{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T18:01:41Z","timestamp":1777053701200,"version":"3.51.4"},"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2020,4,13]],"date-time":"2020-04-13T00:00:00Z","timestamp":1586736000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21AI137843"],"award-info":[{"award-number":["R21AI137843"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"Department of Energy","doi-asserted-by":"crossref","award":["DE-SC0019387"],"award-info":[{"award-number":["DE-SC0019387"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI102922"],"award-info":[{"award-number":["R01AI102922"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007673","type":"journal-article","created":{"date-parts":[[2020,4,13]],"date-time":"2020-04-13T13:23:56Z","timestamp":1586784236000},"page":"e1007673","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":197,"title":["DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8374-6590","authenticated-orcid":true,"given":"Jean-Baptiste","family":"Lugagne","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0437-5902","authenticated-orcid":true,"given":"Haonan","family":"Lin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9261-8216","authenticated-orcid":true,"given":"Mary J.","family":"Dunlop","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,4,13]]},"reference":[{"key":"pcbi.1007673.ref001","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14440\/jbm.2014.36","article-title":"Advanced methods of microscope control using \u03bcManager software","volume":"1","author":"AD Edelstein","year":"2014","journal-title":"J Biol Methods"},{"key":"pcbi.1007673.ref002","doi-asserted-by":"crossref","first-page":"14.21.1","DOI":"10.1002\/0471142727.mb1421s98","article-title":"Use of YouScope to Implement Systematic Microscopy Protocols","volume":"98","author":"M Lang","year":"2012","journal-title":"Curr Protoc Mol Biol"},{"key":"pcbi.1007673.ref003","doi-asserted-by":"crossref","first-page":"15842","DOI":"10.1073\/pnas.1308265110","article-title":"A chemostat array enables the spatio-temporal analysis of the yeast proteome","volume":"110","author":"N D\u00e9nervaud","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi.1007673.ref004","article-title":"Time-resolved imaging-based CRISPRi screening","author":"D Camsund","year":"2019","journal-title":"Nat Methods"},{"key":"pcbi.1007673.ref005","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":"P Wang","year":"2010","journal-title":"Curr Biol"},{"key":"pcbi.1007673.ref006","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1126\/science.aaf4762","article-title":"Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","volume":"356","author":"T Bergmiller","year":"2017","journal-title":"Science"},{"key":"pcbi.1007673.ref007","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1016\/j.cub.2019.04.062","article-title":"Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria","volume":"29","author":"F Si","year":"2019","journal-title":"Curr Biol"},{"key":"pcbi.1007673.ref008","doi-asserted-by":"crossref","first-page":"1420","DOI":"10.1126\/science.aah7084","article-title":"Kinetics of dCas9 target search in Escherichia coli","volume":"357","author":"DL Jones","year":"2017","journal-title":"Science"},{"key":"pcbi.1007673.ref009","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1038\/s41467-017-01683-1","article-title":"Shaping bacterial population behavior through computer-interfaced control of individual cells","volume":"8","author":"R Chait","year":"2017","journal-title":"Nat Commun"},{"key":"pcbi.1007673.ref010","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nature12804","article-title":"Memory and modularity in cell-fate decision making","volume":"503","author":"TM Norman","year":"2013","journal-title":"Nature"},{"key":"pcbi.1007673.ref011","doi-asserted-by":"crossref","first-page":"e0163453","DOI":"10.1371\/journal.pone.0163453","article-title":"Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments","volume":"11","author":"CC Sachs","year":"2016","journal-title":"PLoS One"},{"key":"pcbi.1007673.ref012","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1111\/mmi.13486","article-title":"SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells","volume":"102","author":"S Stylianidou","year":"2016","journal-title":"Mol Microbiol"},{"key":"pcbi.1007673.ref013","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btr095","article-title":"Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software","volume":"27","author":"L Kamentsky","year":"2011","journal-title":"Bioinformatics"},{"key":"pcbi.1007673.ref014","first-page":"230","article-title":"Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro","author":"C Sommer","year":"2011","journal-title":"IEEE"},{"key":"pcbi.1007673.ref015","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":"JW Young","year":"2011","journal-title":"Nat Protoc"},{"key":"pcbi.1007673.ref016","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/978-3-319-12289-2_3","volume-title":"Bayesian and grAphical Models for Biomedical Imaging","author":"F Jug","year":"2014"},{"key":"pcbi.1007673.ref017","doi-asserted-by":"crossref","first-page":"3144","DOI":"10.1038\/s41596-019-0216-9","article-title":"High-throughput detection and tracking of cells and intracellular spots in mother machine experiments","volume":"14","author":"J Ollion","year":"2019","journal-title":"Nat Protoc"},{"key":"pcbi.1007673.ref018","first-page":"4","article-title":"Mother machine image analysis with MM3","author":"JT Sauls","year":"2019","journal-title":"bioRxiv"},{"key":"pcbi.1007673.ref019","doi-asserted-by":"crossref","first-page":"10123","DOI":"10.1038\/s41598-019-46567-0","article-title":"MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine","volume":"9","author":"A Smith","year":"2019","journal-title":"Sci Rep"},{"key":"pcbi.1007673.ref020","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1007\/978-3-319-24574-4_28","volume-title":"Medical Image Computing and Computer-Assisted Intervention\u2014MICCAI 2015","author":"O Ronneberger","year":"2015"},{"key":"pcbi.1007673.ref021","article-title":"Deep learning for cellular image analysis","author":"E Moen","year":"2019","journal-title":"Nat Methods"},{"key":"pcbi.1007673.ref022","article-title":"Deep-learning-based flexible pipeline for segmenting and tracking cells in 3D image time series for whole brain imaging","author":"C Wen","year":"2018","journal-title":"bioRxiv"},{"key":"pcbi.1007673.ref023","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.molcel.2018.04.012","article-title":"An optogenetic platform for real-time, single-cell interrogation of stochastic transcription regulation","volume":"70","author":"M Rullan","year":"2018","journal-title":"Mol Cell"},{"key":"pcbi.1007673.ref024","doi-asserted-by":"crossref","first-page":"14271","DOI":"10.1073\/pnas.1206810109","article-title":"Long-term model predictive control of gene expression at the population and single-cell levels","volume":"109","author":"J Uhlendorf","year":"2012","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi.1007673.ref025","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.coisb.2019.01.001","article-title":"Cell-machine interfaces for characterizing gene regulatory network dynamics","volume":"14","author":"J-B Lugagne","year":"2019","journal-title":"Curr Opin Syst Biol"},{"key":"pcbi.1007673.ref026","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.cell.2018.09.044","article-title":"Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control","volume":"175","author":"P Harrigan","year":"2018","journal-title":"Cell"},{"key":"pcbi.1007673.ref027","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1039\/c3ib40102b","article-title":"Real-time optogenetic control of intracellular protein concentration in microbial cell cultures","volume":"6","author":"J Melendez","year":"2014","journal-title":"Integr Biol"},{"key":"pcbi.1007673.ref028","doi-asserted-by":"crossref","first-page":"5333","DOI":"10.1038\/s41467-018-07702-z","article-title":"Escherichia coli can survive stress by noisy growth modulation","volume":"9","author":"O Patange","year":"2018","journal-title":"Nat Commun"},{"key":"pcbi.1007673.ref029","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1038\/s41467-017-01498-0","article-title":"Balancing a genetic toggle switch by real-time feedback control and periodic forcing","volume":"8","author":"J-B Lugagne","year":"2017","journal-title":"Nat Commun"},{"key":"pcbi.1007673.ref030","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.ymeth.2016.09.016","article-title":"TrackMate: An open and extensible platform for single-particle tracking","volume":"115","author":"J-Y Tinevez","year":"2017","journal-title":"Methods"},{"key":"pcbi.1007673.ref031","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1016\/j.mib.2017.12.004","article-title":"Microfluidics and single-cell microscopy to study stochastic processes in bacteria","volume":"43","author":"L Potvin-Trottier","year":"2018","journal-title":"Curr Opin Microbiol"},{"key":"pcbi.1007673.ref032","doi-asserted-by":"crossref","first-page":"947","DOI":"10.15252\/msb.20177951","article-title":"In situ genotyping of a pooled strain library after characterizing complex phenotypes","volume":"13","author":"MJ Lawson","year":"2017","journal-title":"Mol Syst Biol"},{"key":"pcbi.1007673.ref033","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nmeth.1237","article-title":"Robust single-particle tracking in live-cell time-lapse sequences","volume":"5","author":"K Jaqaman","year":"2008","journal-title":"Nat Methods"},{"key":"pcbi.1007673.ref034","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":"C Versari","year":"2017","journal-title":"J R Soc Interface"},{"key":"pcbi.1007673.ref035","doi-asserted-by":"crossref","first-page":"e0206395","DOI":"10.1371\/journal.pone.0206395","article-title":"A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking","volume":"14","author":"NE Wood","year":"2019","journal-title":"PLoS One"},{"key":"pcbi.1007673.ref036","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/nmeth895","article-title":"A comprehensive library of fluorescent transcriptional reporters for Escherichia coli","volume":"3","author":"A Zaslaver","year":"2006","journal-title":"Nat Methods"},{"key":"pcbi.1007673.ref037","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/B978-0-12-385075-1.00014-7","article-title":"Microfluidics for Synthetic Biology","author":"MS Ferry","year":"2011","journal-title":"Synthetic Biology, Part A"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007673","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,29]],"date-time":"2023-09-29T18:00:05Z","timestamp":1696010405000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007673"}},"subtitle":[],"editor":[{"given":"Anand R.","family":"Asthagiri","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,4,13]]},"references-count":37,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2020,4,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007673","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.737737372.793582045","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/720615","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,4,13]]}}}