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\title{Current Progress and Challenges in Large-scale 3D Mitochondria Instance
Segmentation}



\author[1,1]{Daniel Franco-Barranco }%
\author[2]{Zudi Lin }%
\author[2]{Won-Dong Jang }%
\author[2]{Xueying Wang }%
\author[2]{Qijia Shen }%
\author[2]{Wenjie Yin }%
\author[2]{Yutian Fan }%
\author[2]{Mingxing Li }%
\author[2]{Chang Chen }%
\author[2]{Zhiwei Xiong }%
\author[2]{Rui Xin }%
\author[2]{Hao Liu }%
\author[2]{Huai Chen }%
\author[2]{Zhili Li }%
\author[2]{Jie Zhao }%
\author[2]{Xuejin Chen }%
\author[2]{Constantin Pape }%
\author[2]{Ryan Conrad }%
\author[2]{Jozefus De Folter }%
\author[2]{Luke Nightingale }%
\author[2]{Martin Jones }%
\author[2]{Yanling Liu }%
\author[2]{Dorsa Ziaei }%
\author[2]{Stephan Huschauer }%
\author[2]{Ignacio Arganda-Carreras }%
\author[2]{Hanspeter Pfister }%
\author[2]{Donglai Wei }%
\affil[1]{Donostia International Physics Center}%
\affil[2]{Affiliation not available}%


\vspace{-1em}



  
  \date{April 22, 2026}


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\begin{abstract}
In this paper, we present the results of the MitoEM~challenge on
mitochondria 3D instance segmentation~{from electron microscopy images,
organized in conjunction~}with the IEEE-ISBI 2021 conference. Our
benchmark dataset~{consists of two large-scale 3D volumes, one from
human~}and one from rat cortex tissue, which are 1,986 times~{larger
than previously used datasets. At the time of paper~}submission, 257
participants had registered for the challenge,~{14 teams had submitted
their results, and six teams~participated in the challenge workshop.
Here, we present~}eight top-performing approaches from the challenge
participants,~{along with our own baseline strategies. Posterior to~}the
challenge, annotation errors in the ground truth were corrected without
altering the final ranking. Additionally, we~{present a retrospective
evaluation of the scoring system~}which revealed that (1) the challenge
metric was permissive~{with the false positive predictions and (2) the
size-based~}grouping of instances did not correctly categorize
mitochondria~{of interest. Thus, we propose a new scoring system~}that
better reflects the correctness of the segmentation~results. Although
several of the top methods are compared~{favorably to our own baselines,
substantial errors remain~unsolved for mitochondria with challenging
morphologies.~Thus, the challenge remains open for submission and
automatic~}evaluation, with all volumes available for download.%
\end{abstract}%



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