# Stain Consistency Learning: Handling Stain Variation for Automatic Digital Pathology Segmentation

arXiv: https://arxiv.org/abs/2311.06552 · HTML: https://mlsanity.com/paper/2311.06552/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 47 references that are in the map.
- First posted on arXiv 11 Nov 2023.

## Builds on (most cited first, 20 of 20)

- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [StarGAN: Unified Generative Adversarial Networks for Multi-Domain Image-to-Image Translation](https://mlsanity.com/paper/1711.09020/) (2017)
- [FDA: Fourier Domain Adaptation for Semantic Segmentation](https://mlsanity.com/paper/2004.05498/) (2020)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology](https://mlsanity.com/paper/1902.06543/) (2019)
- [Distribution Matching Losses Can Hallucinate Features in Medical Image Translation](https://mlsanity.com/paper/1805.08841/) (2018)
- [Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification](https://mlsanity.com/paper/2108.11195/) (2021)
- [StainGAN: Stain Style Transfer for Digital Histological Images](https://mlsanity.com/paper/1804.01601/) (2018)
- [Mitosis domain generalization in histopathology images -- The MIDOG challenge](https://mlsanity.com/paper/2204.03742/) (2022)
- [Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks](https://mlsanity.com/paper/1808.05896/) (2018)
- [CoNIC: Colon Nuclei Identification and Counting Challenge 2022](https://mlsanity.com/paper/2111.14485/) (2021)
- [RandStainNA: Learning Stain-Agnostic Features from Histology Slides by Bridging Stain Augmentation and Normalization](https://mlsanity.com/paper/2206.12694/) (2022)
- [Structure-Preserving Multi-Domain Stain Color Augmentation using Style-Transfer with Disentangled Representations](https://mlsanity.com/paper/2107.12357/) (2021)
- [StainNet: a fast and robust stain normalization network](https://mlsanity.com/paper/2012.12535/) (2020)
- [The importance of stain normalization in colorectal tissue classification with convolutional networks](https://mlsanity.com/paper/1702.05931/) (2017)
- [Towards Histopathological Stain Invariance by Unsupervised Domain Augmentation using Generative Adversarial Networks](https://mlsanity.com/paper/2012.12413/) (2020)
- [Test-time image-to-image translation ensembling improves out-of-distribution generalization in histopathology](https://mlsanity.com/paper/2206.09769/) (2022)
- [H&E-adversarial network: a convolutional neural network to learn stain-invariant features through Hematoxylin & Eosin regression](https://mlsanity.com/paper/2201.06329/) (2022)
- [MultiPathGAN: Structure Preserving Stain Normalization using Unsupervised Multi-domain Adversarial Network with Perception Loss](https://mlsanity.com/paper/2204.09782/) (2022)
- [A Laplacian Pyramid Based Generative H&E Stain Augmentation Network](https://mlsanity.com/paper/2305.14301/) (2023)

## Abstract (arXiv)

Stain variation is a unique challenge associated with automated analysis of digital pathology. Numerous methods have been developed to improve the robustness of machine learning methods to stain variation, but comparative studies have demonstrated limited benefits to performance. Moreover, methods to handle stain variation were largely developed for H&E stained data, with evaluation generally limited to classification tasks. Here we propose Stain Consistency Learning, a novel framework combining stain-specific augmentation with a stain consistency loss function to learn stain colour invariant features. We perform the first, extensive comparison of methods to handle stain variation for segmentation tasks, comparing ten methods on Masson's trichrome and H&E stained cell and nuclei datasets, respectively. We observed that stain normalisation methods resulted in equivalent or worse performance, while stain augmentation or stain adversarial methods demonstrated improved performance, with the best performance consistently achieved by our proposed approach. The code is available at: https://github.com/mlyg/stain_consistency_learning