File size: 2,246 Bytes
2a3aff4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 | # 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/)
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