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README.md

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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