README.md · YongchengYAO/OAIZIB-CM at main

metadata

license: cc-by-nc-4.0
task_categories:
  - image-segmentation
language:
  - en
tags:
  - medical
  - image
  - segmentation
  - MRI
  - knee
  - cartilage
pretty_name: oaizib-cm
size_categories:
  - n<1K

Source	link
Huggingface	here (recommended)
Zenodo	here
Google Drive	here

About

This is the official release of OAIZIB-CM dataset

OAIZIB-CM is based on the OAIZIB dataset
- OAIZIB paper: Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative
In OAIZIB-CM, tibial cartilage is split into medial and lateral tibial cartilages.
OAIZIB-CM includes CLAIR-Knee-103R, consisting of
- a template image learned from 103 MR images of subjects without radiographic OA
- corresponding 5-ROI segmentation mask for cartilages and bones
- corresponding 20-ROI atlas for articular cartilages
It is compulsory to cite the paper if you use the dataset
- CartiMorph: A framework for automated knee articular cartilage morphometrics

Changelog 🔥

[27 Feb, 2025] Add the template and atlas CLAIR-Knee-103R
[26 Feb, 2025] Update compulsory citation (CartiMorph) for the dataset
[15 Feb, 2025] Update file imagesTs/oaizib_454_0000.nii.gz
[14 Feb, 2025] Identify corrupted files: case 454

Files

Images & Labels

imagesTr: training images (#404)
labelsTr: training segmentation masks (#404)
imagesTs: testing images (#103)
labelsTs: testing segmentation masks (#103)

Data Split & Info

subInfo_train.xlsx: list of training data
subInfo_test.xlsx: list of testing data
kneeSideInfo.csv: a file containing knee side information, used in CartiMorph Toolbox

Download from Huggingface

#!/bin/bash
pip install --upgrade huggingface-hub[cli]
huggingface-cli login --token $HF_TOKEN

# python
from huggingface_hub import snapshot_download
snapshot_download(repo_id="YongchengYAO/OAIZIB-CM", repo_type='dataset', local_dir="/your/local/folder")

Segmentation Labels

labels_map = {
    "1": "Femur",
    "2": "Femoral Cartilage",
    "3": "Tibia",
    "4": "Medial Tibial Cartilage",
    "5": "Lateral Tibial Cartilage",
}

Papers

The dataset originates from these projects:

CartiMorph: https://github.com/YongchengYAO/CartiMorph
CartiMorph Toolbox:
- https://github.com/YongchengYAO/CartiMorph-Toolbox
- https://github.com/YongchengYAO/CMT-AMAI24paper

@article{YAO2024103035,
title = {CartiMorph: A framework for automated knee articular cartilage morphometrics},
journal = {Medical Image Analysis},
author = {Yongcheng Yao and Junru Zhong and Liping Zhang and Sheheryar Khan and Weitian Chen},
volume = {91},
pages = {103035},
year = {2024},
issn = {1361-8415},
doi = {https://doi.org/10.1016/j.media.2023.103035}
}

@InProceedings{10.1007/978-3-031-82007-6_16,
author="Yao, Yongcheng
and Chen, Weitian",
editor="Wu, Shandong
and Shabestari, Behrouz
and Xing, Lei",
title="Quantifying Knee Cartilage Shape and Lesion: From Image to Metrics",
booktitle="Applications of Medical Artificial Intelligence",
year="2025",
publisher="Springer Nature Switzerland",
address="Cham",
pages="162--172"
}

License

This dataset is released under the CC BY-NC 4.0 license.