Protocols for autoFISH: a modular toolbox for sequential smFISH experiments

This repository provides comprehensive access to all experimental protocols and related resources in the accompanying publication introducing autoFISH (automated Fluorescence in situ Hybridization). AutoFISH establishes a cost-effective, versatile toolbox for conducting automated single-molecule FISH (smFISH) experiments. Included resources enable the full replication of our work by providing validated, step-by-step experimental protocols for both standard and amplified smFISH, as well as analysis pipelines integrated with our FISH-quant package. Crucially, the repository contains the modified tissue clearing protocol, as well as all protocols validated for robustness in cell lines and tissue samples. These resources collectively facilitate the adoption, replication, and extension of the autoFISH framework for spatial transcriptomics research.