Kyle Harrington

Bioimaging and visualization · 2022

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

Ella Bahry, Laura Breimann, Marwan Zouinkhi, Leo Epstein, Klim Kolyvanov, Nicholas Mamrak, Benjamin King, Xi Long, Kyle I. S. Harrington, Timothée Lionnet, Stephan Preibisch

Nature Methods, 19(12)

doi:10.1038/s41592-022-01669-ypdfcode

Abstract

RS-FISH is an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. It offers interactive parameter tuning and 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, making it suitable for single-molecule FISH, spatial transcriptomics, or spatial genomics applications.

RS-FISH is an accurate, fast, and user-friendly software for spot detection in two- and three-dimensional images. It offers interactive parameter tuning and 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, making it suitable for single-molecule FISH, spatial transcriptomics, or spatial genomics applications.