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Terms and Conditions for Using the AbdomenAtlas 1.1 Mini Dataset
1. Acceptance of Terms
Accessing and using the AbdomenAtlas 1.1 Mini dataset implies your agreement to these terms and conditions. If you disagree with any part, please refrain from using the dataset.
2. Permitted Use
- The dataset is intended solely for academic, research, and educational purposes.
- Any commercial exploitation of the dataset without prior permission is strictly forbidden.
- You must adhere to all relevant laws, regulations, and research ethics, including data privacy and protection standards.
3. Data Protection and Privacy
- Acknowledge the presence of sensitive information within the dataset and commit to maintaining data confidentiality.
- Direct attempts to re-identify individuals from the dataset are prohibited.
- Ensure compliance with data protection laws such as GDPR and HIPAA.
4. Attribution
- Cite the dataset and acknowledge the providers in any publications resulting from its use.
- Claims of ownership or exclusive rights over the dataset or derivatives are not permitted.
5. Redistribution
- Redistribution of the dataset or any portion thereof is not allowed.
- Sharing derived data must respect the privacy and confidentiality terms set forth.
6. Disclaimer
The dataset is provided "as is" without warranty of any kind, either expressed or implied, including but not limited to the accuracy or completeness of the data.
7. Limitation of Liability
Under no circumstances will the dataset providers be liable for any claims or damages resulting from your use of the dataset.
8. Access Revocation
Violation of these terms may result in the termination of your access to the dataset.
9. Amendments
The terms and conditions may be updated at any time; continued use of the dataset signifies acceptance of the new terms.
10. Governing Law
These terms are governed by the laws of the location of the dataset providers, excluding conflict of law rules.
Consent:
Accessing and using the AbdomenAtlas 1.1 Mini dataset signifies your acknowledgment and agreement to these terms and conditions.
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Dataset Summary
The largest, fully-annotated abdominal CT dataset to date, including 9,262 CT volumes with annotations for 25 different anatomical structures.
Join the Touchstone Benchmarking Project
The Touchstone Project aims to compare diverse semantic segmentation and pre-training algorithms. We, the CCVL research group at Johns Hopkins University, invite creators of these algorithms to contribute to the initiative. With our support, contributors will train their methodologies on the largest fully-annotated abdominal CT datasets to date. Subsequently, we will evaluate the trained models using a large internal dataset at Johns Hopkins University. If you are the creator of a semantic segmentation or pre-training algorithm and wish to advance medical AI by participating in the Benchmark Project, please reach out to pedro.salvadorbassi2@unibo.it. We will provide you further details on the project and explain your opportunities to collaborate in our future publications!
Note for Touchstone Benchmarking Project
This dataset should be only used for the second round of the Touchstone Project, and not to update first-round checkpoints. The first round dataset (5,195 annotated CT volumes, 9 annotated structures) is available at: AbdomenAtlas1.0Mini and AbdomenAtlas1.0MiniBeta
Downloading Instructions
1- Register at Huggingface, accept our terms and conditions, and create an access token:
Accept our terms and conditions for acessing this dataset: on the top of this page, click on "Expand to review and access", insert your data and click "Agree and access repository")
Create a Huggingface access token and copy it (you will use it in step 3, in paste_your_token_here)
2- Install the Hugging Face library:
pip install huggingface_hub[hf_transfer]==0.24.0
HF_HUB_ENABLE_HF_TRANSFER=1
[Optional] Alternative without HF Trasnsfer (slower)
pip install huggingface_hub==0.24.0
3- Download the dataset:
mkdir AbdomenAtlas
cd AbdomenAtlas
huggingface-cli download BodyMaps/_AbdomenAtlas1.1Mini --token paste_your_token_here --repo-type dataset --local-dir .
[Optional] Resume downloading
In case you had a previous interrupted download, just run the huggingface-cli download command above again.
huggingface-cli download BodyMaps/_AbdomenAtlas1.1Mini --token paste_your_token_here --repo-type dataset --local-dir .
4- Uncompress:
Uncompress:
bash unzip.sh
Check if the folder AbdomenAtlas/uncompressed contains all cases, from BDMAP_00000001 to BDMAP_00009262. If so, you can delete the original compressed files, running:
bash delete.sh
Paper
AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks
Chongyu Qu1, Tiezheng Zhang1, Hualin Qiao2, Jie Liu3, Yucheng Tang4, Alan L. Yuille1, and Zongwei Zhou1,*
1 Johns Hopkins University,
2 Rutgers University,
3 City University of Hong Kong,
4 NVIDIA
NeurIPS 2023
paper | code | dataset | annotation | poster
How Well Do Supervised 3D Models Transfer to Medical Imaging Tasks?
Wenxuan Li, Alan Yuille, and Zongwei Zhou*
Johns Hopkins University
International Conference on Learning Representations (ICLR) 2024 (oral; top 1.2%)
paper | code
Citation
@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},
journal={Advances in Neural Information Processing Systems},
volume={36},
year={2023}
}
@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}
}
Acknowledgements
This work was supported by the Lustgarten Foundation for Pancreatic Cancer Research and partially by the Patrick J. McGovern Foundation Award. We appreciate the effort of the MONAI Team to provide open-source code for the community.
License
AbdomenAtlas 1.1 is licensed under CC BY-NC-SA 4.0.
Uploading AbdomenAtlas to HuggingFace
The file AbdomenAtlasUploadMultipleFolders.ipynb has the code we used to upload AbdomenAtlas to Hugging Face. It may be ncessary to run the script multiple times, until it finishes without an uploading error. The uploading script requires PyTorch, huggingface_hub, and Jupyter Notebook.
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