QuPath for RNAscope Image Analysis

RNAscope is an outstanding tool for the detection and visualization of RNA transcripts with the spatial and morphological context of the tissue. While visualization of an RNA transcript can be powerful by itself, quantification of the RNAscope signal can provide pivotal information on a transcript's expression level in a tissue and/or cell. Several image analysis tools can be used for the quantification of RNAscope signals, with different pipelines having been developed in the last few years. This chapter provides an easy method for the analysis of RNAscope images using QuPath and includes a practical example demonstrating how to perform the analysis for quantifying intestinal stem cells. QuPath is an open-source software for digital pathology and image analysis, with several built-in user-friendly robust tools for image analysis by both dry-lab and wet-lab scientists.