{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T21:46:14Z","timestamp":1787003174885,"version":"build-2736575974"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T00:00:00Z","timestamp":1763337600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T00:00:00Z","timestamp":1763337600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-03826-2018"],"award-info":[{"award-number":["RGPIN-03826-2018"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-03826-2018"],"award-info":[{"award-number":["RGPIN-03826-2018"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Syst Biol Appl"],"DOI":"10.1038\/s41540-025-00600-3","type":"journal-article","created":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T21:37:00Z","timestamp":1763415420000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["TrackRefiner a tool for refinement of bacillus cell tracking data"],"prefix":"10.1038","volume":"11","author":[{"given":"Atiyeh","family":"Ahmadi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alireza","family":"Dostmohammadi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rhyan","family":"Mclean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Ingalls","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,17]]},"reference":[{"key":"600_CR1","doi-asserted-by":"publisher","first-page":"1622","DOI":"10.1126\/science.1099390","volume":"305","author":"NQ Balaban","year":"2004","unstructured":"Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L. & Leibler, S. Bacterial persistence as a phenotypic switch. Science 305, 1622\u20131625 (2004).","journal-title":"Science"},{"key":"600_CR2","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/nature12804","volume":"503","author":"TM Norman","year":"2013","unstructured":"Norman, T. M., Lord, N. D., Paulsson, J. & Losick, R. Memory and modularity in cell-fate decision making. Nature 503, 481\u2013486 (2013).","journal-title":"Nature"},{"key":"600_CR3","first-page":"45","volume":"3","author":"JL Collins","year":"2018","unstructured":"Collins, J. L., Van Knippenberg, B., Ding, K. & Kofman, A. V. Time-lapse microscopy. Cell Cult. 3, 45\u201373 (2018).","journal-title":"Cell Cult."},{"key":"600_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2121-11-24","volume":"11","author":"J Huth","year":"2010","unstructured":"Huth, J. et al. Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system. BMC Cell Biol. 11, 1\u201312 (2010).","journal-title":"BMC Cell Biol."},{"key":"600_CR5","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1038\/s41559-019-0939-6","volume":"3","author":"J van Gestel","year":"2019","unstructured":"van Gestel, J., Ackermann, M. & Wagner, A. Microbial life cycles link global modularity in regulation to mosaic evolution. Nat. Ecol. Evol. 3, 1184\u20131196 (2019).","journal-title":"Nat. Ecol. Evol."},{"key":"600_CR6","doi-asserted-by":"publisher","first-page":"2274","DOI":"10.1038\/ismej.2013.107","volume":"7","author":"D Patzelt","year":"2013","unstructured":"Patzelt, D. et al. You are what you talk: quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae. ISME J. 7, 2274\u20132286 (2013).","journal-title":"ISME J."},{"key":"600_CR7","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/s41592-019-0620-7","volume":"17","author":"S Luro","year":"2020","unstructured":"Luro, S., Potvin-Trottier, L., Okumus, B. & Paulsson, J. Isolating live cells after high-throughput, long-term, time-lapse microscopy. Nat. Methods 17, 93\u2013100 (2020).","journal-title":"Nat. Methods"},{"key":"600_CR8","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-42475-5","volume":"9","author":"M Comes","year":"2019","unstructured":"Comes, M. et al. The influence of spatial and temporal resolutions on the analysis of cell-cell interaction: a systematic study for time-lapse microscopy applications. Sci. Rep. 9, 6789 (2019).","journal-title":"Sci. Rep."},{"key":"600_CR9","doi-asserted-by":"publisher","first-page":"aad3292","DOI":"10.1126\/science.aad3292","volume":"351","author":"M Baym","year":"2016","unstructured":"Baym, M., Stone, L. K. & Kishony, R. Multidrug evolutionary strategies to reverse antibiotic resistance. Science 351, aad3292 (2016).","journal-title":"Science"},{"key":"600_CR10","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/s41564-021-00900-4","volume":"6","author":"S Bakshi","year":"2021","unstructured":"Bakshi, S. et al. Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence. Nat. Microbiol. 6, 783\u2013791 (2021).","journal-title":"Nat. Microbiol."},{"key":"600_CR11","doi-asserted-by":"publisher","first-page":"14734","DOI":"10.1073\/pnas.1906169116","volume":"116","author":"I Levin-Reisman","year":"2019","unstructured":"Levin-Reisman, I., Brauner, A., Ronin, I. & Balaban, N. Q. Epistasis between antibiotic tolerance, persistence, and resistance mutations. Proc. Natl Acad. Sci. USA 116, 14734\u201314739 (2019).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"600_CR12","doi-asserted-by":"publisher","first-page":"e2003853","DOI":"10.1371\/journal.pbio.2003853","volume":"16","author":"SK Govers","year":"2018","unstructured":"Govers, S. K., Mortier, J., Adam, A. & Aertsen, A. Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells. PLoS Biol. 16, e2003853 (2018).","journal-title":"PLoS Biol."},{"key":"600_CR13","doi-asserted-by":"crossref","unstructured":"Lewis, K. Antibiotic Resistance 121\u2013133 (2012).","DOI":"10.1007\/978-3-642-28951-4_8"},{"key":"600_CR14","doi-asserted-by":"publisher","first-page":"aaf4268","DOI":"10.1126\/science.aaf4268","volume":"354","author":"A Harms","year":"2016","unstructured":"Harms, A., Maisonneuve, E. & Gerdes, K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 354, aaf4268 (2016).","journal-title":"Science"},{"key":"600_CR15","doi-asserted-by":"publisher","first-page":"fuaa062","DOI":"10.1093\/femsre\/fuaa062","volume":"45","author":"H Jeckel","year":"2021","unstructured":"Jeckel, H. & Drescher, K. Advances and opportunities in image analysis of bacterial cells and communities. FEMS Microbiol. Rev. 45, fuaa062 (2021).","journal-title":"FEMS Microbiol. Rev."},{"key":"600_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12918-017-0399-z","volume":"11","author":"AD Balomenos","year":"2017","unstructured":"Balomenos, A. D. et al. Image analysis driven single-cell analytics for systems microbiology. BMC Syst. Biol. 11, 1\u201321 (2017).","journal-title":"BMC Syst. Biol."},{"key":"600_CR17","doi-asserted-by":"publisher","first-page":"e00658","DOI":"10.1128\/msphere.00658-22","volume":"8","author":"H Todorov","year":"2023","unstructured":"Todorov, H., Miguel Trabajo, T. & Van der Meer, J. R. Strack: a tool to simply track bacterial cells in microscopy time-lapse images. Msphere 8, e00658\u201322 (2023).","journal-title":"Msphere"},{"key":"600_CR18","doi-asserted-by":"publisher","first-page":"e1009797","DOI":"10.1371\/journal.pcbi.1009797","volume":"18","author":"OM O\u2019Connor","year":"2022","unstructured":"O\u2019Connor, O. M., Alnahhas, R. N., Lugagne, J.-B. & Dunlop, M. J. Delta 2.0: a deep learning pipeline for quantifying single-cell spatial and temporal dynamics. PLoS Comput. Biol. 18, e1009797 (2022).","journal-title":"PLoS Comput. Biol."},{"key":"600_CR19","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1111\/mmi.13486","volume":"102","author":"S Stylianidou","year":"2016","unstructured":"Stylianidou, S., Brennan, C., Nissen, S. B., Kuwada, N. J. & Wiggins, P. A. Supersegger: robust image segmentation, analysis and lineage tracking of bacterial cells. Mol. Microbiol. 102, 690\u2013700 (2016).","journal-title":"Mol. Microbiol."},{"key":"600_CR20","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.ymeth.2016.09.016","volume":"115","author":"J-Y Tinevez","year":"2017","unstructured":"Tinevez, J.-Y. et al. Trackmate: an open and extensible platform for single-particle tracking. Methods 115, 80\u201390 (2017).","journal-title":"Methods"},{"key":"600_CR21","doi-asserted-by":"publisher","first-page":"e00032","DOI":"10.1128\/spectrum.00032-24","volume":"12","author":"A Ahmadi","year":"2024","unstructured":"Ahmadi, A., Courtney, M., Ren, C. & Ingalls, B. A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics. Microbiol. Spectr. 12, e00032\u201324 (2024).","journal-title":"Microbiol. Spectr."},{"key":"600_CR22","doi-asserted-by":"publisher","first-page":"1438","DOI":"10.1038\/s41592-022-01639-4","volume":"19","author":"KJ Cutler","year":"2022","unstructured":"Cutler, K. J. et al. Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Nat. Methods 19, 1438\u20131448 (2022).","journal-title":"Nat. Methods"},{"key":"600_CR23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-021-04344-9","volume":"22","author":"DR Stirling","year":"2021","unstructured":"Stirling, D. R. et al. Cellprofiler 4: improvements in speed, utility and usability. BMC Bioinforma. 22, 1\u201311 (2021).","journal-title":"BMC Bioinforma."},{"key":"600_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2375-z","volume":"19","author":"Y Al-Kofahi","year":"2018","unstructured":"Al-Kofahi, Y., Zaltsman, A., Graves, R., Marshall, W. & Rusu, M. A deep learning-based algorithm for 2-D cell segmentation in microscopy images. BMC Bioinforma. 19, 1\u201311 (2018).","journal-title":"BMC Bioinforma."},{"key":"600_CR25","doi-asserted-by":"publisher","first-page":"1609","DOI":"10.1093\/bioinformatics\/btu080","volume":"30","author":"M Ma\u0161ka","year":"2014","unstructured":"Ma\u0161ka, M. et al. A benchmark for comparison of cell tracking algorithms. Bioinformatics 30, 1609\u20131617 (2014).","journal-title":"Bioinformatics"},{"key":"600_CR26","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/s42003-020-01581-1","volume":"4","author":"J Vacheron","year":"2021","unstructured":"Vacheron, J., Heiman, C. M. & Keel, C. Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion. Commun. Biol. 4, 87 (2021).","journal-title":"Commun. Biol."},{"key":"600_CR27","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41559-019-1080-2","volume":"4","author":"A Dal Co","year":"2020","unstructured":"Dal Co, A., van Vliet, S., Kiviet, D. J., Schlegel, S. & Ackermann, M. Short-range interactions govern the dynamics and functions of microbial communities. Nat. Ecol. Evol. 4, 366\u2013375 (2020).","journal-title":"Nat. Ecol. Evol."},{"key":"600_CR28","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature13582","volume":"514","author":"DJ Kiviet","year":"2014","unstructured":"Kiviet, D. J. et al. Stochasticity of metabolism and growth at the single-cell level. Nature 514, 376\u2013379 (2014).","journal-title":"Nature"},{"key":"600_CR29","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1038\/nmeth.4473","volume":"14","author":"V Ulman","year":"2017","unstructured":"Ulman, V. et al. An objective comparison of cell-tracking algorithms. Nat. Methods 14, 1141\u20131152 (2017).","journal-title":"Nat. Methods"},{"key":"600_CR30","doi-asserted-by":"crossref","unstructured":"Ben-Haim, T. & Raviv, T. R. Graph neural network for cell tracking in microscopy videos. In European Conference on Computer Vision, 610\u2013626 (Springer, 2022).","DOI":"10.1007\/978-3-031-19803-8_36"},{"key":"600_CR31","doi-asserted-by":"crossref","unstructured":"Chatterjee, S. A new method of normal approximation. Ann. Probab. Ann. Probab. 36, 1584\u20131610 (2008).","DOI":"10.1214\/07-AOP370"},{"key":"600_CR32","doi-asserted-by":"publisher","first-page":"1679","DOI":"10.1109\/TAES.2016.140952","volume":"52","author":"DF Crouse","year":"2016","unstructured":"Crouse, D. F. On implementing 2d rectangular assignment algorithms. IEEE Trans. Aerosp. Electron. Syst. 52, 1679\u20131696 (2016).","journal-title":"IEEE Trans. Aerosp. Electron. Syst."}],"container-title":["npj Systems Biology and Applications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41540-025-00600-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41540-025-00600-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41540-025-00600-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T21:37:01Z","timestamp":1763415421000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41540-025-00600-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,17]]},"references-count":32,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["600"],"URL":"https:\/\/doi.org\/10.1038\/s41540-025-00600-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.02.13.637647","asserted-by":"object"}]},"ISSN":["2056-7189"],"issn-type":[{"value":"2056-7189","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,17]]},"assertion":[{"value":"21 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"127"}}