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

Published on Apr 7, 2022in bioRxiv
13.50
· DOI :10.1101/2021.07.20.453024
Arthur Imbert4
Estimated H-index: 4
(ENSMP: Mines ParisTech),
Wei Ouyang8
Estimated H-index: 8
(KTH: Royal Institute of Technology)
+ 5 AuthorsFlorian Mueller27
Estimated H-index: 27
(Institut Pasteur)
Sources
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.
References21
Cited By3
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