{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,20]],"date-time":"2023-08-20T13:31:37Z","timestamp":1692538297585},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The emergence of new microscopy techniques in combination with the increasing resource of bioimaging data has given fresh impetus to utilizing image processing methods for studying biological processes. Cell tracking studies in particular, which are important for a wide range of biological processes such as embryonic development or the immune system, have recently become the focus of attention. These studies typically produce large volumes of data that are hard to investigate manually and therefore call for an automated approach. Due to the large variety of biological cells and the inhomogeneity of applications, however, there exists no widely accepted method or system for cell tracking until today. In this article, we present our publicly available DYNAMIK software environment that allows users to compute a suit of cell features and plot the trajectory of multiple cells over a sequence of frames. Using chemotaxis and Ras pathways as an example, we show how users can employ our software to compute statistics about cell motility and other cell information, and how to evaluate their test series based on the data computed. We see that DYNAMIK's segmentation and tracking compares favorably with the output produced by other software packages.<\/jats:p>\n               <jats:p>Contact: \u00a0jaeger@picb.ac.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp405","type":"journal-article","created":{"date-parts":[[2009,7,5]],"date-time":"2009-07-05T00:13:38Z","timestamp":1246752818000},"page":"2383-2388","source":"Crossref","is-referenced-by-count":8,"title":["DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways"],"prefix":"10.1093","volume":"25","author":[{"given":"Stefan","family":"Jaeger","sequence":"first","affiliation":[{"name":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"}]},{"given":"Qingfeng","family":"Song","sequence":"additional","affiliation":[{"name":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"}]},{"given":"Su-Shing","family":"Chen","sequence":"additional","affiliation":[{"name":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"}]}],"member":"286","published-online":{"date-parts":[[2009,7,4]]},"reference":[{"key":"2023013112115621500_B1","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1242\/jcs.101.2.415","article-title":"Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charge-coupled device camera. low-density lipoprotein and influenza virus receptor mobility at 4 degrees C","volume":"101","author":"Anderson","year":"1992","journal-title":"J. Cell Sci."},{"key":"2023013112115621500_B2","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1016\/S0006-3495(00)76363-6","article-title":"Multiple-particle tracking measurements of heterogeneities in solutions of actin filaments and actin bundles","volume":"79","author":"Apgar","year":"2000","journal-title":"Biophys. J."},{"key":"2023013112115621500_B3","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1145\/235815.235821","article-title":"The Quickhull algorithm for convex hulls","volume":"22","author":"Barber","year":"1996","journal-title":"Trans. Math. Software"},{"key":"2023013112115621500_B4","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1111\/j.1365-2818.2007.01847.x","article-title":"The large-scale digital cell analysis system: an open system for nonperturbing live cell imaging","volume":"228","author":"Davis","year":"2007","journal-title":"J. Microscopy"},{"key":"2023013112115621500_B5","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1007\/BF00133570","article-title":"Snakes: active contour models","volume":"1","author":"Kass","year":"1987","journal-title":"Int. J. Comp. Vision"},{"key":"2023013112115621500_B6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/B978-012077790-7\/50012-6","article-title":"Deformable models","volume-title":"Handbook of Medical Imaging","author":"McInerney","year":"2000"},{"key":"2023013112115621500_B7","first-page":"267","article-title":"Tracking movement in cell biology","volume":"95","author":"Miura","year":"2005","journal-title":"Adv. Biochem. Eng. Biotechnol."},{"key":"2023013112115621500_B8","doi-asserted-by":"crossref","DOI":"10.1186\/1748-7188-4-10","article-title":"Tracking cells in life cell imaging videos using topological alignments","author":"Mosig","year":"2009","journal-title":"Algorithms Mol. Biol."},{"key":"2023013112115621500_B9","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1109\/TIP.2003.819858","article-title":"Level set analysis for leukocyte detection and tracking","volume":"13","author":"Mukherjee","year":"2004","journal-title":"IEEE Trans. Med. Imag."},{"key":"2023013112115621500_B10","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1007\/11864349_84","article-title":"Robust tracking of migrating cells using four-color level set segmentation","volume":"4179","author":"Nath","year":"2006","journal-title":"Advanced Concepts for Intelligent Vision Systems (ACIVS)"},{"key":"2023013112115621500_B11","first-page":"483","article-title":"Moving object segmentation using the flux tensor for biological video microscopy","volume":"4810","author":"Palaniappan","year":"2007","journal-title":"PCM2007 LNCS"},{"key":"2023013112115621500_B12","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/btn247","article-title":"CellTrack: an open-source software for cell tracking and motility analysis","volume":"24","author":"Sacan","year":"2008","journal-title":"Bioinformatics"},{"key":"2023013112115621500_B13","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1083\/jcb.200406177","article-title":"Localized Ras signaling at the leading edge regulates PI3K, cell polarity, and directional cell movement","volume":"167","author":"Sasaki","year":"2004","journal-title":"J. Cell Biol."},{"key":"2023013112115621500_B14","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/S0006-3495(97)78139-6","article-title":"Single-molecule microscopy on model membranes reveals anomalous diffusion","volume":"73","author":"Sch\u00fctz","year":"1997","journal-title":"Biophys. J."},{"key":"2023013112115621500_B15","volume-title":"Level Sets Methods and Fast Searching Methods","author":"Sethian","year":"1999"},{"key":"2023013112115621500_B16","first-page":"25","article-title":"Two- and three-dimensional computer systems for analyzing how animal cells crawl","volume-title":"Motion Analysis of Living Cells","author":"Soll","year":"1998"},{"key":"2023013112115621500_B17","volume-title":"Motion Analysis of Living Cells","author":"Soll","year":"1998"},{"key":"2023013112115621500_B18","doi-asserted-by":"crossref","first-page":"3162","DOI":"10.1016\/S0006-3495(02)75319-8","article-title":"Micromechanical mapping of live cells by multiple particle tracking microrheology","volume":"83","author":"Tseng","year":"2002","journal-title":"Biophys. J."},{"key":"2023013112115621500_B19","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1016\/S0006-3495(03)74564-0","article-title":"Recovery, visualization, and analysis of Actin and Tubulin polymer flow in live cells: a fluorescent speckle microscopy study","volume":"85","author":"Vallotton","year":"2003","journal-title":"Biophys. J."},{"key":"2023013112115621500_B20","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1109\/TMI.2002.806292","article-title":"Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours","volume":"21","author":"Zimmer","year":"2002","journal-title":"IEEE Trans. Med. Imag."},{"key":"2023013112115621500_B21","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1109\/MSP.2006.1628878","article-title":"On the digital trail of mobile cells","volume":"23","author":"Zimmer","year":"2006","journal-title":"Signal Process. Mag."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/18\/2383\/48994407\/bioinformatics_25_18_2383.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/18\/2383\/48994407\/bioinformatics_25_18_2383.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:35:11Z","timestamp":1675200911000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/18\/2383\/196420"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,7,4]]},"references-count":21,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2009,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp405","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,9,15]]},"published":{"date-parts":[[2009,7,4]]}}}