Touchstone

Touchstone

[NeurIPS 2024] Touchstone - Benchmarking AI on 5,172 o.o.d. CT volumes and 9 anatomical structures

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Touchstone Benchmark

Touchstone Benchmark

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We present Touchstone, a large-scale medical segmentation benchmark based on annotated 5,195 CT volumes from 76 hospitals for training, and 6,933 CT volumes from 8 additional hospitals for testing. We invite AI inventors to train their models on AbdomenAtlas, and we independently evaluate their algorithms. We have already collaborated with 14 influential research teams, and we remain accepting new submissions.

Paper

Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?
Pedro R. A. S. Bassi1, Wenxuan Li1, Yucheng Tang2, Fabian Isensee3, ..., Alan Yuille1, Zongwei Zhou1
1Johns Hopkins University, 2NVIDIA, 3DKFZ
NeurIPS 2024
YouTube

Touchstone 1.0 Leaderboard

rank model organization average DSC paper github
🏆 MedNeXt DKFZ 89.2 arXiv GitHub stars
🏆 STU-Net-B Shanghai AI Lab 89.0 arXiv GitHub stars
🏆 MedFormer Rutgers 89.0 arXiv GitHub stars
🏆 nnU-Net ResEncL DKFZ 88.8 arXiv GitHub stars
🏆 UniSeg NPU 88.8 arXiv GitHub stars
🏆 Diff-UNet HKUST 88.5 arXiv GitHub stars
🏆 LHU-Net UR 88.0 arXiv GitHub stars
🏆 NexToU HIT 87.8 arXiv GitHub stars
9 SegVol BAAI 87.1 arXiv GitHub stars
10 U-Net & CLIP CityU 87.1 arXiv GitHub stars
11 Swin UNETR & CLIP CityU 86.7 arXiv GitHub stars
12 Swin UNETR NVIDIA 80.1 arXiv GitHub stars
13 UNesT NVIDIA 79.1 arXiv GitHub stars
14 SAM-Adapter Duke 73.4 arXiv GitHub stars
15 UNETR NVIDIA 64.4 arXiv GitHub stars
Aorta - NexToU 🏆
rank model organization DSC paper github
🏆 NexToU HIT 86.4 arXiv GitHub stars
2 MedNeXt DKFZ 83.1 arXiv GitHub stars
3 UniSeg NPU 82.3 arXiv GitHub stars
4 STU-Net-B Shanghai AI Lab 82.1 arXiv GitHub stars
5 nnU-Net ResEncL DKFZ 81.4 arXiv GitHub stars
6 Diff-UNet HKUST 81.2 arXiv GitHub stars
7 Swin UNETR NVIDIA 81.1 arXiv GitHub stars
8 SegVol BAAI 80.2 arXiv GitHub stars
9 UNesT NVIDIA 78.6 arXiv GitHub stars
10 Swin UNETR & CLIP CityU 78.1 arXiv GitHub stars
11 U-Net & CLIP CityU 77.1 arXiv GitHub stars
12 SAM-Adapter Duke 62.8 arXiv GitHub stars
13 UNETR NVIDIA 52.1 arXiv GitHub stars
Gallbladder - STU-Net-B & MedNeXt 🏆
rank model organization DSC paper github
🏆 STU-Net-B Shanghai AI Lab 85.5 arXiv GitHub stars
🏆 MedNeXt DKFZ 85.3 arXiv GitHub stars
3 nnU-Net ResEncL DKFZ 84.9 arXiv GitHub stars
4 UniSeg NPU 84.7 arXiv GitHub stars
5 Diff-UNet HKUST 83.8 arXiv GitHub stars
6 NexToU HIT 82.3 arXiv GitHub stars
7 U-Net & CLIP CityU 82.1 arXiv GitHub stars
8 Swin UNETR & CLIP CityU 80.2 arXiv GitHub stars
9 SegVol BAAI 79.3 arXiv GitHub stars
10 Swin UNETR NVIDIA 69.2 arXiv GitHub stars
11 UNesT NVIDIA 62.1 arXiv GitHub stars
12 SAM-Adapter Duke 49.4 arXiv GitHub stars
13 UNETR NVIDIA 43.8 arXiv GitHub stars
KidneyL - Diff-UNet 🏆
rank model organization DSC paper github
🏆 Diff-UNet HKUST 91.9 arXiv GitHub stars
2 nnU-Net ResEncL DKFZ 91.9 arXiv GitHub stars
3 STU-Net-B Shanghai AI Lab 91.9 arXiv GitHub stars
4 MedNeXt DKFZ 91.8 arXiv GitHub stars
5 SegVol BAAI 91.8 arXiv GitHub stars
6 UniSeg NPU 91.5 arXiv GitHub stars
7 U-Net & CLIP CityU 91.1 arXiv GitHub stars
8 Swin UNETR & CLIP CityU 91.0 arXiv GitHub stars
9 NexToU HIT 89.6 arXiv GitHub stars
10 SAM-Adapter Duke 87.3 arXiv GitHub stars
11 Swin UNETR NVIDIA 85.5 arXiv GitHub stars
12 UNesT NVIDIA 85.4 arXiv GitHub stars
13 UNETR NVIDIA 63.7 arXiv GitHub stars
KidneyR - Diff-UNet 🏆
rank model organization DSC paper github
🏆 Diff-UNet HKUST 92.8 arXiv GitHub stars
2 MedNeXt DKFZ 92.6 arXiv GitHub stars
3 nnU-Net ResEncL DKFZ 92.6 arXiv GitHub stars
4 STU-Net-B Shanghai AI Lab 92.5 arXiv GitHub stars
5 SegVol BAAI 92.5 arXiv GitHub stars
6 UniSeg NPU 92.2 arXiv GitHub stars
7 U-Net & CLIP CityU 91.9 arXiv GitHub stars
8 Swin UNETR & CLIP CityU 91.7 arXiv GitHub stars
9 SAM-Adapter Duke 90.4 arXiv GitHub stars
10 NexToU HIT 90.1 arXiv GitHub stars
11 UNesT NVIDIA 83.6 arXiv GitHub stars
12 Swin UNETR NVIDIA 81.7 arXiv GitHub stars
13 UNETR NVIDIA 69.6 arXiv GitHub stars
Liver - MedNeXt 🏆
rank model organization DSC paper github
🏆 MedNeXt DKFZ 96.3 arXiv GitHub stars
2 nnU-Net ResEncL DKFZ 96.3 arXiv GitHub stars
3 Diff-UNet HKUST 96.2 arXiv GitHub stars
4 STU-Net-B Shanghai AI Lab 96.2 arXiv GitHub stars
5 UniSeg NPU 96.1 arXiv GitHub stars
6 U-Net & CLIP CityU 96.0 arXiv GitHub stars
7 SegVol BAAI 96.0 arXiv GitHub stars
8 Swin UNETR & CLIP CityU 95.8 arXiv GitHub stars
9 NexToU HIT 95.7 arXiv GitHub stars
10 SAM-Adapter Duke 94.1 arXiv GitHub stars
11 UNesT NVIDIA 93.6 arXiv GitHub stars
12 Swin UNETR NVIDIA 93.5 arXiv GitHub stars
13 UNETR NVIDIA 90.5 arXiv GitHub stars
Pancreas - MedNeXt 🏆
rank model organization DSC paper github
🏆 MedNeXt DKFZ 83.3 arXiv GitHub stars
2 STU-Net-B Shanghai AI Lab 83.2 arXiv GitHub stars
3 nnU-Net ResEncL DKFZ 82.9 arXiv GitHub stars
4 UniSeg NPU 82.7 arXiv GitHub stars
5 Diff-UNet HKUST 81.9 arXiv GitHub stars
6 U-Net & CLIP CityU 80.8 arXiv GitHub stars
7 Swin UNETR & CLIP CityU 80.2 arXiv GitHub stars
8 NexToU HIT 80.2 arXiv GitHub stars
9 SegVol BAAI 79.1 arXiv GitHub stars
10 Swin UNETR NVIDIA 68.5 arXiv GitHub stars
11 UNesT NVIDIA 68.3 arXiv GitHub stars
12 UNETR NVIDIA 55.1 arXiv GitHub stars
13 SAM-Adapter Duke 50.2 arXiv GitHub stars
Postcava - STU-Net-B & MedNeXt 🏆
rank model organization DSC paper github
🏆 STU-Net-B Shanghai AI Lab 81.3 arXiv GitHub stars
🏆 MedNeXt DKFZ 81.3 arXiv GitHub stars
3 UniSeg NPU 81.2 arXiv GitHub stars
4 Diff-UNet HKUST 80.8 arXiv GitHub stars
5 nnU-Net ResEncL DKFZ 80.5 arXiv GitHub stars
6 U-Net & CLIP CityU 78.5 arXiv GitHub stars
7 NexToU HIT 78.1 arXiv GitHub stars
8 SegVol BAAI 77.8 arXiv GitHub stars
9 Swin UNETR & CLIP CityU 76.8 arXiv GitHub stars
10 Swin UNETR NVIDIA 69.9 arXiv GitHub stars
11 UNesT NVIDIA 66.2 arXiv GitHub stars
12 UNETR NVIDIA 53.9 arXiv GitHub stars
13 SAM-Adapter Duke 48.0 arXiv GitHub stars
Spleen - nnU-Net ResEncL 🏆
rank model organization DSC paper github
🏆 nnU-Net ResEncL DKFZ 95.2 arXiv GitHub stars
2 MedNeXt DKFZ 95.2 arXiv GitHub stars
3 STU-Net-B Shanghai AI Lab 95.1 arXiv GitHub stars
4 Diff-UNet HKUST 95.0 arXiv GitHub stars
5 UniSeg NPU 94.9 arXiv GitHub stars
6 SegVol BAAI 94.5 arXiv GitHub stars
7 NexToU HIT 94.7 arXiv GitHub stars
8 U-Net & CLIP CityU 94.3 arXiv GitHub stars
9 Swin UNETR & CLIP CityU 94.1 arXiv GitHub stars
10 SAM-Adapter Duke 90.5 arXiv GitHub stars
11 Swin UNETR NVIDIA 87.9 arXiv GitHub stars
12 UNesT NVIDIA 86.7 arXiv GitHub stars
13 UNETR NVIDIA 76.5 arXiv GitHub stars
Stomach - STU-Net-B & MedNeXt & nnU-Net ResEncL 🏆
rank model organization DSC paper github
🏆 STU-Net-B Shanghai AI Lab 93.5 arXiv GitHub stars
🏆 MedNeXt DKFZ 93.5 arXiv GitHub stars
🏆 nnU-Net ResEncL DKFZ 93.4 arXiv GitHub stars
4 UniSeg NPU 93.3 arXiv GitHub stars
5 Diff-UNet HKUST 93.1 arXiv GitHub stars
6 NexToU HIT 92.7 arXiv GitHub stars
7 SegVol BAAI 92.5 arXiv GitHub stars
8 U-Net & CLIP CityU 92.4 arXiv GitHub stars
9 Swin UNETR & CLIP CityU 92.2 arXiv GitHub stars
10 SAM-Adapter Duke 88.0 arXiv GitHub stars
11 UNesT NVIDIA 87.6 arXiv GitHub stars
12 Swin UNETR NVIDIA 84.1 arXiv GitHub stars
13 UNETR NVIDIA 74.2 arXiv GitHub stars

Touchstone 1.0 Dataset

Training set

Test set

metadata

Figure 1. Metadata distribution in the test set.

Touchstone 1.0 Model

[!NOTE] We are releasing the trained AI models evaluated in Touchstone right here. Stay tuned!

rank model average DSC parameter infer. speed download
🏆 MedNeXt 89.2 61.8M ★☆☆☆☆
🏆 STU-Net-B 89.0 58.3M ★★☆☆☆ checkpoint
🏆 MedFormer 89.0 38.5M ★★★☆☆
🏆 nnU-Net ResEncL 88.8 102.0M ★★★★☆ checkpoint
🏆 UniSeg 88.8 31.0M ☆☆☆☆☆
🏆 Diff-UNet 88.5 434.0M ★★★☆☆
🏆 LHU-Net 88.0 8.6M ★★★★★
🏆 NexToU 87.8 81.9M ★★★★☆ checkpoint
9 SegVol 87.1 181.0M ★★★★☆ checkpoint
10 U-Net & CLIP 87.1 19.1M ★★★☆☆
11 Swin UNETR & CLIP 86.7 62.2M ★★★☆☆
12 Swin UNETR 80.1 72.8M ★★★★★
13 UNesT 79.1 87.2M ★★★★★
14 SAM-Adapter 73.4 11.6M ★★★★☆
15 UNETR 64.4 101.8M ★★★★★

Citation

Please cite the following papers if you find our study helpful.

@article{bassi2024touchstone,
  title={Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?},
  author={Bassi, Pedro RAS and Li, Wenxuan and Tang, Yucheng and Isensee, Fabian and Wang, Zifu and Chen, Jieneng and Chou, Yu-Cheng and Kirchhoff, Yannick and Rokuss, Maximilian and Huang, Ziyan and Ye, Jin and He, Junjun and Wald, Tassilo and Ulrich, Constantin and Baumgartner, Michael and Roy, Saikat and Maier-Hein, Klaus H. and Jaeger, Paul and Ye, Yiwen and Xie, Yutong and Zhang, Jianpeng and Chen, Ziyang and Xia, Yong and Xing, Zhaohu and Zhu, Lei and Sadegheih, Yousef and Bozorgpour, Afshin and Kumari, Pratibha and Azad, Reza and Merhof, Dorit and Shi, Pengcheng and Ma, Ting and Du, Yuxin and Bai, Fan and Huang, Tiejun and Zhao, Bo and Wang, Haonan and Li, Xiaomeng and Gu, Hanxue and Dong, Haoyu and Yang, Jichen and Mazurowski, Maciej A. and Gupta, Saumya and Wu, Linshan and Zhuang, Jiaxin and Chen, Hao and Roth, Holger and Xu, Daguang and Blaschko, Matthew B. and Decherchi, Sergio and Cavalli, Andrea and Yuille, Alan L. and Zhou, Zongwei},
  journal={Conference on Neural Information Processing Systems},
  year={2024},
  utl={https://github.com/MrGiovanni/Touchstone}
}

@article{li2024abdomenatlas,
  title={AbdomenAtlas: A large-scale, detailed-annotated, \& multi-center dataset for efficient transfer learning and open algorithmic benchmarking},
  author={Li, Wenxuan and Qu, Chongyu and Chen, Xiaoxi and Bassi, Pedro RAS and Shi, Yijia and Lai, Yuxiang and Yu, Qian and Xue, Huimin and Chen, Yixiong and Lin, Xiaorui and others},
  journal={Medical Image Analysis},
  pages={103285},
  year={2024},
  publisher={Elsevier}
}

@inproceedings{li2024well,
  title={How Well Do Supervised Models Transfer to 3D Image Segmentation?},
  author={Li, Wenxuan and Yuille, Alan and Zhou, Zongwei},
  booktitle={The Twelfth International Conference on Learning Representations},
  year={2024}
}

@article{qu2023abdomenatlas,
  title={Abdomenatlas-8k: Annotating 8,000 CT volumes for multi-organ segmentation in three weeks},
  author={Qu, Chongyu and Zhang, Tiezheng and Qiao, Hualin and Tang, Yucheng and Yuille, Alan L and Zhou, Zongwei and others},
  journal={Advances in Neural Information Processing Systems},
  volume={36},
  year={2023}
}

Acknowledgement

This work was supported by the Lustgarten Foundation for Pancreatic Cancer Research and the McGovern Foundation. Paper content is covered by patents pending.

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