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Art"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>As one of the most widely used assays in biological research, an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process. To speed up the colony counting, a machine learning method is presented for counting the colony forming units (CFUs), which is referred to as CFUCounter. This cell-counting program processes digital images and segments bacterial colonies. The algorithm combines unsupervised machine learning, iterative adaptive thresholding, and local-minima-based watershed segmentation to enable an accurate and robust cell counting. Compared to a manual counting method, CFUCounter supports color-based CFU classification, allows plates containing heterologous colonies to be counted individually, and demonstrates overall performance (slope 0.996, SD 0.013, 95%CI: 0.97\u20131.02, p value\u2009&lt;\u20091e-11, r\u2009=\u20090.999) indistinguishable from the gold standard of point-and-click counting. This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.<\/jats:p>","DOI":"10.1186\/s42492-022-00122-3","type":"journal-article","created":{"date-parts":[[2022,11,5]],"date-time":"2022-11-05T06:02:31Z","timestamp":1667628151000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Machine learning for enumeration of cell colony forming units"],"prefix":"10.1186","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4524-8213","authenticated-orcid":false,"given":"Louis","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,11,5]]},"reference":[{"key":"122_CR1","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.tube.2017.05.002","volume":"105","author":"GJ de Knegt","year":"2017","unstructured":"de Knegt GJ, Dickinson L, Pertinez H, Evangelopoulos D, McHugh TD, Bakker-Woudenberg IAJM et al (2017) Assessment of treatment response by colony forming units, time to culture positivity and the molecular bacterial load assay compared in a mouse tuberculosis model. 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