Image analysis of Arabidopsis trichome patterning in 4D confocal datasets
In this article, we present an approach for the automated extraction of quantitative information about trichome patterning on leaves of Arabidopsis thaliana. Time series of growing rosette leaves (4D confocal datasets, 3D + time) are used for this work. At first, significant anatomical structures, i...
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| creator | Bensch, R. Ronneberger, O. Greese, B. Fleck, C. Wester, K. Hulskamp, M. Burkhardt, H. |
| description | In this article, we present an approach for the automated extraction of quantitative information about trichome patterning on leaves of Arabidopsis thaliana. Time series of growing rosette leaves (4D confocal datasets, 3D + time) are used for this work. At first, significant anatomical structures, i.e. leaf surface and midplane are extracted robustly. Using the extracted anatomical structures, a biological reference coordinate system is registered to the leaves. The performed registration allows to determine intra- as well as inter-series spatiotemporal correspondences. Trichomes are localized by first detecting candidates using Hough transform. Then, local 3D invariants are extracted and the candidates are validated using a Support Vector Machine (SVM). |
| doi_str_mv | 10.1109/ISBI.2009.5193154 |
| format | Conference Proceeding |
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Then, local 3D invariants are extracted and the candidates are validated using a Support Vector Machine (SVM).</description><subject>Anatomical structure</subject><subject>Arabidopsis trichome patterning</subject><subject>Biology</subject><subject>Computed tomography</subject><subject>Data mining</subject><subject>Image analysis</subject><subject>Optimized production technology</subject><subject>registration</subject><subject>Robustness</subject><subject>Support vector machines</subject><subject>surface extraction</subject><subject>Surface morphology</subject><subject>symmetry plane</subject><subject>trichome localization</subject><subject>X-ray imaging</subject><issn>1945-7928</issn><issn>1945-8452</issn><isbn>1424439310</isbn><isbn>9781424439317</isbn><isbn>1424439329</isbn><isbn>9781424439324</isbn><fulltext>true</fulltext><rsrctype>conference_proceeding</rsrctype><creationdate>2009</creationdate><recordtype>conference_proceeding</recordtype><sourceid>6IE</sourceid><sourceid>RIE</sourceid><recordid>eNpFkMlOwzAQhs0mUUofAHHxCySMlzj2sbQskSpxAM7VxEsxyqY4l749QVRiLqPRJ_365ifkjkHOGJiH6v2xyjmAyQtmBCvkGblhkkspjODmnCyYkUWmZcEv_gGDyxMoDdfXZJXSN8xTzhTkglRViwdPscPmmGKifaDrEevo-uH3nMZov_rW0wGnyY9d7A40dlRuqe270FtsqMMJk5_SLbkK2CS_Ou0l-Xx--ti8Zru3l2qz3mWWKzVlQUOtvUINQrlSWV5ojkYpNgu52ZkHIVBwjTVYQO39_IirmRRBeHCCiyW5_8uN3vv9MMYWx-P-VIn4ATXAT-E</recordid><startdate>200906</startdate><enddate>200906</enddate><creator>Bensch, R.</creator><creator>Ronneberger, O.</creator><creator>Greese, B.</creator><creator>Fleck, C.</creator><creator>Wester, K.</creator><creator>Hulskamp, M.</creator><creator>Burkhardt, H.</creator><general>IEEE</general><scope>6IE</scope><scope>6IL</scope><scope>CBEJK</scope><scope>RIE</scope><scope>RIL</scope></search><sort><creationdate>200906</creationdate><title>Image analysis of Arabidopsis trichome patterning in 4D confocal datasets</title><author>Bensch, R. ; Ronneberger, O. ; Greese, B. ; Fleck, C. ; Wester, K. ; Hulskamp, M. ; Burkhardt, H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c266t-f80b8e6a8036d76c2582a9661443d2442f33a328ab0c0a8ee424db143f3e0d323</frbrgroupid><rsrctype>conference_proceedings</rsrctype><prefilter>conference_proceedings</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Anatomical structure</topic><topic>Arabidopsis trichome patterning</topic><topic>Biology</topic><topic>Computed tomography</topic><topic>Data mining</topic><topic>Image analysis</topic><topic>Optimized production technology</topic><topic>registration</topic><topic>Robustness</topic><topic>Support vector machines</topic><topic>surface extraction</topic><topic>Surface morphology</topic><topic>symmetry plane</topic><topic>trichome localization</topic><topic>X-ray imaging</topic><toplevel>online_resources</toplevel><creatorcontrib>Bensch, R.</creatorcontrib><creatorcontrib>Ronneberger, O.</creatorcontrib><creatorcontrib>Greese, B.</creatorcontrib><creatorcontrib>Fleck, C.</creatorcontrib><creatorcontrib>Wester, K.</creatorcontrib><creatorcontrib>Hulskamp, M.</creatorcontrib><creatorcontrib>Burkhardt, H.</creatorcontrib><collection>IEEE Electronic Library (IEL) Conference Proceedings</collection><collection>IEEE Proceedings Order Plan All Online (POP All Online) 1998-present by volume</collection><collection>IEEE Xplore All Conference Proceedings</collection><collection>IEEE Xplore</collection><collection>IEEE Proceedings Order Plans (POP All) 1998-Present</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Bensch, R.</au><au>Ronneberger, O.</au><au>Greese, B.</au><au>Fleck, C.</au><au>Wester, K.</au><au>Hulskamp, M.</au><au>Burkhardt, H.</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>Image analysis of Arabidopsis trichome patterning in 4D confocal datasets</atitle><btitle>2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro</btitle><stitle>ISBI</stitle><date>2009-06</date><risdate>2009</risdate><spage>742</spage><epage>745</epage><pages>742-745</pages><issn>1945-7928</issn><eissn>1945-8452</eissn><isbn>1424439310</isbn><isbn>9781424439317</isbn><eisbn>1424439329</eisbn><eisbn>9781424439324</eisbn><abstract>In this article, we present an approach for the automated extraction of quantitative information about trichome patterning on leaves of Arabidopsis thaliana. 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| fulltext | fulltext_linktorsrc |
| identifier | ISSN: 1945-7928 |
| ispartof | 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009, p.742-745 |
| issn | 1945-7928 1945-8452 |
| language | eng |
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| source | IEEE Electronic Library (IEL) Conference Proceedings |
| subjects | Anatomical structure Arabidopsis trichome patterning Biology Computed tomography Data mining Image analysis Optimized production technology registration Robustness Support vector machines surface extraction Surface morphology symmetry plane trichome localization X-ray imaging |
| title | Image analysis of Arabidopsis trichome patterning in 4D confocal datasets |
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