{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T09:30:59Z","timestamp":1777714259358,"version":"3.51.4"},"reference-count":9,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-148","type":"journal-article","created":{"date-parts":[[2011,5,12]],"date-time":"2011-05-12T19:16:32Z","timestamp":1305227792000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":240,"title":["HTPheno: An image analysis pipeline for high-throughput plant phenotyping"],"prefix":"10.1186","volume":"12","author":[{"given":"Anja","family":"Hartmann","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"Czauderna","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roberto","family":"Hoffmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nils","family":"Stein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Falk","family":"Schreiber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,5,12]]},"reference":[{"key":"4527_CR1","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1111\/j.1469-8137.2005.01609.x","volume":"169","author":"C Granier","year":"2006","unstructured":"Granier C, Aguirrezabal L, Chenu L, Cookson SJ, Dauzat M, Hamard P, Thioux JJ, Rolland G, Bouchier-Combaud S, Lebaudy A, Muller B, Simonneau T, Tardieu F: PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in Arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytologist 2006, 169: 623\u2013635. 10.1111\/j.1469-8137.2005.01609.x","journal-title":"New Phytologist"},{"key":"4527_CR2","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1111\/j.1469-8137.2007.02002.x","volume":"174","author":"A Walter","year":"2007","unstructured":"Walter A, Scharr H, Gilmer F, Zierer R, Nagel KA, Ernst M, Wiese A, Virnich O, Christ MM, Uhlig B, Juenger S, Schurr U: Dynamics of seedling growth acclimation towards altered light conditions can be quantified via GROWSCREEN: a setup and procedure designed for rapid optical phenotyping of different plant species. New Phytologist 2007, 174: 447\u2013455. 10.1111\/j.1469-8137.2007.02002.x","journal-title":"New Phytologist"},{"key":"4527_CR3","first-page":"753","volume":"5","author":"C Reuzeau","year":"2005","unstructured":"Reuzeau C, Pen J, Frankard V, de Wolf J, Peerbolte R, Broekaert W, van Camp W: TraitMill\u2122: a Discovery Engine for Identifying Yield-enhancement Genes in Cereals. 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Journal of Information Science and Engineering 2001, 17: 713\u2013727.","journal-title":"Journal of Information Science and Engineering"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-148.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T13:59:13Z","timestamp":1630504753000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-148"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,12]]},"references-count":9,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4527"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-148","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,12]]},"assertion":[{"value":"29 October 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2011","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2011","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"148"}}