Stain Consistency Learning: Handling Stain Variation for Automatic
  Digital Pathology Segmentation
Michael Yeung Todd Watts Sean YW Tan Pedro F. Ferreira Andrew D. Scott Sonia Nielles-Vallespin Guang Yang
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