Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes Articles uri icon

publication date

  • April 2022

start page

  • 437

end page

  • 450


  • 2


  • 20

International Standard Serial Number (ISSN)

  • 1539-2791

Electronic International Standard Serial Number (EISSN)

  • 1559-0089


  • Electron microscopy (EM) allows the identifcation of intracellular organelles such as mitochondria, providing insights for clinical and scientifc studies. In recent years, a number of novel deep learning architectures have been published reporting superior performance, or even human-level accuracy, compared to previous approaches on public mitochondria segmentation datasets. Unfortunately, many of these publications make neither the code nor the full training details public, leading to reproducibility issues and dubious model comparisons. Thus, following a recent code of best practices in the feld, we present an extensive study of the state-of-the-art architectures and compare them to diferent variations of U-Net-like models for this task. To unveil the impact of architectural novelties, a common set of pre- and post-processing operations has been implemented and tested with each approach. Moreover, an exhaustive sweep of hyperparameters has been performed, running each confguration multiple times to measure their stability. Using this methodology, we found very stable architectures and training confgurations that consistently obtain state-of-the-art results in the well-known EPFL Hippocampus mitochondria segmentation dataset and outperform all previous works on two other available datasets: Lucchi++ and Kasthuri++. The code and its documentation are publicly available at


  • Biology and Biomedicine
  • Education
  • Electronics
  • Materials science and engineering
  • Mechanical Engineering
  • Medicine
  • Naval Engineering
  • Robotics and Industrial Informatics
  • Statistics


  • electron microscopy; mitochondria; semantic segmentation; deep learning; bioimage analysis