# Semi-Supervised Segmentation of Mitochondria from Electron Microscopy Images Using Spatial Continuity

arXiv: https://arxiv.org/abs/2206.02392 · HTML: https://mlsanity.com/paper/2206.02392/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 8 of its 21 references that are in the map.
- First posted on arXiv 6 Jun 2022.

## Builds on (most cited first, 8 of 8)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Do Vision Transformers See Like Convolutional Neural Networks?](https://mlsanity.com/paper/2108.08810/) (2021)
- [Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentation](https://mlsanity.com/paper/1705.08302/) (2017)
- [ConvNets vs. Transformers: Whose Visual Representations are More Transferable?](https://mlsanity.com/paper/2108.05305/) (2021)
- [Cardiac Segmentation from LGE MRI Using Deep Neural Network Incorporating Shape and Spatial Priors](https://mlsanity.com/paper/1906.07347/) (2019)
- [EM-NET: Centerline-Aware Mitochondria Segmentation in EM Images via Hierarchical View-Ensemble Convolutional Network](https://mlsanity.com/paper/1912.00201/) (2019)

## Built on by (most cited first, 1 of 1)

- [Adapting Open-Weight MLLMs to Generate Point Prompts for Electron Microscopy Segmentation](https://mlsanity.com/paper/2609.14080/) (2026)

## Abstract (arXiv)

Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at the nanometer scale. Fully supervised deep learning models developed for this task achieve excellent performance but require substantial amounts of annotated data for training. However, manual annotation of EM images is laborious and time-consuming because of their large volumes, limited contrast, and low signal-to-noise ratios (SNRs). To overcome this challenge, we propose a semi-supervised deep learning model that segments mitochondria by leveraging the spatial continuity of their structural, morphological, and contextual information in both labeled and unlabeled images. We use random piecewise affine transformation to synthesize comprehensive and realistic mitochondrial morphology for augmentation of training data. Experiments on the EPFL dataset show that our model achieves performance similar as that of state-of-the-art fully supervised models but requires only ~20% of their annotated training data. Our semi-supervised model is versatile and can also accurately segment other spatially continuous structures from EM images. Data and code of this study are openly accessible at https://github.com/cbmi-group/MPP.