratory](https://colab.research.google.com/) - - Run the [`playing_with_pytorch.ipynb`][playing_with_pytorch] notebook. [![Open In Colab][colab-badge]][playing_with_pytorch]