Overcoming Variability in RNAscope Image Analysis: A HALO-Based Approach

Advances in digital pathology (DP) and whole slide imaging (WSI) are transforming the application of image analysis (IA) techniques for interpreting in situ hybridisation (ISH) results. However, a multitude of complexities can arise during image acquisition, leading to downstream challenges in image analysis. Overcoming these issues requires an understanding of both the biological question and the techniques available to achieve the best outcome. This protocol describes the use of different HALO modules for the analysis of multiplex RNAscope images, depending on sample-to-sample variations in probe expression and image quality.Keywords .