The RNAscope™ assay, based on ACD’s technology for signal amplification and background suppression, was optimized on LabSat® to result in well-preserved morphology, uniform staining with excellent signal-to-noise ratio, and readily detectable punctate signal dots – comparable to the manual assay on mouse and human FFPE samples. Concomitantly, the assay turnaround time was shortened with respect to the manual and other automated CISH protocols. Overall, we have proven the capability of the microfluidic platform LabSat® to automate the RNAscope™2.5 HD-BROWN CISH assay with reproducible staining results. The microfluidic platform brings the benefits of a shorter run time and reliability of a compact desktop system.