FISH-quant v2: a scalable and modular tool for smFISH image analysis.
Arthur ImbertWei OuyangAdham SafieddineEmeline ColenoChristophe ZimmerEdouard BertrandThomas WalterFlorian MuellerPublished in: RNA (New York, N.Y.) (2022)
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 quantitative studies of gene expression and its regulatory mechanisms. Today, these methods are applicable at a large scale, which in turn come with a need for adequate tools for data analysis and exploration. Here, we present FISH-quant v2, a highly modular tool accessible for both experts and non-experts. Our user-friendly package allows the user to segment nuclei and cells, detect isolated RNAs, decompose dense RNA clusters, quantify RNA localization patterns and visualize these results both at the single-cell level and variations within the cell population. This tool was validated and applied on large-scale smFISH image data sets, revealing diverse subcellular RNA localization patterns and a surprisingly high degree of cell-to-cell heterogeneity.
Keyphrases
- single cell
- single molecule
- gene expression
- rna seq
- data analysis
- living cells
- high throughput
- cell therapy
- dna methylation
- high resolution
- nucleic acid
- deep learning
- mesenchymal stem cells
- induced apoptosis
- signaling pathway
- cell proliferation
- photodynamic therapy
- microbial community
- endoplasmic reticulum stress
- energy transfer