Skip to content

Commit

Permalink
README: update information
Browse files Browse the repository at this point in the history
  • Loading branch information
woctezuma authored Nov 10, 2023
1 parent 0ff4a5e commit ba03ea3
Showing 1 changed file with 5 additions and 7 deletions.
12 changes: 5 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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]

Expand Down

0 comments on commit ba03ea3

Please sign in to comment.