RS-FISH: precise, interactive, fast, and scalable FISH spot detection


  • E. Bahry
  • L. Breimann
  • M. Zouinkhi
  • L. Epstein
  • K. Kolyvanov
  • N. Mamrak
  • B. King
  • Xi Long
  • K.I.S. Harrington
  • T. Lionnet
  • S. Preibisch


  • Nature Methods


  • Nat Methods 19 (12): 1563-1567


  • 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.