Datasets:
Tasks:
Image Segmentation
Formats:
imagefolder
Size:
< 1K
Tags:
medical-imaging
electron-microscopy
FIB-SEM
3D-segmentation
mitochondria
organelle-segmentation
License:
File size: 2,520 Bytes
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---
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
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