Several FISH-,qPCR- or RNA sequencing-based methods can measureRNA expression at the single-cell level. One technique that is suitablefor high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH.

Analyzing microscopic image datasets is difficult. It is even more so with the rapid increase of PixelBiotech’s customer base. We are con-stantly receiving requests for HuluREAD to analyze datasets that are acquired using different microscopes, under various imaging conditions and on different species. In this article,we discuss important lessons we learned in building HuluREAD into an efficient and scalable algorith-mic platform for customized HuluFISH image data analysis.