MedCAGD-Dataset-Collection - Medical Image Segmentation Datasets

This repo contains multiple publicly available medical image segmentation (Semantic Segmentation) datasets used for training and evaluation of the segmentation models. Each subfolder corresponds to a specific dataset and follows its original structure or a standardized format used in this project. These datasets are used for benchmarking segmentation performance across multiple medical imaging modalities including CT, MRI, dermoscopy, endoscopy, ultrasound, fundus imaging, and microscopy.

Citation

If you use this, please cite the following paper (MCADS) *:

@inproceedings{wazir2025rethinking,
  title={Rethinking decoder design: Improving biomarker segmentation using depth-to-space restoration and residual linear attention},
  author={Wazir, Saad and Kim, Daeyoung},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={30861--30871},
  year={2025},
  doi = {10.48550/arXiv.2506.18335},
  url = {https://doi.org/10.48550/arXiv.2506.18335}
}

MCADS-Decoder - Rethinking decoder design: Improving biomarker segmentation using depth-to-space restoration and residual linear attentionImproving Biomarker Segmentation Using Depth-to-Space Restoration and Residual Linear Attention - CVPR 2025 - GitHub | Paper

Research Note *

This dataset collection provides early access to the datasets used for benchmarking segmentation models across multiple medical imaging datasets. The segmentation benchmarks associated with this dataset collection are part of ongoing research related to the MCADS decoder and the upcoming MedCAGD framework. The full benchmark results and evaluation protocols will appear in the MedCAGD paper, which is currently under review, and additional results will be released after the review process.

---

Included Datasets:

ACDC-2D-Slices 2D cardiac MRI slices from the ACDC dataset used for cardiac structure segmentation.

Synapse Multi-Organ Segmentation Dataset-8 abdominal organs-2D-Slices
2D slices from the Synapse multi-organ CT segmentation dataset containing annotations for eight abdominal organs.

ThyroidXL
Thyroid ultrasound dataset for thyroid nodule segmentation.

ISIC2017
Skin lesion segmentation dataset from the ISIC 2017 challenge.

ISIC2018
Skin lesion segmentation dataset from the ISIC 2018 challenge.

BKAI
Gastrointestinal polyp segmentation dataset released by BKAI.

ClinicDB
Colonoscopy polyp segmentation dataset from the CVC-ClinicDB benchmark.

ColonDB
Colonoscopy polyp segmentation dataset commonly used for evaluating polyp detection models.

ETIS
ETIS-Larib polyp dataset containing challenging colonoscopy images with pixel-level annotations.

Kvasir
Kvasir-SEG dataset for gastrointestinal polyp segmentation.

BUSI
Breast ultrasound dataset used for tumor segmentation.

DRIVE
Retinal vessel segmentation dataset from the DRIVE challenge.

FIVES
Fundus Image Vessel Segmentation dataset for retinal blood vessel analysis.

CHASEDB Retinal vessel segmentation dataset from the CHASE_DB1 benchmark.

LES-AV
Dataset for retinal artery and vein segmentation.

STARE
Retinal vessel segmentation dataset from the STARE benchmark.

UOA-DR
Diabetic retinopathy dataset with retinal lesion annotations.

CellSeg
Microscopy cell segmentation dataset used for cell instance or semantic segmentation.

---

Acknowledgement

We gratefully acknowledge the prior contributions of the research community, which have provided the foundation for our framework.