Update README.md

README.md

@@ -62,4 +62,91 @@ superior mesenteric vein
 Merlin Plus presents annotations for the CT scans in the original Merlin dataset. To download these CT scans, please visit this website: https://stanfordaimi.azurewebsites.net/datasets/60b9c7ff-877b-48ce-96c3-0194c8205c40
 
 ### Merlin Dataset
-Merlin Abdominal CT Dataset is an abdominal CT dataset consisting of 25,494 scans from 18,317 patients. Each scan is paired with its corresponding radiology report. The dataset includes abdominal and pelvis CT exams conducted between 2012 and 2018 at the Stanford Hospital Emergency Department, selected using CPT codes (72192, 72193, 72194, 74150, 74160, 74170, 74176, 74177, and 74178) through the STARR tool. For each exam, the DICOM series with the largest slice count was converted into NIfTI format, compressing the scans and removing patient-identifiable metadata.
+Merlin Abdominal CT Dataset is an abdominal CT dataset consisting of 25,494 scans from 18,317 patients. Each scan is paired with its corresponding radiology report. The dataset includes abdominal and pelvis CT exams conducted between 2012 and 2018 at the Stanford Hospital Emergency Department, selected using CPT codes (72192, 72193, 72194, 74150, 74160, 74170, 74176, 74177, and 74178) through the STARR tool. For each exam, the DICOM series with the largest slice count was converted into NIfTI format, compressing the scans and removing patient-identifiable metadata.
+
+
+# Papers
+
+<b>Learning Segmentation from Radiology Reports</b> <br/>
+[Pedro R. A. S. Bassi](https://scholar.google.com/citations?user=NftgL6gAAAAJ&hl=en), [Wenxuan Li](https://scholar.google.com/citations?hl=en&user=tpNZM2YAAAAJ), [Jieneng Chen](https://scholar.google.com/citations?user=yLYj88sAAAAJ&hl=zh-CN), Zheren Zhu, Tianyu Lin, [Sergio Decherchi](https://scholar.google.com/citations?user=T09qQ1IAAAAJ&hl=it), [Andrea Cavalli](https://scholar.google.com/citations?user=4xTOvaMAAAAJ&hl=en), [Kang Wang](https://radiology.ucsf.edu/people/kang-wang), [Yang Yang](https://scholar.google.com/citations?hl=en&user=6XsJUBIAAAAJ), [Alan Yuille](https://www.cs.jhu.edu/~ayuille/), [Zongwei Zhou](https://www.zongweiz.com/)* <br/>
+*Johns Hopkins University* <br/>
+MICCAI 2025 <br/>
+<b>Finalist, Best Paper and Young Scientist Awards</b>  <br/>
+<a href='https://www.cs.jhu.edu/~zongwei/publication/bassi2025learning.pdf'><img src='https://img.shields.io/badge/Paper-PDF-purple'></a>
+
+<b>Merlin: A Vision Language Foundation Model for 3D Computed Tomography</b> <br/>
+Louis Blankemeier, Joseph Paul Cohen, Ashwin Kumar, Dave Van Veen, Syed Jamal Safdar Gardezi, Magdalini Paschali, Zhihong Chen, Jean-Benoit Delbrouck, Eduardo Reis, Cesar Truyts, Christian Bluethgen, Malte Engmann Kjeldskov Jensen, Sophie Ostmeier, Maya Varma, Jeya Maria Jose Valanarasu, Zhongnan Fang, Zepeng Huo, Zaid Nabulsi, Diego Ardila, Wei-Hung Weng, Edson Amaro Junior, Neera Ahuja, Jason Fries, Nigam H. Shah, Andrew Johnston, Robert D. Boutin, Andrew Wentland, Curtis P. Langlotz, Jason Hom, Sergios Gatidis, Akshay S. Chaudhari  <br/>
+*Stanford University * <br/>
+<a href='https://arxiv.org/pdf/2406.06512v1'><img src='https://img.shields.io/badge/Paper-PDF-purple'></a>
+
+# Download
+
+You can manually download and unzip the Merlin Plus annotations, or you can save the script below as download.sh and execute it with 'bash download.sh'.
+
+```bash
+#!/bin/bash
+set -e
+
+cd data/
+
+echo "Downloading README.md..."
+wget -O README.md "https://huggingface.co/datasets/AbdomenAtlas/MerlinPlus/resolve/main/README.md?download=true"
+
+mkdir -p MerlinMasks
+
+# Download and extract the 1,000-case shards (00000001 → 00025000)
+for i in {1..25}; do
+    start=$(printf "%08d" $(( (i - 1) * 1000 + 1 )))
+    end=$(printf "%08d" $(( i * 1000 )))
+    file="MerlinMasks_BDMAP_${start}_${end}.tar.gz"
+    url="https://huggingface.co/datasets/AbdomenAtlas/MerlinPlus/resolve/main/${file}?download=true"
+
+    echo "[${i}/25] Downloading $file..."
+    wget --show-progress -O "$file" "$url"
+
+    echo "Extracting $file..."
+    tar -xzf "$file" -C MerlinMasks
+    rm "$file"
+done
+
+# Download and extract the final partial shard (00025001 → 00025456)
+file="MerlinMasks_BDMAP_00025001_00025456.tar.gz"
+url="https://huggingface.co/datasets/AbdomenAtlas/MerlinPlus/resolve/main/${file}?download=true"
+echo "Downloading final shard..."
+wget --show-progress -O "$file" "$url"
+echo "Extracting $file..."
+tar -xzf "$file" -C MerlinMasks
+rm "$file"
+
+cd ..
+```
+
+
+# Citations
+If you use this data, please cite the 3 paper below (model and datasets):
+
+```
+@article{bassi2025learning,
+  title={Learning Segmentation from Radiology Reports},
+  author={Bassi, Pedro RAS and Li, Wenxuan and Chen, Jieneng and Zhu, Zheren and Lin, Tianyu and Decherchi, Sergio and Cavalli, Andrea and Wang, Kang and Yang, Yang and Yuille, Alan L and others},
+  journal={arXiv preprint arXiv:2507.05582},
+  year={2025}
+}
+
+@article{li2025pants,
+  title={PanTS: The Pancreatic Tumor Segmentation Dataset},
+  author={Li, Wenxuan and Zhou, Xinze and Chen, Qi and Lin, Tianyu and Bassi, Pedro RAS and Plotka, Szymon and Cwikla, Jaroslaw B and Chen, Xiaoxi and Ye, Chen and Zhu, Zheren and others},
+  journal={arXiv preprint arXiv:2507.01291},
+  year={2025},
+  url={https://github.com/MrGiovanni/PanTS}
+}
+
+@article{blankemeier2024merlin,
+  title={Merlin: A vision language foundation model for 3d computed tomography},
+  author={Blankemeier, Louis and Cohen, Joseph Paul and Kumar, Ashwin and Van Veen, Dave and Gardezi, Syed Jamal Safdar and Paschali, Magdalini and Chen, Zhihong and Delbrouck, Jean-Benoit and Reis, Eduardo and Truyts, Cesar and others},
+  journal={Research Square},
+  pages={rs--3},
+  year={2024}
+}
+
+```