HAL will be down for maintenance from Friday, June 10 at 4pm through Monday, June 13 at 9am. More information
Skip to Main content Skip to Navigation
Preprints, Working Papers, ...

FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis

Abstract : Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in-situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling a quantitative understanding of gene expression and its regulatory mechanisms. Recent progress in experimental techniques provides larger data-sets, requiring adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular analysis tool accessible both for non-experts and experts, which we validated and applied on large-scale smFISH image datasets. Our package allows the user to detect isolated and clustered mRNA spots, segment nuclei and cells, quantify RNA localization patterns and visualize these results at the single-cell level.
Complete list of metadata

Contributor : Thomas Walter Connect in order to contact the contributor
Submitted on : Tuesday, January 18, 2022 - 10:55:58 PM
Last modification on : Tuesday, May 17, 2022 - 2:18:04 PM


Files produced by the author(s)



Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, et al.. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. 2021. ⟨hal-03533689⟩



Record views


Files downloads