diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000000000000000000000000000000000..1ef325f1b111266a6b26e0196871bd78baa8c2f3 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,59 @@ +*.7z filter=lfs diff=lfs merge=lfs -text +*.arrow filter=lfs diff=lfs merge=lfs -text +*.bin filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.ckpt filter=lfs diff=lfs merge=lfs -text +*.ftz filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.h5 filter=lfs diff=lfs merge=lfs -text +*.joblib filter=lfs diff=lfs merge=lfs -text +*.lfs.* filter=lfs diff=lfs merge=lfs -text +*.lz4 filter=lfs diff=lfs merge=lfs -text +*.mds filter=lfs diff=lfs merge=lfs -text +*.mlmodel filter=lfs diff=lfs merge=lfs -text +*.model filter=lfs diff=lfs merge=lfs -text +*.msgpack filter=lfs diff=lfs merge=lfs -text +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.onnx filter=lfs diff=lfs merge=lfs -text +*.ot filter=lfs diff=lfs merge=lfs -text +*.parquet filter=lfs diff=lfs merge=lfs -text +*.pb filter=lfs diff=lfs merge=lfs -text +*.pickle filter=lfs diff=lfs merge=lfs -text +*.pkl filter=lfs diff=lfs merge=lfs -text +*.pt filter=lfs diff=lfs merge=lfs -text +*.pth filter=lfs diff=lfs merge=lfs -text +*.rar filter=lfs diff=lfs merge=lfs -text +*.safetensors filter=lfs diff=lfs merge=lfs -text +saved_model/**/* filter=lfs diff=lfs merge=lfs -text +*.tar.* filter=lfs diff=lfs merge=lfs -text +*.tar filter=lfs diff=lfs merge=lfs -text +*.tflite filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.wasm filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text +*tfevents* filter=lfs diff=lfs merge=lfs -text +# Audio files - uncompressed +*.pcm filter=lfs diff=lfs merge=lfs -text +*.sam filter=lfs diff=lfs merge=lfs -text +*.raw filter=lfs diff=lfs merge=lfs -text +# Audio files - compressed +*.aac filter=lfs diff=lfs merge=lfs -text +*.flac filter=lfs diff=lfs merge=lfs -text +*.mp3 filter=lfs diff=lfs merge=lfs -text +*.ogg filter=lfs diff=lfs merge=lfs -text +*.wav filter=lfs diff=lfs merge=lfs -text +# Image files - uncompressed +*.bmp filter=lfs diff=lfs merge=lfs -text +*.gif filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.tiff filter=lfs diff=lfs merge=lfs -text +# Image files - compressed +*.jpg filter=lfs diff=lfs merge=lfs -text +*.jpeg filter=lfs diff=lfs merge=lfs -text +*.webp filter=lfs diff=lfs merge=lfs -text +# Video files - compressed +*.mp4 filter=lfs diff=lfs merge=lfs -text +*.webm filter=lfs diff=lfs merge=lfs -text diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..24a66c6866343f156b475a56db840bf2a56eb5ba --- /dev/null +++ b/README.md @@ -0,0 +1,103 @@ +--- +license: cc-by-4.0 +task_categories: +- image-segmentation +tags: +- medical +- CT +- multi-organ +- segmentation +size_categories: +- n<1K +configs: +- config_name: default + data_files: + - split: train + path: train.jsonl +--- + +# Beyond the Cranial Vault Dataset + +## Dataset Description + +The Beyond the Cranial Vault dataset for multi-organ abdominal CT segmentation. This dataset contains CT scans with dense segmentation annotations. + +### Dataset Details + +- **Modality**: CT +- **Target**: 13 abdominal organs +- **Format**: NIfTI (.nii.gz) + +### Dataset Structure + +Each sample in the JSONL file contains: +```json +{ + "image": "path/to/image.nii.gz", + "mask": "path/to/mask.nii.gz", + "label": ["organ1", "organ2", ...], + "modality": "CT", + "dataset": "BTCV", + "official_split": "train", + "patient_id": "patient_id" +} +``` + +## Usage + +### Load Metadata + +```python +from datasets import load_dataset + +# Load the dataset +ds = load_dataset("Angelou0516/btcv") + +# Access a sample +sample = ds['train'][0] +print(f"Patient ID: {sample['patient_id']}") +print(f"Labels: {sample['label']}") +``` + +### Load Images + +```python +from huggingface_hub import snapshot_download +import nibabel as nib +import os + +# Download the full dataset +local_path = snapshot_download( + repo_id="Angelou0516/btcv", + 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 + +```bibtex +@article{btcv, + title={Multi-Atlas Labeling Beyond the Cranial Vault}, + year={2023} +} +``` + +## License + +CC-BY-4.0 + +## Dataset Homepage + +https://www.synapse.org/#!Synapse:syn3193805 diff --git a/RawData/Training/img/img0001.nii.gz b/RawData/Training/img/img0001.nii.gz new file mode 100644 index 0000000000000000000000000000000000000000..81fca78997f7b4a6aad75622a0c709b4fa53044a --- /dev/null +++ b/RawData/Training/img/img0001.nii.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:aac170731db3b7a89d21562e726f8de1847690874249a94e84511470d0d99dd1 +size 44418042 diff --git a/RawData/Training/img/img0002.nii.gz 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