{"entity": "publication", "iuid": "10b5b7a1918d4b41946b103a175f76c0", "timestamp": "2026-08-22T06:57:16.751Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/10b5b7a1918d4b41946b103a175f76c0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/10b5b7a1918d4b41946b103a175f76c0"}}, "title": "FISH-quant v2: a scalable and modular tool for smFISH image analysis.", "authors": [{"family": "Imbert", "given": "Arthur", "initials": "A"}, {"family": "Ouyang", "given": "Wei", "initials": "W"}, {"family": "Safieddine", "given": "Adham", "initials": "A", "orcid": "0000-0002-9324-9037", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9631fea704c2481dba933e59b12873d5.json"}}, {"family": "Coleno", "given": "Emeline", "initials": "E"}, {"family": "Zimmer", "given": "Christophe", "initials": "C"}, {"family": "Bertrand", "given": "Edouard", "initials": "E"}, {"family": "Walter", "given": "Thomas", "initials": "T"}, {"family": "Mueller", "given": "Florian", "initials": "F", "orcid": "0000-0002-9622-4396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8df07352fbd44ef39300b8067904c5c7.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "RNA", "issn": "1469-9001", "volume": "28", "issue": "6", "pages": "786-795", "issn-l": "1355-8382"}, "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 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.", "doi": "10.1261/rna.079073.121", "pmid": "35347070", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9074904"}, {"db": "pii", "key": "rna.079073.121"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2026-08-21T12:42:59.122Z", "modified": "2026-08-21T12:42:59.179Z"}