Duplicate from YongchengYAO/OAIZIB-CM

Co-authored-by: Yongcheng Yao <YongchengYAO@users.noreply.huggingface.co>

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README.md

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+---
+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
+---
+
+
+![HF-OAIZIB-CM](HF-OAIZIB-CM.png)
+
+
+## Summary 🌟
+**OAIZIB-CM: 507 knee MRIs and segmentation masks of [5 ROIs](https://huggingface.co/datasets/YongchengYAO/OAIZIB-CM/blob/main/README.md#segmentation-labels)** 
+
+## Data
+| Source       | link                                                         |
+| ------------ | ------------------------------------------------------------ |
+| Huggingface  | [main](https://huggingface.co/datasets/YongchengYAO/OAIZIB-CM/tree/main) |
+|              | [load_dataset-support](https://huggingface.co/datasets/YongchengYAO/OAIZIB-CM/tree/load_dataset-support) | 
+| Zenodo       | [here](https://zenodo.org/records/14934086)
+| Google Drive | [here](https://drive.google.com/drive/folders/13_afAKSH7ZMOI_Nk2gfoihbJKwafw1l9?usp=share_link) |
+- Huggingface Dataset Branch:
+  - `main`: The main branch contains the same files as those in Zenodo and Google Drive
+  - `load_dataset-support`: We added HF `load_dataset()` support in this branch (ref: [intended usage 2](https://huggingface.co/datasets/YongchengYAO/OAIZIB-CM#2-load-dataset-or-iterabledataset-from-the-load_dataset-support-branch-%EF%B8%8F))
+
+
+## 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](https://doi.org/10.1016/j.media.2018.11.009)
+- In OAIZIB-CM, tibial cartilage is split into medial and lateral tibial cartilages.
+- OAIZIB-CM includes [CLAIR-Knee-103R](https://github.com/YongchengYAO/CartiMorph/blob/main/Documents/TemplateAtlas.md), 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](https://doi.org/10.1016/j.media.2023.103035)
+
+
+## Changelog 🔥
+- [10 Oct, 2025] This dataset is integrated into 🔥[MedVision](https://huggingface.co/datasets/YongchengYAO/MedVision)🔥
+- [09 Jul, 2025] `trust_remote_code` is no longer supported in datasets==4.0.0, install with `pip install datasets==3.6.0`
+- [22 Mar, 2025] Add HF `load_dataset()` support in the `load_dataset-support` branch.
+- [27 Feb, 2025] Add the template and atlas [CLAIR-Knee-103R](https://github.com/YongchengYAO/CartiMorph/blob/main/Documents/TemplateAtlas.md)
+- [26 Feb, 2025] Update compulsory citation ([CartiMorph](https://doi.org/10.1016/j.media.2023.103035)) 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`: list of training data
+- `subInfo_test`: list of testing data
+- `kneeSideInfo`: a file containing knee side information, used in CartiMorph Toolbox
+
+
+## Intended Usage
+### 1. Download Files from the `main` or `load_dataset-support` Branch
+```bash
+#!/bin/bash
+pip install --upgrade huggingface-hub[cli]
+huggingface-cli login --token $HF_TOKEN
+```
+```python
+# python
+from huggingface_hub import snapshot_download
+snapshot_download(repo_id="YongchengYAO/OAIZIB-CM", repo_type='dataset', local_dir="/your/local/folder")
+```
+```python
+# python
+from huggingface_hub import snapshot_download
+snapshot_download(repo_id="YongchengYAO/OAIZIB-CM", repo_type='dataset', revision="load_dataset-support", local_dir="/your/local/folder")
+```
+
+### 2. Load `Dataset` or `IterableDataset` from the `load_dataset-support` Branch ‼️
+‼️ Require datasets<=3.6.0
+```python
+>>> from datasets import load_dataset
+
+# Load Dataset
+>>> dataset_test = load_dataset("YongchengYAO/OAIZIB-CM", revision="load_dataset-support", trust_remote_code=True, split="test")
+>>> type(dataset_test)
+<class 'datasets.arrow_dataset.Dataset'>
+
+# Convert Dataset to IterableDataset: use .to_iterable_dataset()
+>>> iterdataset_test = dataset_test.to_iterable_dataset()
+>>> type(iterdataset_test)
+<class 'datasets.iterable_dataset.IterableDataset'>
+
+# Load IterableDataset: add streaming=True
+>>> iterdataset_train = load_dataset("YongchengYAO/OAIZIB-CM", revision="load_dataset-support", trust_remote_code=True, streaming=True, split="train")
+>>> type(iterdataset_train)
+<class 'datasets.iterable_dataset.IterableDataset'>
+```
+
+- 🔥 [Differences between Dataset and IterableDataset](https://huggingface.co/docs/datasets/about_mapstyle_vs_iterable#downloading-and-streaming)
+
+
+## Segmentation Labels
+```python
+labels_map = {
+    "1": "Femur",
+    "2": "Femoral Cartilage",
+    "3": "Tibia",
+    "4": "Medial Tibial Cartilage",
+    "5": "Lateral Tibial Cartilage",
+}
+```
+
+## Citations
+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.

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