{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T01:39:03Z","timestamp":1775612343176,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T00:00:00Z","timestamp":1557964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Science and Engineering Research Council"},{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canadian Foundation for Innovation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>YeastSpotter is available at http:\/\/yeastspotter.csb.utoronto.ca\/. Code is available at https:\/\/github.com\/alexxijielu\/yeast_segmentation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz402","type":"journal-article","created":{"date-parts":[[2019,5,7]],"date-time":"2019-05-07T23:26:09Z","timestamp":1557271569000},"page":"4525-4527","source":"Crossref","is-referenced-by-count":94,"title":["YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9568-3155","authenticated-orcid":false,"given":"Alex X","family":"Lu","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Toronto , Toronto, ON, Canada"}]},{"given":"Taraneh","family":"Zarin","sequence":"additional","affiliation":[{"name":"Department of Cells and Systems Biology, University of Toronto , Toronto, ON, Canada"}]},{"given":"Ian S","family":"Hsu","sequence":"additional","affiliation":[{"name":"Department of Cells and Systems Biology, University of Toronto , Toronto, ON, Canada"}]},{"given":"Alan M","family":"Moses","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Toronto , Toronto, ON, Canada"},{"name":"Department of Cells and Systems Biology, University of Toronto , Toronto, ON, Canada"},{"name":"Center for Analysis of Genome Evolution and Function, University of Toronto , Toronto, ON, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,5,16]]},"reference":[{"key":"2023062712534299700_btz402-B1","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1093\/bioinformatics\/btx550","article-title":"Morphologically constrained and data informed cell segmentation of budding yeast","volume":"34","author":"Bakker","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062712534299700_btz402-B2","doi-asserted-by":"crossref","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","article-title":"CellProfiler: image analysis software for identifying and quantifying cell phenotypes","volume":"7","author":"Carpenter","year":"2006","journal-title":"Genome Biol"},{"key":"2023062712534299700_btz402-B3","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1016\/j.cell.2015.04.051","article-title":"Yeast proteome dynamics from single cell imaging and automated analysis","volume":"161","author":"Chong","year":"2015","journal-title":"Cell"},{"key":"2023062712534299700_btz402-B4","doi-asserted-by":"crossref","first-page":"2644","DOI":"10.1093\/bioinformatics\/btu302","article-title":"Accurate cell segmentation in microscopy images using membrane patterns","volume":"30","author":"Dimopoulos","year":"2014","journal-title":"Bioinformatics"},{"key":"2023062712534299700_btz402-B5","doi-asserted-by":"crossref","first-page":"D1245","DOI":"10.1093\/nar\/gky941","article-title":"YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries","volume":"47","author":"Dubreuil","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062712534299700_btz402-B6","doi-asserted-by":"crossref","first-page":"e1003085.","DOI":"10.1371\/journal.pcbi.1003085","article-title":"Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins","volume":"9","author":"Handfield","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023062712534299700_btz402-B7","author":"He","year":"2017"},{"key":"2023062712534299700_btz402-B8","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1534\/g3.115.017830","article-title":"CYCLoPs: a comprehensive database constructed from automated analysis of protein abundance and subcellular localization patterns in Saccharomyces cerevisiae","volume":"5","author":"Koh","year":"2015","journal-title":"G3 (Bethesda)"},{"key":"2023062712534299700_btz402-B9","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1177\/1087057113503553","article-title":"Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment","volume":"18","author":"Ljosa","year":"2013","journal-title":"J. Biomol. Screen"},{"key":"2023062712534299700_btz402-B10","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1109\/MSP.2012.2204190","article-title":"Cell segmentation: 50 Years down the road [life sciences]","volume":"29","author":"Meijering","year":"2012","journal-title":"IEEE Signal Process Mag"},{"key":"2023062712534299700_btz402-B11","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1186\/1471-2105-11-263","article-title":"The yeast resource center public image repository: a large database of fluorescence microscopy images","volume":"11","author":"Riffle","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023062712534299700_btz402-B12","doi-asserted-by":"crossref","first-page":"20160705.","DOI":"10.1098\/rsif.2016.0705","article-title":"Long-term tracking of budding yeast cells in brightfield microscopy: cellStar and the evaluation platform","volume":"14","author":"Versari","year":"2017","journal-title":"J. R. Soc. Interface"},{"key":"2023062712534299700_btz402-B13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1117\/1.JBO.23.12.125002","article-title":"Segmentation of yeast cell\u2019s bright-field image with an edge-tracing algorithm","volume":"23","author":"Wang","year":"2018","journal-title":"J. Biomed. Opt"},{"key":"2023062712534299700_btz402-B14","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/s41592-018-0044-9","article-title":"Genome-wide SWAp-Tag yeast libraries for proteome exploration","volume":"15","author":"Weill","year":"2018","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz402\/28756709\/btz402.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4525\/50721947\/bioinformatics_35_21_4525.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4525\/50721947\/bioinformatics_35_21_4525.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:55:12Z","timestamp":1687870512000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4525\/5490207"}},"subtitle":[],"editor":[{"given":"Robert","family":"Murphy","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,16]]},"references-count":14,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz402","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,5,16]]}}}