Angelou0516/msd-colon

Medical Segmentation Decathlon: Colon

Dataset Description

This is the Colon dataset from the Medical Segmentation Decathlon (MSD) challenge. The dataset contains CT scans with segmentation annotations for colon cancer segmentation.

Dataset Details

• Modality: CT
• Task: Task10_Colon
• Target: colon cancer
• Format: NIfTI (.nii.gz)

Dataset Structure

Each sample in the JSONL file contains:

{
  "image": "path/to/image.nii.gz",
  "mask": "path/to/mask.nii.gz",
  "label": ["label1", "label2", ...],
  "modality": "CT",
  "dataset": "MSD_Colon",
  "official_split": "train",
  "patient_id": "patient_id"
}

Data Organization

Task10_Colon/
├── imagesTr/          # Training images
│   └── *.nii.gz
└── labelsTr/          # Training labels
    └── *.nii.gz

Usage

Load Metadata

from datasets import load_dataset

# Load the dataset
ds = load_dataset("Angelou0516/msd-colon")

# Access a sample
sample = ds['train'][0]
print(f"Image: {sample['image']}")
print(f"Mask: {sample['mask']}")
print(f"Labels: {sample['label']}")
print(f"Modality: {sample['modality']}")

Load Images

from huggingface_hub import snapshot_download
import nibabel as nib
import os

# Download the full dataset
local_path = snapshot_download(
    repo_id="Angelou0516/msd-colon",
    repo_type="dataset"
)

# Load a sample
sample = ds['train'][0]
image = nib.load(os.path.join(local_path, sample['image']))
mask = nib.load(os.path.join(local_path, sample['mask']))

# Get numpy arrays
image_data = image.get_fdata()
mask_data = mask.get_fdata()

print(f"Image shape: {image_data.shape}")
print(f"Mask shape: {mask_data.shape}")

Citation

If you use this dataset, please cite the Medical Segmentation Decathlon paper:

@article{antonelli2022medical,
  title={A large annotated medical image dataset for the development and evaluation of segmentation algorithms},
  author={Antonelli, Michela and Reinke, Annika and Bakas, Spyridon and others},
  journal={Nature Communications},
  volume={13},
  number={1},
  pages={1--13},
  year={2022},
  publisher={Nature Publishing Group}
}

License

CC-BY-SA-4.0

Dataset Homepage

http://medicaldecathlon.com/