Using QuPath to analyze RNAscope™, BaseScope™ and miRNAscope™ images

QuPath, short for Quantitative Pathology, is an open-source software that provides automated quantitative and semi-quantitative analysis of whole slide images. By using the built-in algorithms, QuPath offers a complete workflow for spatial RNA analysis - starting from color deconvolution, through stages of cell detection, subcellular probe identification, and classification, all the way to the final cell-by-cell RNA quantification.

This Technical note provides a guide to using QuPath for image analysis.