# Deep learning based domain adaptation for mitochondria segmentation on EM volumes

arXiv: https://arxiv.org/abs/2202.10773 · HTML: https://mlsanity.com/paper/2202.10773/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 44 of its 79 references that are in the map.
- First posted on arXiv 22 Feb 2022.

## Builds on (most cited first, 30 of 44)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Delving Deep into Rectifiers: Surpassing Human-Level Performance on ImageNet Classification](https://mlsanity.com/paper/1502.01852/) (2015)
- [Unsupervised Learning of Visual Representations by Solving Jigsaw Puzzles](https://mlsanity.com/paper/1603.09246/) (2016)
- [Contrastive Learning for Unpaired Image-to-Image Translation](https://mlsanity.com/paper/2007.15651/) (2020)
- [Deep Visual Domain Adaptation: A Survey](https://mlsanity.com/paper/1802.03601/) (2018)
- [A Survey of Unsupervised Deep Domain Adaptation](https://mlsanity.com/paper/1812.02849/) (2018)
- [Domain Adaptation for Medical Image Analysis: A Survey](https://mlsanity.com/paper/2102.09508/) (2021)
- [Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images](https://mlsanity.com/paper/1808.08114/) (2018)
- [Generative Adversarial Network in Medical Imaging: A Review](https://mlsanity.com/paper/1809.07294/) (2018)
- [GAN-based Synthetic Medical Image Augmentation for increased CNN Performance in Liver Lesion Classification](https://mlsanity.com/paper/1803.01229/) (2018)
- [Super-Convergence: Very Fast Training of Neural Networks Using Large Learning Rates](https://mlsanity.com/paper/1708.07120/) (2017)
- [High-Quality Self-Supervised Deep Image Denoising](https://mlsanity.com/paper/1901.10277/) (2019)
- [Data augmentation using learned transformations for one-shot medical image segmentation](https://mlsanity.com/paper/1902.09383/) (2019)
- [3D Self-Supervised Methods for Medical Imaging](https://mlsanity.com/paper/2006.03829/) (2020)
- [GAN Augmentation: Augmenting Training Data using Generative Adversarial Networks](https://mlsanity.com/paper/1810.10863/) (2018)
- [Translating and Segmenting Multimodal Medical Volumes with Cycle- and Shape-Consistency Generative Adversarial Network](https://mlsanity.com/paper/1802.09655/) (2018)
- [StainGAN: Stain Style Transfer for Digital Histological Images](https://mlsanity.com/paper/1804.01601/) (2018)
- [SynSeg-Net: Synthetic Segmentation Without Target Modality Ground Truth](https://mlsanity.com/paper/1810.06498/) (2018)
- [Unsupervised Cross-Modality Domain Adaptation of ConvNets for Biomedical Image Segmentations with Adversarial Loss](https://mlsanity.com/paper/1804.10916/) (2018)
- [Unsupervised Reverse Domain Adaptation for Synthetic Medical Images via Adversarial Training](https://mlsanity.com/paper/1711.06606/) (2017)
- [Multimodal Self-Supervised Learning for Medical Image Analysis](https://mlsanity.com/paper/1912.05396/) (2019)
- [Probabilistic Noise2Void: Unsupervised Content-Aware Denoising](https://mlsanity.com/paper/1906.00651/) (2019)
- [Self-Loop Uncertainty: A Novel Pseudo-Label for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2007.09854/) (2020)
- [Few-shot 3D Multi-modal Medical Image Segmentation using Generative Adversarial Learning](https://mlsanity.com/paper/1810.12241/) (2018)
- [Synthetic Medical Images from Dual Generative Adversarial Networks](https://mlsanity.com/paper/1709.01872/) (2017)
- [Deep CT to MR Synthesis using Paired and Unpaired Data](https://mlsanity.com/paper/1805.10790/) (2018)
- [Unpaired Brain MR-to-CT Synthesis using a Structure-Constrained CycleGAN](https://mlsanity.com/paper/1809.04536/) (2018)
- [LT-Net: Label Transfer by Learning Reversible Voxel-wise Correspondence for One-shot Medical Image Segmentation](https://mlsanity.com/paper/2003.07072/) (2020)
- [Self-Supervised training for blind multi-frame video denoising](https://mlsanity.com/paper/2004.06957/) (2020)

## Built on by (most cited first, 2 of 2)

- [MitoSeg: Mitochondria Segmentation Tool](https://mlsanity.com/paper/2409.11974/) (2024)
- [NeuroADDA: Active Discriminative Domain Adaptation in Connectomic](https://mlsanity.com/paper/2503.06196/) (2025)

## Abstract (arXiv)

Accurate segmentation of electron microscopy (EM) volumes of the brain is essential to characterize neuronal structures at a cell or organelle level. While supervised deep learning methods have led to major breakthroughs in that direction during the past years, they usually require large amounts of annotated data to be trained, and perform poorly on other data acquired under similar experimental and imaging conditions. This is a problem known as domain adaptation, since models that learned from a sample distribution (or source domain) struggle to maintain their performance on samples extracted from a different distribution or target domain. In this work, we address the complex case of deep learning based domain adaptation for mitochondria segmentation across EM datasets from different tissues and species. We present three unsupervised domain adaptation strategies to improve mitochondria segmentation in the target domain based on (1) state-of-the-art style transfer between images of both domains; (2) self-supervised learning to pre-train a model using unlabeled source and target images, and then fine-tune it only with the source labels; and (3) multi-task neural network architectures trained end-to-end with both labeled and unlabeled images. Additionally, we propose a new training stopping criterion based on morphological priors obtained exclusively in the source domain. We carried out all possible cross-dataset experiments using three publicly available EM datasets. We evaluated our proposed strategies on the mitochondria semantic labels predicted on the target datasets. The methods introduced here outperform the baseline methods and compare favorably to the state of the art. In the absence of validation labels, monitoring our proposed morphology-based metric is an intuitive and effective way to stop the training process and select in average optimal models.