RS-FISH: Precise, interactive and scalable smFISH spot detection using Radial Symmetry

Studying transcription using single-molecule RNA-FISH (smFISH) is a powerful method to gain insights into gene regulation on a single cell basis, which relies on accurate identification of sub-resolution fluorescent spots in microscopy images. Here we present Radial Symmetry-FISH (RS-FISH), which can robustly and quickly detect even close smFISH spots in two and three dimensions with high precision, allows interactive parameter tuning, and can easily be applied to large sets of images.RS-FISH is an open-source implementation written in Java/ImgLib2 and provided as a macro-scriptable Fiji plugin. Source code, tutorial, documentation, and example images are available at: https://github.com/PreibischLab/RadialSymmetryLocalization