{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T05:37:46Z","timestamp":1773898666340,"version":"3.50.1"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T00:00:00Z","timestamp":1743724800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Bacterial interactions in clinically relevant settings remain challenging to quantify, especially in systems with multiple species or varied material properties. Quantitative image analysis methods based on machine learning show promise to overcome this challenge and support the development of novel antimicrobial treatments, but are limited by a lack of high-quality training data. Here, novel experimental and image analysis techniques for high-fidelity single-cell segmentation of bacterial colonies are developed. Machine learning-based segmentation models are trained solely using synthetic microscopy images that are processed to look realistic using a state-of-the-art image-to-image translation method (cycleGAN), requiring no biophysical modeling. Accurate single-cell segmentation is achieved for densely packed single-species colonies and multi-species colonies of common pathogenic bacteria, even under suboptimal imaging conditions and for both brightfield and confocal laser scanning microscopy. The resulting data provide quantitative insights into the self-organization of bacteria on soft surfaces. Thanks to their high adaptability and relatively simple implementation, these methods promise to greatly facilitate quantitative descriptions of bacterial infections in varied environments, and may be used for the development of rapid diagnostic tools in clinical settings.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012874","type":"journal-article","created":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T17:55:01Z","timestamp":1743789301000},"page":"e1012874","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2928-9568","authenticated-orcid":true,"given":"Vincent","family":"Hickl","sequence":"first","affiliation":[]},{"given":"Abid","family":"Khan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0946-682X","authenticated-orcid":true,"given":"Ren\u00e9 M.","family":"Rossi","sequence":"additional","affiliation":[]},{"given":"Bruno F. B.","family":"Silva","sequence":"additional","affiliation":[]},{"given":"Katharina","family":"Maniura-Weber","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2025,4,4]]},"reference":[{"issue":"23","key":"pcbi.1012874.ref001","doi-asserted-by":"crossref","first-page":"e2310079","DOI":"10.1002\/advs.202310079","article-title":"Optogenetic control of bacterial cell-cell adhesion dynamics: unraveling the influence on biofilm architecture and functionality","volume":"11","author":"JJ Quispe Haro","year":"2024","journal-title":"Adv Sci (Weinh)"},{"issue":"1","key":"pcbi.1012874.ref002","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1038\/s41467-018-03446-y","article-title":"Asymmetric adhesion of rod-shaped bacteria controls microcolony morphogenesis","volume":"9","author":"M-C Duvernoy","year":"2018","journal-title":"Nat Commun"},{"issue":"5","key":"pcbi.1012874.ref003","doi-asserted-by":"crossref","first-page":"pgac269","DOI":"10.1093\/pnasnexus\/pgac269","article-title":"Tilt-induced polar order and topological defects in growing bacterial populations","volume":"1","author":"T Shimaya","year":"2022","journal-title":"PNAS Nexus"},{"issue":"3","key":"pcbi.1012874.ref004","first-page":"031065","article-title":"Geometry and mechanics of microdomains in growing bacterial colonies","volume":"8","author":"Z You","year":"2018","journal-title":"Phys Rev X"},{"key":"pcbi.1012874.ref005","unstructured":"Langeslay B, Juarez G. Growth-induced phase changes in swimming bacteria at finite liquid interfaces; 2023. 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