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kits21

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The official repository of the 2021 Kidney and Kidney Tumor Segmentation Challenge

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## NEW: The KiTS23 Challenge is Underway!

See the [KiTS23 Homepage](https://kits-challenge.org/kits23/) for more details, including:

- A larger dataset
- Additional contrast phases

# KiTS21

The official repository of the 2021 Kidney and Kidney Tumor Segmentation Challenge

**Current dataset version: `2.2.3` -- Official Frozen Training Set** (see [changelog](changelog.md))

[Challenge Homepage](https://kits-challenge.org/kits21/)

## Timeline

- **Mar 1 - Jul 1**: Annotation, Release, and Refinement of Training Data (*now published!*)
- **July 15**: Further refinement of training set will be complete
- **Aug 23**: Deadline for Intention to Submit & Required Paper (formerly Aug 9)
- **Aug 30 - Sep 13**: Submissions Accepted (formerly Aug 16 - 30)
- **Sep 15**: Results Announced (formerly Sep 1)
- **Sep 27**: Satellite Event at MICCAI 2021

## News

- **July 15, 2021**: The training set has been frozen!
- **July 1, 2021**: The training set has been released! Also we are adding a two-week buffer for final edits to be made based on community feedback, and we are pushing the challenge timeline by two weeks (see above).
- **June 17, 2021**: We've changed the set of classes for the challenge. See [this forum post](https://discourse.kits-challenge.org/t/kits21-challenge-update/354) for details
- **Apr 7, 2021**: We've started using tags and a changelog to keep track of the dataset version
- **Mar 23, 2021**: A draft of the postprocessing code and some preliminary data has been merged into the master branch.
- **Mar 9, 2021**: A preliminary challenge homepage has been published at [kits-challenge.org](https://kits-challenge.org). You can keep tabs on the data annotation process there.
- **Mar 29, 2020**: A second edition of KiTS was accepted to be held in conjunction with MICCAI 2021 in Strasbourg! More information will be posted here and on the [discussion forum](https://discourse.kits-challenge.org/) when it becomes available.

## Usage

### Installation

1) Install dependency for surface dice:\
`pip install git+https://github.com/JoHof/surface-distance.git` (the original [DeepMind repository](https://github.com/deepmind/surface-distance) is currently not working due to a [missing line comment](https://github.com/deepmind/surface-distance/blob/4315531eb2d449310d47c0850f334cc6a6580543/surface_distance/metrics.py#L102))
2) Clone this repository
3) Install this repository by running `pip install -e .` in the folder where the setup.py file is located

### Download

Start by cloning this repository, but note that **the imaging is not stored here**, it must be downloaded using one of the `get_imaging` scripts in the `starter_code` directory. Currently there are implementations in:

- **python3**: `python3 kits21/starter_code/get_imaging.py`
- **MATLAB**: `matlab kits21/starter_code/get_imaging.m`
- **bash**: `bash kits21/starter_code/get_imaging.sh`
- **julia**: `julia kits21/starter_code/get_imaging.jl`

If you would like to request another implementation of `get_imaging`, please [submit an issue](https://github.com/neheller/kits21/issues/new).

These scripts download imaging from the
[`neheller/KiTS-Challenge-Imaging`](https://huggingface.co/datasets/neheller/KiTS-Challenge-Imaging)
Hugging Face dataset into the local `data/` folder.

## Folder Structure

### `data/`

This is different from [KiTS19](https://github.com/neheller/kits19) because unlike 2019, we now have multiple annotations per "instance" and multiple instances per region.

Consider the "kidney" label in a scan: most patients have two kidneys (i.e., two "instances" of kidney), and each instance was annotated by three independent people. That case's `segmentations/` we would thus have

- `kidney_instance-1_annotation-1.nii.gz`
- `kidney_instance-1_annotation-2.nii.gz`
- `kidney_instance-1_annotation-3.nii.gz`
- `kidney_instance-2_annotation-1.nii.gz`
- `kidney_instance-2_annotation-2.nii.gz`
- `kidney_instance-2_annotation-3.nii.gz`

along with similar collections for `cyst`, and `tumor` regions. The `aggregated_<X>_seg.nii.gz` file is a result of aggregating all of these files by various methods indicated by \<X\>:

- **OR**: A voxel-wise "or" or "union" operator
- **AND**: A voxel-wise "and" or "intersection" operator
- **MAJ**: Voxel-wise majority voting

### `starter_code/`

This folder holds code snippets for viewing and manipulating the data. See [Usage](#Usage) for more information.

### `annotation/`

This folder contains code used to process and import data from the annotation platform. As a participant, there's no reason you should need to run this code, it's only meant to serve as a reference.

## Challenge Information

This challenge will feature significantly more data, several annotations per case, and a number of additional annotated regions. The accepted proposal can be found [on Zenodo](https://doi.org/10.5281/zenodo.3714971), but the most up-to-date information about the challenge can be found on [the KiTS21 homepage](https://kits-challenge.org/kits21/).

## Previous KiTS Challenges

KiTS was first held in conjunction with MICCAI 2019 in Shenzhen. A paper describing that challenge was published in Medical Image Analysis \[[html](https://www.sciencedirect.com/science/article/abs/pii/S1361841520301857)\] \[[pdf](https://arxiv.org/pdf/1912.01054.pdf)\].

```bibtex
@article{heller2020state,
  title={The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge},
  author={Heller, Nicholas and Isensee, Fabian and Maier-Hein, Klaus H and Hou, Xiaoshuai and Xie, Chunmei and Li, Fengyi and Nan, Yang and Mu, Guangrui and Lin, Zhiyong and Han, Miofei and others},
  journal={Medical Image Analysis},
  pages={101821},
  year={2020},
  publisher={Elsevier}
}
```

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