Stain Normalisation Does Not Consistently Improve Matched-Location Retrieval with Pathology Foundation Models

Abstract

Pathology foundation models provide reusable representations for computational pathology, but staining- and scanner-induced variation may compromise the robustness and reproducibility of embedding-based analyses across acquisition settings. Stain normalisation is widely used to mitigate such colour variation, yet whether it improves retrieval with modern self-supervised pathology encoders remains unclear. We test whether stain normalisation improves cross-scanner and cross-staining image retrieval using the PLISM whole-slide image subset, comprising 13 co-registered images of serial sections prepared under different staining conditions and digitised using seven scanners (91 whole-slide images). We sample 400 matched locations across the 91 images, yielding 36,400 tile instances. We compare two DINOv2-based encoders, Phikon-v2 (1,024-dimensional) and Midnight-12k (3,072-dimensional), with Reinhard and Macenko normalisation against an unnormalised baseline. Performance is measured using paired top-1 nearest-neighbour retrieval accuracy in two settings: cross-scanner retrieval of the same physical section digitised by different scanners, and cross-staining retrieval across co-registered images of serial sections, which differ in staining condition and may also contain section-level morphological variation. Neither normalisation method consistently improves top-1 retrieval relative to no normalisation, while Macenko reduces accuracy by up to 18.3 percentage points. An exploratory UMAP of unnormalised Midnight-12k slide-level mean embeddings showed partial overlap between scanner groups in a two-dimensional projection. These results challenge the routine use of stain normalisation in foundation-model retrieval pipelines and support validating preprocessing choices for each encoder and retrieval setting.