This digital resource is a workflow protocol specifically designed for in situ hybridization (ISH) using the Tecan GenePaint system. The Tecan GenePaint system is an automated platform for high-throughput, standardized molecular pathology applications, including ISH. This protocol provides step-by-step instructions for performing ISH experiments, ensuring consistency and reproducibility. The workflow details the necessary reagents, equipment settings, and procedural steps for preparing samples, performing hybridization, and detecting target nucleic acids (DNA or RNA) within tissue sections or whole mounts. It likely covers critical parameters such as probe preparation, hybridization temperatures, washing conditions, and signal detection methods, all optimized for the automated GenePaint platform. This automation minimizes manual variability and increases throughput. Researchers in molecular biology, developmental biology, and pathology can utilize this protocol to reliably visualize gene expression patterns or chromosomal locations within cells and tissues. The standardization offered by the Tecan GenePaint system and this accompanying workflow is particularly beneficial for large-scale studies, drug discovery, and biomarker validation, where consistent results across many samples are paramount. As a proprietary protocol associated with a specific automated system, it ensures optimal performance and integration with the Tecan GenePaint hardware and software. It serves as a critical guide for users of the system, enabling them to achieve high-quality, reproducible in situ hybridization results for various research and diagnostic applications.