{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T00:36:28Z","timestamp":1753922188810,"version":"3.37.3"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T00:00:00Z","timestamp":1525824000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["MOST 104-2628-E-006-004-MY3"],"award-info":[{"award-number":["MOST 104-2628-E-006-004-MY3"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2166-6","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T13:57:04Z","timestamp":1525874224000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["An automatic method to calculate heart rate from zebrafish larval cardiac videos"],"prefix":"10.1186","volume":"19","author":[{"given":"Chia-Pin","family":"Kang","sequence":"first","affiliation":[]},{"given":"Hung-Chi","family":"Tu","sequence":"additional","affiliation":[]},{"given":"Tzu-Fun","family":"Fu","sequence":"additional","affiliation":[]},{"given":"Jhe-Ming","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Po-Hsun","family":"Chu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9119-4231","authenticated-orcid":false,"given":"Darby Tien-Hao","family":"Chang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,5,9]]},"reference":[{"issue":"1","key":"2166_CR1","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.ccell.2008.10.001","volume":"21","author":"SL Sadowski","year":"2009","unstructured":"Sadowski SL. Congenital cardiac disease in the newborn infant: past, present, and future. Crit Care Nurs Clin North Am. 2009;21(1):37\u201348.","journal-title":"Crit Care Nurs Clin North Am"},{"key":"2166_CR2","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/0168-9525(89)90103-0","volume":"5","author":"CB Kimmel","year":"1989","unstructured":"Kimmel CB. Genetics and early development of zebrafish. Trends Genet. 1989;5:283\u20138.","journal-title":"Trends Genet"},{"issue":"5","key":"2166_CR3","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nrg2091","volume":"8","author":"GJ Lieschke","year":"2007","unstructured":"Lieschke GJ, Currie PD. Animal models of human disease: zebrafish swim into view. Nat Rev Genet. 2007;8(5):353\u201367.","journal-title":"Nat Rev Genet"},{"issue":"6","key":"2166_CR4","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1161\/CIRCRESAHA.111.246504","volume":"110","author":"J Liu","year":"2012","unstructured":"Liu J, Stainier DY. Zebrafish in the study of early cardiac development. Circ Res. 2012;110(6):870\u20134.","journal-title":"Circ Res"},{"issue":"5\u20136","key":"2166_CR5","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1007\/BF00755773","volume":"10","author":"V Gervais-Pingot","year":"1994","unstructured":"Gervais-Pingot V, Legrand J, Nasr G, Schoevaert D. In vitro quantification by image analysis of inotropic and chronotropic effects of drugs on cultures of cardiac myocytes. Cell Biol Toxicol. 1994;10(5\u20136):297\u2013300.","journal-title":"Cell Biol Toxicol"},{"issue":"1","key":"2166_CR6","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1242\/dev.123.1.285","volume":"123","author":"D Stainier","year":"1996","unstructured":"Stainier D, Fouquet B, Chen J-N, Warren KS, Weinstein BM, Meiler SE, Mohideen M, Neuhauss S, Solnica-Krezel L, Schier AF. Mutations affecting the formation and function of the cardiovascular system in the zebrafish embryo. Development. 1996;123(1):285\u201392.","journal-title":"Development"},{"issue":"8","key":"2166_CR7","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1242\/jeb.00249","volume":"206","author":"T Schwerte","year":"2003","unstructured":"Schwerte T, \u00dcberbacher D, Pelster B. Non-invasive imaging of blood cell concentration and blood distribution in zebrafish Danio rerio incubated in hypoxic conditions in vivo. J Exp Biol. 2003;206(8):1299\u2013307.","journal-title":"J Exp Biol"},{"key":"2166_CR8","first-page":"3615","volume-title":"Engineering in medicine and biology society, 2004 IEMBS'04 26th annual international conference of the IEEE","author":"A Forouhar","year":"2004","unstructured":"Forouhar A, Hove J, Calvert C, Flores J, Jadvar H, Gharib M. Electrocardiographic characterization of embryonic zebrafish. In: Engineering in medicine and biology society, 2004 IEMBS'04 26th annual international conference of the IEEE; 2004. p. 3615\u20137."},{"issue":"5","key":"2166_CR9","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/nchembio732","volume":"1","author":"CG Burns","year":"2005","unstructured":"Burns CG, Milan DJ, Grande EJ, Rottbauer W, MacRae CA, Fishman MC. High-throughput assay for small molecules that modulate zebrafish embryonic heart rate. Nat Chem Biol. 2005;1(5):263.","journal-title":"Nat Chem Biol"},{"issue":"2","key":"2166_CR10","doi-asserted-by":"publisher","first-page":"101","DOI":"10.2144\/000113078","volume":"46","author":"M Fink","year":"2009","unstructured":"Fink M, Callol-Massot C, Chu A, Ruiz-Lozano P, Belmonte JCI, Giles W, Bodmer R, Ocorr K. A new method for detection and quantification of heartbeat parameters in Drosophila, zebrafish, and embryonic mouse hearts. BioTechniques. 2009;46(2):101.","journal-title":"BioTechniques"},{"key":"2166_CR11","doi-asserted-by":"crossref","unstructured":"Ocorr K, Fink M, Cammarato A, Bernstein SI, Bodmer R: Semi-automated optical heartbeat analysis of small hearts. Journal of visualized experiments: JoVE 2009;(31):e1435.","DOI":"10.3791\/1435"},{"key":"2166_CR12","doi-asserted-by":"publisher","first-page":"1549","DOI":"10.1109\/ISBI.2011.5872696","volume-title":"Biomedical imaging: from Nano to macro, 2011 IEEE international symposium on","author":"J Ohn","year":"2011","unstructured":"Ohn J, Liebling M. In vivo, high-throughput imaging for functional characterization of the embryonic zebrafish heart. In: Biomedical imaging: from Nano to macro, 2011 IEEE international symposium on; 2011. p. 1549\u201352. IEEE."},{"issue":"19","key":"2166_CR13","doi-asserted-by":"publisher","first-page":"11302","DOI":"10.1021\/es403360y","volume":"47","author":"KL Yozzo","year":"2013","unstructured":"Yozzo KL, Isales GM, Raftery TD, Volz DC. High-content screening assay for identification of chemicals impacting cardiovascular function in zebrafish embryos. Environmental science & technology. 2013;47(19):11302\u201310.","journal-title":"Environmental science & technology"},{"issue":"1","key":"2166_CR14","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1472-6750-9-11","volume":"9","author":"PK Chan","year":"2009","unstructured":"Chan PK, Lin CC, Cheng SH. Noninvasive technique for measurement of heartbeat regularity in zebrafish (Danio rerio) embryos. BMC Biotechnol. 2009;9(1):11.","journal-title":"BMC Biotechnol"},{"key":"2166_CR15","doi-asserted-by":"publisher","first-page":"4898","DOI":"10.1038\/srep04898","volume":"4","author":"E De Luca","year":"2014","unstructured":"De Luca E, Zaccaria GM, Hadhoud M, Rizzo G, Ponzini R, Morbiducci U, Santoro MM. ZebraBeat: a flexible platform for the analysis of the cardiac rate in zebrafish embryos. Sci Rep. 2014;4:4898.","journal-title":"Sci Rep"},{"issue":"4","key":"2166_CR16","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1089\/zeb.2014.1002","volume":"11","author":"C Pylatiuk","year":"2014","unstructured":"Pylatiuk C, Sanchez D, Mikut R, Alshut R, Reischl M, Hirth S, Rottbauer W, Just S. Automatic zebrafish heartbeat detection and analysis for zebrafish embryos. Zebrafish. 2014;11(4):379\u201383.","journal-title":"Zebrafish"},{"key":"2166_CR17","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1109\/IPTA.2015.7367171","volume-title":"Image processing theory, tools and applications (IPTA), 2015 international conference on","author":"E Puybareau","year":"2015","unstructured":"Puybareau E, Talbot H, L\u00e9onard M. Automated heart rate estimation in fish embryo. In: Image processing theory, tools and applications (IPTA), 2015 international conference on; 2015. p. 379\u201384. IEEE."},{"issue":"16\u201318","key":"2166_CR18","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1080\/15287394.2017.1352212","volume":"80","author":"R Nepstad","year":"2017","unstructured":"Nepstad R, Davies E, Altin D, Nordtug T, Hansen BH. Automatic determination of heart rates from microscopy videos of early life stages of fish. J Toxic Environ Health A. 2017;80(16\u201318):932\u201340.","journal-title":"J Toxic Environ Health A"},{"key":"2166_CR19","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.compbiomed.2016.12.007","volume":"81","author":"\u00c9 Puybareau","year":"2017","unstructured":"Puybareau \u00c9, Genest D, Barbeau E, L\u00e9onard M, Talbot H. An automated assay for the assessment of cardiac arrest in fish embryo. Comput Biol Med. 2017;81:32\u201344.","journal-title":"Comput Biol Med"},{"key":"2166_CR20","doi-asserted-by":"crossref","unstructured":"Krishna S, Chatti K, Galigekere RR: Automatic and robust estimation of heart rate in zebrafish larvae. IEEE transactions on automation science and engineering 2017.","DOI":"10.1109\/TASE.2017.2705240"},{"issue":"1","key":"2166_CR21","doi-asserted-by":"publisher","first-page":"e29740","DOI":"10.1371\/journal.pone.0029740","volume":"7","author":"C Kanan","year":"2012","unstructured":"Kanan C, Cottrell GW. Color-to-grayscale: does the method matter in image recognition? PLoS One. 2012;7(1):e29740.","journal-title":"PLoS One"},{"key":"2166_CR22","unstructured":"Jack K. Video Demystified-forth edition. Newnes: Elsevier; 2007."},{"key":"2166_CR23","first-page":"857","volume-title":"Digital signal processing proceedings, 1997 DSP 97, 1997 13th international conference on","author":"B Cramariuc","year":"1997","unstructured":"Cramariuc B, Gabbouj M, Astola J. Clustering based region growing algorithm for color image segmentation. In: Digital signal processing proceedings, 1997 DSP 97, 1997 13th international conference on; 1997. p. 857\u201360. IEEE."},{"issue":"7","key":"2166_CR24","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1016\/S0031-3203(96)00147-1","volume":"30","author":"A Tremeau","year":"1997","unstructured":"Tremeau A, Borel N. A region growing and merging algorithm to color segmentation. Pattern Recogn. 1997;30(7):1191\u2013203.","journal-title":"Pattern Recogn"},{"key":"2166_CR25","first-page":"163","volume-title":"International conference on information technology: coding and computing (ITCC'05)-volume II","author":"ME Celebi","year":"2005","unstructured":"Celebi ME, Aslandogan YA, Bergstresser PR. Mining biomedical images with density-based clustering. In: International conference on information technology: coding and computing (ITCC'05)-volume II; 2005. p. 163\u20138. IEEE."},{"key":"2166_CR26","first-page":"226","volume-title":"Kdd","author":"M Ester","year":"1996","unstructured":"Ester M, Kriegel H-P, Sander J, Xu X. A density-based algorithm for discovering clusters in large spatial databases with noise. In: Kdd; 1996. p. 226\u201331."},{"key":"2166_CR27","doi-asserted-by":"crossref","unstructured":"Hartigan JA, Wong MA. Algorithm AS 136: a k-means clustering algorithm. Appl Stat. 1979:100\u20138.","DOI":"10.2307\/2346830"},{"key":"2166_CR28","doi-asserted-by":"crossref","unstructured":"Huang NE, Shen SS: Hilbert-Huang transform and its applications, vol. 5. Singapore: World Scientific; 2005.","DOI":"10.1142\/9789812703347"},{"key":"2166_CR29","unstructured":"lun Chou Y: Statistical Analysis. Mishawaka: Holt International 1975."},{"issue":"3","key":"2166_CR30","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1007\/s10462-015-9447-5","volume":"45","author":"MD Awheda","year":"2016","unstructured":"Awheda MD, Schwartz HM. Exponential moving average based multiagent reinforcement learning algorithms. Artif Intell Rev. 2016;45(3):299\u2013332.","journal-title":"Artif Intell Rev"},{"issue":"4","key":"2166_CR31","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.jalgor.2009.04.003","volume":"64","author":"A Burkov","year":"2009","unstructured":"Burkov A, Chaib-draa B. Effective learning in the presence of adaptive counterparts. Journal of Algorithms. 2009;64(4):127\u201338.","journal-title":"Journal of Algorithms"},{"key":"2166_CR32","unstructured":"Westerfield M: The zebrafish book: a guide for the laboratory use of zebrafish (Brachydanio rerio). Eugene: University of Oregon Press; 1995."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2166-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2166-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2166-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,22]],"date-time":"2022-08-22T23:34:40Z","timestamp":1661211280000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2166-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,9]]},"references-count":32,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2166"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2166-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2018,5,9]]},"assertion":[{"value":"7 February 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 April 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 May 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"This work prepared 32 zebrafish (Danio rerio, AB strain) larvae that were treated with 0.003% 1-phenyl 2-thiourea (PTU) at 24-h post-fertilization (hpf) to prevent melanogenesis. At 3 dpf, the zebrafish larvae were placed on concavity slides and mounted in 3% methylcellulose without anesthesia for recording. The zebrafish maintenance followed the standard husbandry procedures []. All the zebrafish experiments were approved by the Affidavit of Approval of Animal Use Protocol of National Cheng Kung University (IACUC Approval NO. 96062). The larval cardiac videos were recorded by Leica Z16 APO microscope equipped with Canon EOS 550D megapixel digital single-lens reflex camera. The videos used for analysis were recorded in 60 frames per second (fps) with a resolution of 1280 X 720.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"169"}}