Towards a unified pipeline for tissue-scale localization and identification of individual RNA molecules

Single-molecule fluorescent in situ hybridization (smFISH) is a leading method for gene transcription analysis at the cellular level, yielding information on gene expression levels and spatial RNA distributions. When extended to the tissue or organ level, this information helps guide development of targeted treatments for disease, such as personalized cancer therapies. However, smFISH data is inherently hindered by inhomogeneous background, detector noise, optical aberrations, clustering of RNA transcripts at transcription sites, and the inherently stochastic nature of probe binding.