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

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:

@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 license.

Source

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