Update README.md

README.md

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----
-license: apache-2.0
----
+---
+license: cc-by-nc-sa-4.0
+task_categories:
+- image-segmentation
+tags:
+- medical
+pretty_name: AbdomenAtlas 1.0 Mini
+size_categories:
+- 1K<n<10K
+extra_gated_prompt: >
+  ## 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.
+extra_gated_fields:
+  Name: text
+  Institution: text
+  Email: text
+  I have read and agree with Terms and Conditions for using the dataset: checkbox
+---
+
+# 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 [email protected]. 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](https://huggingface.co/datasets/AbdomenAtlas/AbdomenAtlas1.0Mini) and
+[AbdomenAtlas1.0MiniBeta](https://huggingface.co/datasets/AbdomenAtlas/AbdomenAtlas1.0MiniBeta)
+
+---
+
+# Downloading Instructions
+
+#### 1- Register at Huggingface, accept our terms and conditions, and create an access token:
+
+[Create a Huggingface account](https://huggingface.co/join)
+
+[Log in](https://huggingface.co/login)
+
+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](https://huggingface.co/settings/tokens) and copy it (you will use it in step 3, in paste_your_token_here)
+
+
+#### 2- Install the Hugging Face library:
+```bash
+pip install huggingface_hub[hf_transfer]==0.24.0
+HF_HUB_ENABLE_HF_TRANSFER=1
+```
+<details>
+<summary style="margin-left: 25px;">[Optional] Alternative without HF Trasnsfer (slower)</summary>
+<div style="margin-left: 25px;">
+  
+```bash
+pip install huggingface_hub==0.24.0
+```
+
+</div>
+</details>
+
+#### 3- Download the dataset:
+```bash
+mkdir AbdomenAtlas
+cd AbdomenAtlas
+huggingface-cli download BodyMaps/AbdomenAtlas1.0Mini --token paste_your_token_here --repo-type dataset --local-dir .
+```
+
+<details>
+<summary style="margin-left: 25px;">[Optional] Resume downloading</summary>
+<div style="margin-left: 25px;">
+
+In case you had a previous interrupted download, just run the huggingface-cli download command above again.
+```bash
+huggingface-cli download BodyMaps/AbdomenAtlas1.0Mini --token paste_your_token_here --repo-type dataset --local-dir .
+```
+</div>
+</details>
+
+### 4- Uncompress:
+Uncompress:
+```bash
+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
+bash delete.sh
+```
+
+---
+
+## Paper
+
+<b>AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks</b> <br/>
+[Chongyu Qu](https://github.com/Chongyu1117)<sup>1</sup>, [Tiezheng Zhang](https://github.com/ollie-ztz)<sup>1</sup>, [Hualin Qiao](https://www.linkedin.com/in/hualin-qiao-a29438210/)<sup>2</sup>, [Jie Liu](https://ljwztc.github.io/)<sup>3</sup>, [Yucheng Tang](https://scholar.google.com/citations?hl=en&user=0xheliUAAAAJ)<sup>4</sup>, [Alan L. Yuille](https://www.cs.jhu.edu/~ayuille/)<sup>1</sup>, and [Zongwei Zhou](https://www.zongweiz.com/)<sup>1,*</sup> <br/>
+<sup>1 </sup>Johns Hopkins University,  <br/>
+<sup>2 </sup>Rutgers University,  <br/>
+<sup>3 </sup>City University of Hong Kong,   <br/>
+<sup>4 </sup>NVIDIA <br/>
+NeurIPS 2023 <br/>
+[paper](https://www.cs.jhu.edu/~alanlab/Pubs23/qu2023abdomenatlas.pdf) | [code](https://github.com/MrGiovanni/AbdomenAtlas) | [dataset](https://huggingface.co/datasets/AbdomenAtlas/AbdomenAtlas1.0Mini) | [annotation](https://www.dropbox.com/scl/fi/28l5vpxrn212r2ejk32xv/AbdomenAtlas.tar.gz?rlkey=vgqmao4tgv51hv5ew24xx4xpm&dl=0) | [poster](document/neurips_poster.pdf)
+
+<b>How Well Do Supervised 3D Models Transfer to Medical Imaging Tasks?</b> <br/>
+[Wenxuan Li](https://scholar.google.com/citations?hl=en&user=tpNZM2YAAAAJ), [Alan Yuille](https://www.cs.jhu.edu/~ayuille/), and [Zongwei Zhou](https://www.zongweiz.com/)<sup>*</sup> <br/>
+Johns Hopkins University  <br/>
+International Conference on Learning Representations (ICLR) 2024 (oral; top 1.2%) <br/>
+[paper](https://www.cs.jhu.edu/~alanlab/Pubs23/li2023suprem.pdf) | [code](https://github.com/MrGiovanni/SuPreM) 
+
+## Citation 
+
+```
+@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},
+  url={https://github.com/MrGiovanni/AbdomenAtlas}
+}
+
+@misc{bassi2024touchstonebenchmarkrightway,
+      title={Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?}, 
+      author={Pedro R. A. S. Bassi and Wenxuan Li and Yucheng Tang and Fabian Isensee and Zifu Wang and Jieneng Chen and Yu-Cheng Chou and Yannick Kirchhoff and Maximilian Rokuss and Ziyan Huang and Jin Ye and Junjun He and Tassilo Wald and Constantin Ulrich and Michael Baumgartner and Saikat Roy and Klaus H. Maier-Hein and Paul Jaeger and Yiwen Ye and Yutong Xie and Jianpeng Zhang and Ziyang Chen and Yong Xia and Zhaohu Xing and Lei Zhu and Yousef Sadegheih and Afshin Bozorgpour and Pratibha Kumari and Reza Azad and Dorit Merhof and Pengcheng Shi and Ting Ma and Yuxin Du and Fan Bai and Tiejun Huang and Bo Zhao and Haonan Wang and Xiaomeng Li and Hanxue Gu and Haoyu Dong and Jichen Yang and Maciej A. Mazurowski and Saumya Gupta and Linshan Wu and Jiaxin Zhuang and Hao Chen and Holger Roth and Daguang Xu and Matthew B. Blaschko and Sergio Decherchi and Andrea Cavalli and Alan L. Yuille and Zongwei Zhou},
+      year={2024},
+      eprint={2411.03670},
+      archivePrefix={arXiv},
+      primaryClass={cs.CV},
+      url={https://arxiv.org/abs/2411.03670}, 
+}
+
+@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},
+  journal={Advances in Neural Information Processing Systems},
+  volume={36},
+  year={2023}
+}
+```
+
+## 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</a> is licensed under <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY-NC-SA 4.0.</a></p>
+
+## 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.