| # 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/) | |