A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics

Abstract

The analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is essential for the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly adopted into diagnostic guidelines and routine workflows to assess the status of several established biomarkers, including ER, PGR, HER2 and KI67. Biomarker assessment can also be facilitated by computational pathology image analysis methods, which have made numerous substantial advances recently, often based on publicly available whole slide image (WSI) data sets. However, the field is still considerably limited by the sparsity of public data sets. In particular, there are no large, high quality publicly available data sets with WSIs of matching IHC and H&E-stained tissue sections from the same tumour. Here, we publish the currently largest publicly available data set of WSIs of tissue sections from surgical resection specimens from female primary breast cancer patients with matched WSIs of corresponding H&E and IHC-stained tissue, consisting of 4,212 WSIs from 1,153 patients.

Fig. 1

Example of an H&E-stained tissue region with corresponding IHC-stained tissue with all four routine diagnostic stains available in this data set. (a) shows H&E, (b) ER, (c) HER2, (d) Ki67 and (e) PGR. (f) shows an example of a WSI that was excluded since it contains multiple tissue sections.