README.md

---
license: cc-by-4.0
task_categories:
  - image-segmentation
tags:
  - medical-imaging
  - electron-microscopy
  - FIB-SEM
  - 3D-segmentation
  - mitochondria
  - organelle-segmentation
size_categories:
  - n<1K
---

# UroCell FIB-SEM Dataset

## Dataset Description

UroCell is a 3D electron microscopy dataset acquired using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) 
for segmentation of subcellular organelles in urothelial cells.

### Imaging Modality
- **Modality**: FIB-SEM (Focused Ion Beam Scanning Electron Microscopy)
- **Resolution**: ~16nm × 16nm × 15nm (nearly isotropic)
- **Volume Size**: 256 × 256 × 256 voxels per volume

### Data Contents

| Folder | Description | Files |
|--------|-------------|-------|
| `data/` | Raw FIB-SEM volumes | 8 NIfTI files |
| `mito/binary/` | Binary mitochondria masks | 5 NIfTI files |
| `mito/instance/` | Instance mitochondria masks | 5 NIfTI files |
| `mito/branched/` | Branched mitochondria annotations | 5 NIfTI files |
| `mito/contacting/` | Contacting mitochondria annotations | 5 NIfTI files |
| `mito/mesh/` | 3D mesh reconstructions | OBJ files |
| `lyso/binary/` | Binary endolysosome masks | 5 NIfTI files |
| `lyso/mesh/` | 3D mesh reconstructions | OBJ files |
| `golgi/` | Golgi apparatus annotations | NIfTI + OBJ files |
| `fv/` | Fusiform vesicles annotations | OBJ mesh files |

### Annotated Volumes
5 of 8 volumes have segmentation annotations:
- fib1-0-0-0
- fib1-1-0-3
- fib1-3-2-1
- fib1-3-3-0
- fib1-4-3-0

### File Format
- **Volumes & Masks**: NIfTI format (`.nii.gz`)
- **3D Meshes**: Wavefront OBJ format (`.obj`)

## Usage

```python
from huggingface_hub import hf_hub_download
import nibabel as nib

# Download a volume
volume_path = hf_hub_download(
    repo_id="Angelou0516/UroCell",
    filename="data/fib1-0-0-0.nii.gz",
    repo_type="dataset"
)

# Load with nibabel
volume = nib.load(volume_path).get_fdata()
print(f"Volume shape: {volume.shape}")  # (256, 256, 256)
```

## Citation

If you use this dataset, please cite:

```bibtex
@article{urocell2024,
  title={UroCell: A FIB-SEM Dataset for 3D Organelle Segmentation},
  author={MancaZeworksLabs},
  year={2024},
  url={https://github.com/MancaZeworksLabs/UroCell}
}
```

## License

This dataset is released under the [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) license.

## Source

Original repository: https://github.com/MancaZeworksLabs/UroCell