Segmentation of glandular epithelium in colorectal tumours to automatically compartmentalise IHC biomarker quantification: A deep learning approach

•We propose a method to automate glandular epithelium segmentation.•Our approach combines Deep Learning and a new method of data augmentation.•Our algorithm efficiently processes H&E as well as IHC images.•Our algorithm achieves state-of-the-art performances.•Our method enables to automate the compartmentalisation of IHC biomarker analyses.