# Stable deep neural network architectures for mitochondria segmentation on electron microscopy volumes

arXiv: https://arxiv.org/abs/2104.03577 · HTML: https://mlsanity.com/paper/2104.03577/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 31 of its 63 references that are in the map.
- First posted on arXiv 8 Apr 2021.

## Builds on (most cited first, 30 of 31)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Rethinking the Inception Architecture for Computer Vision](https://mlsanity.com/paper/1512.00567/) (2015)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Going Deeper with Convolutions](https://mlsanity.com/paper/1409.4842/) (2014)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Identity Mappings in Deep Residual Networks](https://mlsanity.com/paper/1603.05027/) (2016)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [Image Segmentation Using Deep Learning: A Survey](https://mlsanity.com/paper/2001.05566/) (2020)
- [R-FCN: Object Detection via Region-based Fully Convolutional Networks](https://mlsanity.com/paper/1605.06409/) (2016)
- [Learning Deconvolution Network for Semantic Segmentation](https://mlsanity.com/paper/1505.04366/) (2015)
- [Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images](https://mlsanity.com/paper/1808.08114/) (2018)
- [CE-Net: Context Encoder Network for 2D Medical Image Segmentation](https://mlsanity.com/paper/1903.02740/) (2019)
- [LinkNet: Exploiting Encoder Representations for Efficient Semantic Segmentation](https://mlsanity.com/paper/1707.03718/) (2017)
- [MultiResUNet : Rethinking the U-Net Architecture for Multimodal Biomedical Image Segmentation](https://mlsanity.com/paper/1902.04049/) (2019)
- [Show Your Work: Improved Reporting of Experimental Results](https://mlsanity.com/paper/1909.03004/) (2019)
- [Revisiting ResNets: Improved Training and Scaling Strategies](https://mlsanity.com/paper/2103.07579/) (2021)
- [The One Hundred Layers Tiramisu: Fully Convolutional DenseNets for Semantic Segmentation](https://mlsanity.com/paper/1611.09326/) (2016)
- [Concurrent Spatial and Channel Squeeze & Excitation in Fully Convolutional Networks](https://mlsanity.com/paper/1803.02579/) (2018)
- [DUNet: A deformable network for retinal vessel segmentation](https://mlsanity.com/paper/1811.01206/) (2018)
- [Recalibrating Fully Convolutional Networks with Spatial and Channel 'Squeeze & Excitation' Blocks](https://mlsanity.com/paper/1808.08127/) (2018)
- [Joint Optic Disc and Cup Segmentation Based on Multi-label Deep Network and Polar Transformation](https://mlsanity.com/paper/1801.00926/) (2018)
- [LadderNet: Multi-path networks based on U-Net for medical image segmentation](https://mlsanity.com/paper/1810.07810/) (2018)

## Built on by (most cited first, 6 of 6)

- [Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey](https://mlsanity.com/paper/2206.07171/) (2022)
- [Deep learning based domain adaptation for mitochondria segmentation on EM volumes](https://mlsanity.com/paper/2202.10773/) (2022)
- [Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?](https://mlsanity.com/paper/2602.08505/) (2026)
- [MitoSeg: Mitochondria Segmentation Tool](https://mlsanity.com/paper/2409.11974/) (2024)
- [Towards Generalized Synapse Detection Across Invertebrate Species](https://mlsanity.com/paper/2509.17041/) (2025)
- [μMatch: Foundation Models for Semi-supervised Learning and Domain Adaptation in EM](https://mlsanity.com/paper/2606.21605/) (2026)

## Abstract (arXiv)

Electron microscopy (EM) allows the identification of intracellular organelles such as mitochondria, providing insights for clinical and scientific 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 do not make neither the code nor the full training details public to support the results obtained, leading to reproducibility issues and dubious model comparisons. For that reason, and following a recent code of best practices for reporting experimental results, we present an extensive study of the state-of-the-art deep learning architectures for the segmentation of mitochondria on EM volumes, and evaluate the impact in performance of different variations of 2D and 3D U-Net-like models for this task. To better understand the contribution of each component, a common set of pre- and post-processing operations has been implemented and tested with each approach. Moreover, an exhaustive sweep of hyperparameters values for all architectures have been performed and each configuration has been run multiple times to report the mean and standard deviation values of the evaluation metrics. Using this methodology, we found very stable architectures and hyperparameter configurations that consistently obtain state-of-the-art results in the well-known EPFL Hippocampus mitochondria segmentation dataset. Furthermore, we have benchmarked our proposed models on two other available datasets, Lucchi++ and Kasthuri++, where they outperform all previous works. The code derived from this research and its documentation are publicly available.