{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T02:34:54Z","timestamp":1722738894474},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1201,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Advances in high-resolution microscopy have recently made possible the analysis of gene expression at the level of individual cells. The fixed lineage of cells in the adult worm Caenorhabditis elegans makes this organism an ideal model for studying complex biological processes like development and aging. However, annotating individual cells in images of adult C.elegans typically requires expertise and significant manual effort. Automation of this task is therefore critical to enabling high-resolution studies of a large number of genes.<\/jats:p>\n               <jats:p>Results: In this article, we describe an automated method for annotating a subset of 154 cells (including various muscle, intestinal and hypodermal cells) in high-resolution images of adult C.elegans. We formulate the task of labeling cells within an image as a combinatorial optimization problem, where the goal is to minimize a scoring function that compares cells in a test input image with cells from a training atlas of manually annotated worms according to various spatial and morphological characteristics. We propose an approach for solving this problem based on reduction to minimum-cost maximum-flow and apply a cross-entropy\u2013based learning algorithm to tune the weights of our scoring function. We achieve 84% median accuracy across a set of 154 cell labels in this highly variable system. These results demonstrate the feasibility of the automatic annotation of microscopy-based images in adult C.elegans.<\/jats:p>\n               <jats:p>Contact: saerni@cs.stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt223","type":"journal-article","created":{"date-parts":[[2013,6,27]],"date-time":"2013-06-27T05:33:26Z","timestamp":1372311206000},"page":"i18-i26","source":"Crossref","is-referenced-by-count":10,"title":["Automated cellular annotation for high-resolution images of adult <i>Caenorhabditis elegans<\/i>"],"prefix":"10.1093","volume":"29","author":[{"given":"Sarah J.","family":"Aerni","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuong B.","family":"Do","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel S.","family":"Gross","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andy","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephen D.","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuhui","family":"Long","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanchuan","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart S.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serafim","family":"Batzoglou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,6,19]]},"reference":[{"key":"2023062614325938100_btt223-B1","article-title":"Handbook of C. elegans Anatomy","volume-title":"WormAtlas.org","author":"Altun","year":"2008"},{"key":"2023062614325938100_btt223-B2","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1073\/pnas.0511111103","article-title":"Automated cell lineage tracing in Caenorhabditis elegans","volume":"103","author":"Bao","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023062614325938100_btt223-B3","first-page":"1","article-title":"Learning graph matching","volume":"0","author":"Caetano","year":"2007","journal-title":"IEEE 11th International Conference on Computer Vision 2007"},{"key":"2023062614325938100_btt223-B4","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1109\/TPAMI.2009.28","article-title":"Learning Graph Matching","volume":"31","author":"Caetano","year":"2009","journal-title":"IEEE Trans. Pattern Anal. Mach. Intelligence"},{"key":"2023062614325938100_btt223-B5","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s10479-005-5724-z","article-title":"A Tutorial on the cross-entropy method","volume":"134","author":"de Boer","year":"2005","journal-title":"Ann. Oper. Res."},{"key":"2023062614325938100_btt223-B6","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.entcs.2011.06.003","article-title":"LEMON\u2013an open source C++ graph template library","volume":"264","author":"Dezs","year":"2011","journal-title":"Electron Notes Theor Comput Sci"},{"key":"2023062614325938100_btt223-B7","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1145\/321694.321699","article-title":"Theoretical improvements in algorithmic efficiency for network flow problems","volume":"19","author":"Edmonds","year":"1972","journal-title":"J. ACM"},{"key":"2023062614325938100_btt223-B8","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.cell.2008.01.053","article-title":"A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm","volume":"133","author":"Fowlkes","year":"2008","journal-title":"Cell"},{"key":"2023062614325938100_btt223-B9","doi-asserted-by":"crossref","first-page":"R124","DOI":"10.1186\/gb-2006-7-12-r124","article-title":"Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics","volume":"7","author":"Ker\u00e4nen","year":"2006","journal-title":"Genome Biol."},{"key":"2023062614325938100_btt223-B10","article-title":"An experimental study of minimum cost flow algorithm","volume-title":"8th International Conference on Applied Informatics. Eger, Hungary, 2010","author":"Kir\u00e1ly","year":"2010"},{"key":"2023062614325938100_btt223-B11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF01585755","article-title":"A strongly polynomial algorithm for the transportation problem","volume":"68","author":"Kleinschmidt","year":"1995","journal-title":"Math. Program."},{"key":"2023062614325938100_btt223-B12","article-title":"Direct optimization of ranking measures","author":"Le","year":"2007","journal-title":"Mach. Learn."},{"key":"2023062614325938100_btt223-B13","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2121-8-40","article-title":"3D cell nuclei segmentation based on gradient flow tracking","volume":"8","author":"Li","year":"2007","journal-title":"BMC Cell Biol."},{"key":"2023062614325938100_btt223-B14","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.cell.2009.08.044","article-title":"Analysis of cell fate from single-cell gene expression profiles in C. elegans","volume":"139","author":"Liu","year":"2009","journal-title":"Cell"},{"key":"2023062614325938100_btt223-B15","first-page":"128","article-title":"Automatic Recognition of Cells (ARC) for 3D images of C. elegans","volume-title":"Research in Computational Molecular Biology, Volume 4955 of Lecture Notes in Computer Science","author":"Long","year":"2008"},{"key":"2023062614325938100_btt223-B16","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/nmeth.1366","article-title":"A 3D digital atlas of C. elegans and its application to single-cell analyses","volume":"6","author":"Long","year":"2009","journal-title":"Nat. Meth."},{"key":"2023062614325938100_btt223-B17","doi-asserted-by":"crossref","first-page":"R123","DOI":"10.1186\/gb-2006-7-12-r123","article-title":"Three-dimensiondal morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline","volume":"7","author":"Luengo Hendriks","year":"2006","journal-title":"Genome Biol."},{"key":"2023062614325938100_btt223-B18","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/nmeth.1228","article-title":"Automated analysis of embryonic gene expression with cellular resolution in C. elegans","volume":"5","author":"Murray","year":"2008","journal-title":"Nat. Methods."},{"key":"2023062614325938100_btt223-B19","volume-title":"Exponential Family Graph Matching and Ranking","author":"Petterson","year":"2009"},{"key":"2023062614325938100_btt223-B20","doi-asserted-by":"crossref","first-page":"2895","DOI":"10.1093\/bioinformatics\/btr480","article-title":"Simultaneous recognition and segmentation of cells: application in C. elegans","volume":"27","author":"Qu","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062614325938100_btt223-B21","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-4321-0","volume-title":"The Cross-Entropy Method: A Unified Approach to Combinatorial Optimization, Monte-Carlo Simulation and Machine Learning","author":"Rubinstein","year":"2004"},{"key":"2023062614325938100_btt223-B22","article-title":"Learning structured prediction models: a large margin approach","author":"Taskar","year":"2004"},{"key":"2023062614325938100_btt223-B23","doi-asserted-by":"crossref","DOI":"10.1145\/1102351.1102464","article-title":"Learning structured prediction models: a large margin approach","volume-title":"Proceedings of the 22nd international conference on Machine learning","author":"Taskar","year":"2005"},{"key":"2023062614325938100_btt223-B24","first-page":"1453","article-title":"Large margin methods for structured and interdependent output variables","volume":"6","author":"Tsochantaridis","year":"2005","journal-title":"J. Mach. Learning Res."},{"key":"2023062614325938100_btt223-B25","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.ydbio.2007.11.015","article-title":"Comparative analysis of embryonic cell lineage between Caenorhabditis briggsae and Caenorhabditis elegans","volume":"314","author":"Zhao","year":"2008","journal-title":"Dev. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/13\/i18\/50703439\/bioinformatics_29_13_i18.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/13\/i18\/50703439\/bioinformatics_29_13_i18.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T15:33:57Z","timestamp":1687793637000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/13\/i18\/192623"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,19]]},"references-count":25,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt223","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2013,7]]},"published":{"date-parts":[[2013,6,19]]}}}