The invention is notably directed to a computer-implemented method for normalizing medical images, e.g., whole slide images. This method includes steps performed for each image of a first subset of images of a dataset. Actual quantities are estimated for each image, including actual stain vectors and, possibly, robust maximum stain concentrations (typically hematoxylin and eosin stain vectors and concentrations). The actual quantities estimated are assessed by comparing them to reference data based on reference quantities estimated for one or more images of a second subset of images of the dataset, where the second subset of images differ from the first subset of images. The reference quantities include reference stain vectors. For each image, either the actual quantities or the reference quantities for the dataset are selected as effective quantities, based on an outcome of the previous assessment of the actual quantities. Each image is then normalized.