# CREMI - Circuit Reconstruction from Electron Microscopy Images

## Dataset Description

CREMI is a benchmark dataset for evaluating algorithms for automatic reconstruction of neurons and neuronal connectivity from serial section electron microscopy data.

### Modality
- Serial section Transmission Electron Microscopy (ssTEM)

### Anatomy
- Adult Drosophila melanogaster brain

### Segmentation Targets
- **Neuron segmentation** (`volumes/labels/neuron_ids`)
- **Synaptic cleft segmentation** (`volumes/labels/clefts`)

### Volume Size
- 125 slices × 1250 × 1250 pixels per sample
- Resolution: 4×4×40 nm (x,y,z)

## Dataset Structure

```
CREMI/
└── train/
    ├── sample_A.hdf    # 167 MB
    ├── sample_B.hdf    # 160 MB
    └── sample_C.hdf    # 165 MB
```

Note: Test files (A+, B+, C+) are not included as they have no labels.

## HDF5 Structure

Each training file contains:
- `volumes/raw`: (125, 1250, 1250) uint8 - grayscale EM images
- `volumes/labels/neuron_ids`: (125, 1250, 1250) uint64 - neuron instance segmentation
- `volumes/labels/clefts`: (125, 1250, 1250) uint64 - synaptic cleft segmentation
- `annotations/` - synaptic partner annotations

## Usage

```python
import h5py
from huggingface_hub import hf_hub_download

# Download a training volume
path = hf_hub_download(
    repo_id="Angelou0516/CREMI",
    filename="train/sample_A.hdf",
    repo_type="dataset"
)

# Load data
with h5py.File(path, 'r') as f:
    raw = f['volumes/raw'][:]  # (125, 1250, 1250)
    neuron_ids = f['volumes/labels/neuron_ids'][:]  # (125, 1250, 1250)
    clefts = f['volumes/labels/clefts'][:]  # (125, 1250, 1250)
```

## Citation

```bibtex
@misc{cremi2016,
    title={CREMI: MICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images},
    author={Funke, Jan and Saalfeld, Stephan and Bock, Davi and Turaga, Srini and Perlman, Eric},
    year={2016},
    url={https://cremi.org/}
}
```

## License

Please refer to the original dataset website: https://cremi.org/

## Links
- [CREMI Challenge Website](https://cremi.org/)
- [CREMI Data Page](https://cremi.org/data/)
- [CREMI Metrics](https://cremi.org/metrics/)