Cmito: Mitochondria detection in C. elegans EM images

Cmito is a tool that enables dense reconstruction of mitochondria in C. elegans electron microscopy (EM) image stacks using convolutional neural network (CNN).

Setup

# Clone repository
git clone https://github.com/jabae/Cmito.git
cd Cmito

# Install requirements
pip install -r requirements

Cmito pipeline

Mitochondria reconstructions

Stage	Link to reconstructions	Source
L1	L1 reconstructions	Witvliet et al. (2021)1 Dataset 2
L2	L2 reconstructions	Witvliet et al. (2021)1 Dataset 5
L3	L3 reconstructions	Witvliet et al. (2021)1 Dataset 6
Adult	Adult reconstructions	Witvliet et al. (2021)1 Dataset 8
Dauer	Dauer reconstructions	Yim et al. (2024)2 Dataset

Footnotes

1. Witvliet, D., Mulcahy, B., Mitchell, J.K., Meirovitch, Y., Berger, D.R., Wu, Y., Liu, Y., Koh, W.X., Parvathala, R., Holmyard, D., et al. (2021). Connectomes across development reveal principles of brain maturation. Nature 596, 257–261. ↩ ↩² ↩³ ↩⁴

2. Yim, H., Choe, D.T., Bae, J.A., Choi, M.-K., Kang, H.-M., Nguyen, K.C.Q., Ahn, S., Bahn, S.-K., Yang, H., Hall, D.H., et al. (2024). Comparative connectomics of dauer reveals developmental plasticity. Nat. Commun. 15, 1546. ↩