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

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Nature Methods. 2022 Nov 17;19(12):1563-7. doi: 10.1038/s41592-022-01669-y
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RS-FISH: Precise, interactive, fast, and scalable FISH spot detection Scientific Computing
Bahry Ella, Breimann Laura, Zouinkhi Marwan, Epstein Leo, Kolyvanov Klim, Long Xi, Harrington Kyle, Lionnet Timothée, Preibisch Stephan
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Abstract

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.

PMID: 36396787 [PubMed - indexed for MEDLINE]

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Previous bioRxiv PrePrint https://doi.org/10.1101/2021.03.09.434205

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Janelia Authors

Marwan Zouinkhi
Xi Salina Long
Stephan Preibisch
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