RT Journal Article
SR Electronic
T1 RS-FISH: Precise, interactive, fast, and scalable FISH spot detection
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.03.09.434205
DO 10.1101/2021.03.09.434205
A1 Bahry, Ella
A1 Breimann, Laura
A1 Zouinkhi, Marwan
A1 Epstein, Leo
A1 Kolyvanov, Klim
A1 Long, Xi
A1 Harrington, Kyle I S
A1 Lionnet, Timothée
A1 Preibisch, Stephan
YR 2021
UL http://biorxiv.org/content/early/2021/10/18/2021.03.09.434205.abstract
AB Fluorescent in-situ hybridization (FISH)-based methods are powerful tools to study molecular processes with subcellular resolution, relying on accurate identification and localization of diffraction-limited spots in microscopy images. We developed the Radial Symmetry-FISH (RS-FISH) software that accurately, robustly, and quickly detects single-molecule spots in two and three dimensions, making it applicable to several key assays, including single-molecule FISH (smFISH), spatial transcriptomics, and spatial genomics. RS-FISH allows interactive parameter tuning and scales to large sets of images as well as tera-byte sized image volumes such as entire brain scans using straight-forward distributed processing on workstations, clusters, and in the cloud.Competing Interest StatementThe authors have declared no competing interest.