biostudies-literatureBahry EHoward Hughes Medical InstituteNCI NIH HHSNIGMS NIH HHS1563-1567https://www.ebi.ac.uk/biostudies/studies/S-EPMC9718671biostudies-literatureUnknown19(12)Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challenging task. We present Radial Symmetry-FISH (RS-FISH), an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. RS-FISH offers interactive parameter tuning and readily scales to large datasets and image volumes of cleared or expanded samples using distributed processing on workstations, clusters, or the cloud. RS-FISH maintains high detection accuracy and low localization error across a wide range of signal-to-noise ratios, a key feature for single-molecule FISH, spatial transcriptomics, or spatial genomics applications.Nature methodsRS-FISH: precise, interactive, fast, and scalable FISH spot detection.PMC9718671R01 GM127538F32 CA239394Long XPreibisch SBahry ELionnet TKolyvanov KMamrak NZouinkhi MHarrington KISBreimann LEpstein LKing BfalseRS-FISH: precise, interactive, fast, and scalable FISH spot detection.Fluorescent in-situ hybridization (FISH)-based methods extract spatially resolved genetic and epigenetic information from biological samples by detecting fluorescent spots in microscopy images, an often challenging task. We present Radial Symmetry-FISH (RS-FISH), an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. RS-FISH offers interactive parameter tuning and readily scales to large datasets and image volumes of cleared or expanded samples using distributed processing on workstations, clusters, or the cloud. RS-FISH maintains high detection accuracy and low localization error across a wide range of signal-to-noise ratios, a key feature for single-molecule FISH, spatial transcriptomics, or spatial genomics applications.2022-01-01T00:00:00Z2022 Dec2026-06-04T05:57:49.098Z2025-04-05T11:27:22.078ZS-EPMC97186713639678710.1038/s41592-022-01669-y