MitoEM Challenge: Large-scale 3D Mitochondria Instance Segmentation

This challenge is part of ISBI 2021taking place on April 13-16th, 2021.  The top teams will be invited for writing an overview paper after the challenge. More information about the MitoEM dataset can be found in our MICCAI 2020 paper

Note: we keep the online evaluation open for new submissions, but only results submitted before March 1, 2021, are considered for the ISBI challenge workshop.

Explore it in your browser! [MitoEM-H], [MitoEM-R]

(navigation tips: [manual] [youtube video])


The task is the 3D mitochondria instance segmentation on two 30x30x30 um datasets, 1000x4096x4096 in voxels at 30x8x8 nm resolution. The image volumes are acquired from a rat (Mito-R) and a human (Mito-H) tissue, respectively. The mitochondria can display a complex morphology, e.g., (a) mitochondria-on-a-string (MOAS) instances are connected by thin microtubules, and (b) multiple instances can entangle with each other.

Dataset [Link]

MitoEM-{H, R}.zip

  •  im/: 1,000 consecutive 3D slices for each dataset
  •  mito_{train, val}/: ground truth mitochondria instance labels for the first 500 slices split between train (0-399) / val (400-499) subfolders.

All the mitochondria instances in the ground-truth annotation are at least 2,000 voxels. The annotation is not perfect. Please email the (x,y,z) location of erroneous segmentation to refine it together :) The subject of the email: "[MitoEM Error]"

Starter Code

  • Deep learning baseline method: [link]
  • Submission utility functions: [link]

Important Dates

  • 01 Nov 2020: Challenge Website Launch
  • 08 Nov 2020: Registration open
  • 26 Nov 2020: Training/Val/Test Data Release (Images + Training/Val Ground truth)
  • 28 Feb 2021: Test set results submission deadline.
  • 10 Mar 2021: 4-page Paper submission deadline for top-performing teams.
  • 15 Mar 2021: Off-site leaderboard update and call for participation of top-performing teams (subjected to ISBI registration)
  • 18 Mar 2021: ISBI registration deadline
  • 20 Mar 2021: Final Off-site leaderboard update and the display of top teams upon participation confirmation.
  • 13 April 2021: On-site challenge at ISBI 2021.


Number of participants: 231


  title={MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images},
  author={D. Wei, Z. Lin, D. Barranco, N. Wendt, X. Liu, W. Yin, X. Huang, A. Gupta,
W. Jang, X. Wang, I. Arganda-Carreras, J. Lichtman, H. Pfister}, booktitle={International Conference on Medical Image Computing and Computer Assisted Intervention}, year={2020} }

Organizing committee