{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:18:21Z","timestamp":1762298301305},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Single cell time-lapse microscopy is a powerful method for investigating heterogeneous cell behavior. Advances in microfluidic lab-on-a-chip technologies and live-cell imaging render the parallel observation of the development of individual cells in hundreds of populations possible. While image analysis tools are available for cell detection and tracking, biologists are still confronted with the challenge of exploring and evaluating this data.<\/jats:p>\n               <jats:p>Results: We present the software tool Vizardous that assists scientists with explorative analysis and interpretation tasks of single cell data in an interactive, configurable and visual way. With Vizardous, lineage tree drawings can be augmented with various, time-resolved cellular characteristics. Associated statistical moments bridge the gap between single cell and the population-average level.<\/jats:p>\n               <jats:p>Availability and implementation: The software, including documentation and examples, is available as executable Java archive as well as in source form at https:\/\/github.com\/modsim\/vizardous.<\/jats:p>\n               <jats:p>Contact: \u00a0k.noeh@fz-juelich.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv468","type":"journal-article","created":{"date-parts":[[2015,8,11]],"date-time":"2015-08-11T01:50:30Z","timestamp":1439257830000},"page":"3875-3877","source":"Crossref","is-referenced-by-count":9,"title":["Vizardous: interactive analysis of microbial populations with single cell resolution"],"prefix":"10.1093","volume":"31","author":[{"given":"Stefan","family":"Helfrich","sequence":"first","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charaf E.","family":"Azzouzi","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Probst","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Seiffarth","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Gr\u00fcnberger","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolfgang","family":"Wiechert","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dietrich","family":"Kohlheyer","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katharina","family":"N\u00f6h","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum J\u00fclich GmbH, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,8,10]]},"reference":[{"key":"2023020202420485900_btv468-B1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nmeth.1896","article-title":"OMERO: flexible, model-driven data management for experimental biology","volume":"9","author":"Allan","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020202420485900_btv468-B2","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1126\/science.1099390","article-title":"Bacterial persistence as a phenotypic switch","volume":"305","author":"Balaban","year":"2004","journal-title":"Science"},{"key":"2023020202420485900_btv468-B3","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1039\/C4IB00027G","article-title":"Light-responsive control of bacterial gene expression: precise triggering of the lac promoter activity using photocaged IPTG","volume":"6","author":"Binder","year":"2014","journal-title":"Integr. Biol. (Camb)."},{"key":"2023020202420485900_btv468-B4","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1016\/j.cell.2014.11.022","article-title":"A constant size extension drives bacterial cell size homeostasis","volume":"159","author":"Campos","year":"2014","journal-title":"Cell"},{"key":"2023020202420485900_btv468-B5","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.copbio.2014.02.008","article-title":"Single-cell microfluidics: opportunity for bioprocess development","volume":"29","author":"Gr\u00fcnberger","year":"2014","journal-title":"Curr. Opin. Biotechnol."},{"key":"2023020202420485900_btv468-B6","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/1471-2105-10-356","article-title":"phyloXML: XML for evolutionary biology and comparative genomics","volume":"10","author":"Han","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020202420485900_btv468-B7","doi-asserted-by":"crossref","first-page":"1251821","DOI":"10.1126\/science.1251821","article-title":"Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria","volume":"346","author":"Hol","year":"2014","journal-title":"Science"},{"key":"2023020202420485900_btv468-B8","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature13582","article-title":"Stochasticity of metabolism and growth at the single-cell level","volume":"514","author":"Kiviet","year":"2014","journal-title":"Nature"},{"key":"2023020202420485900_btv468-B9","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1126\/science.1239999","article-title":"Functional roles of pulsing in genetic circuits","volume":"342","author":"Levine","year":"2013","journal-title":"Science"},{"key":"2023020202420485900_btv468-B10","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/nrmicro2056","article-title":"Using movies to analyse gene circuit dynamics in single cells","volume":"7","author":"Locke","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"2023020202420485900_btv468-B11","doi-asserted-by":"crossref","first-page":"e85731","DOI":"10.1371\/journal.pone.0085731","article-title":"Application of a genetically encoded biosensor for live cell imaging of l-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains","volume":"9","author":"Mustafi","year":"2014","journal-title":"PLoS One"},{"key":"2023020202420485900_btv468-B12","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1128\/JB.01018-13","article-title":"Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level","volume":"196","author":"Nanda","year":"2014","journal-title":"J. Bacteriol."},{"key":"2023020202420485900_btv468-B13","doi-asserted-by":"crossref","first-page":"e93466","DOI":"10.1371\/journal.pone.0093466","article-title":"Long-term single cell analysis of S.pombe on a microfluidic microchemostat array","volume":"9","author":"Nobs","year":"2014","journal-title":"PLoS One"},{"key":"2023020202420485900_btv468-B14","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1039\/C4AY02257B","article-title":"Rapid inoculation of single bacteria into parallel picoliter fermentation chambers","volume":"7","author":"Probst","year":"2015","journal-title":"Anal. Methods"},{"key":"2023020202420485900_btv468-B15","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/ng.1048","article-title":"Following evolution of bacterial antibiotic resistance in real time","volume":"44","author":"Rosenthal","year":"2012","journal-title":"Nat. Genet."},{"key":"2023020202420485900_btv468-B16","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/nature13118","article-title":"The present and future role of microfluidics in biomedical research","volume":"507","author":"Sackmann","year":"2014","journal-title":"Nature"},{"key":"2023020202420485900_btv468-B17","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.cub.2014.12.009","article-title":"Cell-size control and homeostasis in bacteria","volume":"25","author":"Taheri-Araghi","year":"2014","journal-title":"Curr. Biol."},{"key":"2023020202420485900_btv468-B18","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1016\/j.cub.2010.04.045","article-title":"Robust growth of Escherichia coli","volume":"20","author":"Wang","year":"2010","journal-title":"Curr. Biol."},{"key":"2023020202420485900_btv468-B19","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1038\/nprot.2011.432","article-title":"Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy","volume":"7","author":"Young","year":"2012","journal-title":"Nat. Protoc."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3875\/49036361\/bioinformatics_31_23_3875.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/23\/3875\/49036361\/bioinformatics_31_23_3875.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:57:12Z","timestamp":1675310232000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/23\/3875\/209371"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8,10]]},"references-count":19,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2015,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv468","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,1]]},"published":{"date-parts":[[2015,8,10]]}}}