Descarpentrie, J.; Bernard, F.; Souleyreau, W.; Brisson, L.; Mathivet, T.; Pateras, I. S.; Martin, O. C.; Frisan, T.

Fluorescence-based in-situ hybridization methods such as RNAscope technology enable highly sensitive and specific visualization of individual RNA molecules (identified as fluorescent specks) within intact cells, enabling precise spatial and cellular localization of RNA transcripts. However, manual analysis of images is time-consuming. We developed a novel, open-source, user-friendly tool to facilitate high-throughput applications for specks-like staining. The protocol seamlessly integrates automated processes, offering a universal solution for efficient transcriptomic analysis, such as, but not limited to, RNAscope in various biological contexts.