A Multicentric Dataset for Training and Benchmarking Breast Cancer Segmentation in H&E Slides

Automated semantic segmentation of whole-slide images (WSIs) stained with hematoxylin and eosin (H&E) is essential for large-scale artificial intelligence-based biomarker analysis in breast cancer. However, existing public datasets for breast cancer segmentation lack the morphological diversity needed to support model generalizability and robust biomarker validation across heterogeneous patient cohorts. We introduce BrEast cancEr hisTopathoLogy sEgmentation (BEETLE), a dataset for multiclass semantic segmentation of H&E-stained breast cancer WSIs. It consists of 587 biopsies and resections from three collaborating clinical centers and two public datasets, digitized using seven scanners, and covers all molecular subtypes and histological grades. Using diverse annotation strategies, we collected annotations across four classes - invasive epithelium, non-invasive epithelium, necrosis, and other - with particular focus on morphologies underrepresented in existing datasets, such as ductal carcinoma in situ and dispersed lobular tumor cells. The dataset's diversity and relevance to the rapidly growing field of automated biomarker quantification in breast cancer ensure its high potential for reuse. Finally, we provide a well-curated, multicentric external evaluation set to enable standardized benchmarking of breast cancer segmentation models.

Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology

Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invariant CNNs. The latter aims to match training and test color distributions in order to reduce stain variation. For the first time, we compared some of these techniques and quantified their effect on CNN classification performance using a heterogeneous dataset of hematoxylin and eosin histopathology images from 4 organs and 9 pathology laboratories. Additionally, we propose a novel unsupervised method to perform stain color normalization using a neural network. Based on our experimental results, we provide practical guidelines on how to use stain color augmentation and stain color normalization in future computational pathology applications.