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

import h5py
from huggingface_hub import hf_hub_download

# Download a training volume
path = hf_hub_download(
    repo_id="MedOtter/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

@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/}
}

Links

• CREMI Challenge Website
• CREMI Data Page
• CREMI Metrics

License

CC BY-NC 4.0

Redistribution is permitted for non-commercial research use under the terms below; commercial use is not.

Source of the terms: https://www.temca2data.org/

Audit note (verbatim from the MedOtter dataset card):

CREMI EM data is the FAFB adult-Drosophila ssTEM volume (Zheng, Lauritzen et al. 2018) whose authoritative source temca2data.org releases it under CC-BY-NC 4.0. NC restricts only commercial use, not non-commercial research redistribution; only gap is the missing HF tag.