Quantifying Liver Fibrosis with QuPath

Fibrosis quantification was performed with the QuPath software package (version 0.3.2, QuPath, Edinburgh, UK) [34 (link)]. Two sagittal sections of an entire liver lobe per animal were included in the analysis. Whole slide images with Masson’s Trichrome stain were scanned with the Zeiss Axioscan.Z1 Microscope Slide Scanner (Carl Zeiss AG, Jena, Germany). Parts of the slide containing tissue were detected in QuPath using the createAnntationFromPixelClassifier function. The thereby created annotations were manually assessed and cleaned to only include liver tissue without large vessels or purely fibrotic tissue. Next, parts of the whole slide image containing fibrotic tissue, stained in blue, were quantified with a manually trained tissue thresholder. Once more, the thereby detected fibrotic tissue was assessed blindly to only include fibrotic tissue. The relative surface of fibrosis was calculated as the surface of the whole slide image classified as fibrosis divided by the total surface of the whole slide image.