RootScan: Software for high-throughput analysis of root anatomical traits
Background and aims RootScan is a program for semi-automated image analysis of anatomical traits in root cross-sections. Methods RootScan uses pixel thresholds to separate the cross-section from its background and to divide it into tissue regions. Area measurements and object counts are performed wi...
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| Veröffentlicht in: | Plant and soil 2012-08, Vol.357 (1-2), p.189-203 |
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| creator | Burton, Amy L. Williams, Michael Lynch, Jonathan P. Brown, Kathleen M. |
| description | Background and aims RootScan is a program for semi-automated image analysis of anatomical traits in root cross-sections. Methods RootScan uses pixel thresholds to separate the cross-section from its background and to divide it into tissue regions. Area measurements and object counts are performed within various regions of interest. A graphical user interface permits the user to see which regions are selected, to edit those selections, and to rate and comment on the data. The structure of the program allows for organized workflow and increased data collection efficiency. Results The program collects data on more than 20 variables per image including areas of the cross-section, stele, cortex, aerenchyma lacunae, xylem vessels, and counts of cortical cells and cell files. An increased rate of data collection allows collection of four times more variables in less time than is possible with current methods. Correlation analysis shows that RootScan data is equal or greater in accuracy than data collected with Photoshop. Conclusions Compared with currently available tools, this software offers considerable improvements in the amount and quality of data, ease of use, and time needed for data collection. RootScan permits phenotypic scoring of physiologically and agronomically important traits on a large number of genotypes. |
| doi_str_mv | 10.1007/s11104-012-1138-2 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_1032892240</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A362726738</galeid><jstor_id>24370309</jstor_id><sourcerecordid>A362726738</sourcerecordid><originalsourceid>FETCH-LOGICAL-c506t-9a4acbe06f6cd34a2840127e60b1d903e77234bf3a2a4e31dad4a3e878442d9b3</originalsourceid><addsrcrecordid>eNp1kV1rFDEUhoNYcK3-AC-EARG8ST352GTGu1KqLRSEfoB34Wwm2c0yO1mTDNJ_b4YpVgTJRcjJ876c9xxC3jE4YwD6c2aMgaTAOGVMtJS_ICu21oKuQaiXZAUgOAXd_XhFXue8h_nN1Ipc38ZY7iyOX5q76MsvTK7xMTW7sN3Rsktx2u6OU2lwxOExh9xE36QqmQslHoLFoSkJQ8lvyInHIbu3T_cpefh6eX9xRW--f7u-OL-hdg2q0A4l2o0D5ZXthUTeytq0dgo2rO9AOK25kBsvkKN0gvXYSxSu1a2UvO824pR8WnyPKf6cXC7mELJ1w4Cji1M2rCZrO84lVPTDP-g-TqkmmSmulOYKVKXOFmqLgzNh9LEGsvX0ruaLo_Oh1s-F4pXXoq0Ctghsijkn580xhQOmx-pq5m2YZRumBjPzNgyvmo9PrWCuM_MJRxvyHyFXrONSy8rxhcv1a9y69HfL_zd_v4j2ucT0bCqFBgGd-A1i06HK</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1026672606</pqid></control><display><type>article</type><title>RootScan: Software for high-throughput analysis of root anatomical traits</title><source>JSTOR Archive Collection A-Z Listing</source><source>SpringerLink Journals - AutoHoldings</source><creator>Burton, Amy L. ; Williams, Michael ; Lynch, Jonathan P. ; Brown, Kathleen M.</creator><creatorcontrib>Burton, Amy L. ; Williams, Michael ; Lynch, Jonathan P. ; Brown, Kathleen M.</creatorcontrib><description>Background and aims RootScan is a program for semi-automated image analysis of anatomical traits in root cross-sections. Methods RootScan uses pixel thresholds to separate the cross-section from its background and to divide it into tissue regions. Area measurements and object counts are performed within various regions of interest. A graphical user interface permits the user to see which regions are selected, to edit those selections, and to rate and comment on the data. The structure of the program allows for organized workflow and increased data collection efficiency. Results The program collects data on more than 20 variables per image including areas of the cross-section, stele, cortex, aerenchyma lacunae, xylem vessels, and counts of cortical cells and cell files. An increased rate of data collection allows collection of four times more variables in less time than is possible with current methods. Correlation analysis shows that RootScan data is equal or greater in accuracy than data collected with Photoshop. Conclusions Compared with currently available tools, this software offers considerable improvements in the amount and quality of data, ease of use, and time needed for data collection. RootScan permits phenotypic scoring of physiologically and agronomically important traits on a large number of genotypes.</description><identifier>ISSN: 0032-079X</identifier><identifier>EISSN: 1573-5036</identifier><identifier>DOI: 10.1007/s11104-012-1138-2</identifier><identifier>CODEN: PLSOA2</identifier><language>eng</language><publisher>Dordrecht: Springer</publisher><subject>Agronomy ; Agronomy. Soil science and plant productions ; Animal, plant and microbial ecology ; Biological and medical sciences ; Biomedical and Life Sciences ; Corn ; Correlation analysis ; Cross-sections ; Data collection ; Ecology ; Fundamental and applied biological sciences. Psychology ; General agronomy. Plant production ; Genotype & phenotype ; Genotypes ; Image analysis ; Image contrast ; Life Sciences ; Phenotypic traits ; Pixels ; Plant Physiology ; Plant roots ; Plant Sciences ; Plants ; Regular Article ; Root stele ; Software ; Soil Science & Conservation ; Soil-plant relationships. Soil fertility ; Soil-plant relationships. Soil fertility. Fertilization. Amendments ; Xylem vessels</subject><ispartof>Plant and soil, 2012-08, Vol.357 (1-2), p.189-203</ispartof><rights>Springer Science+Business Media B.V. 2012</rights><rights>2015 INIST-CNRS</rights><rights>COPYRIGHT 2012 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c506t-9a4acbe06f6cd34a2840127e60b1d903e77234bf3a2a4e31dad4a3e878442d9b3</citedby><cites>FETCH-LOGICAL-c506t-9a4acbe06f6cd34a2840127e60b1d903e77234bf3a2a4e31dad4a3e878442d9b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/24370309$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/24370309$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,27924,27925,41488,42557,51319,58017,58250</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26192474$$DView record in Pascal Francis$$Hfree_for_read</backlink></links><search><creatorcontrib>Burton, Amy L.</creatorcontrib><creatorcontrib>Williams, Michael</creatorcontrib><creatorcontrib>Lynch, Jonathan P.</creatorcontrib><creatorcontrib>Brown, Kathleen M.</creatorcontrib><title>RootScan: Software for high-throughput analysis of root anatomical traits</title><title>Plant and soil</title><addtitle>Plant Soil</addtitle><description>Background and aims RootScan is a program for semi-automated image analysis of anatomical traits in root cross-sections. Methods RootScan uses pixel thresholds to separate the cross-section from its background and to divide it into tissue regions. Area measurements and object counts are performed within various regions of interest. A graphical user interface permits the user to see which regions are selected, to edit those selections, and to rate and comment on the data. The structure of the program allows for organized workflow and increased data collection efficiency. Results The program collects data on more than 20 variables per image including areas of the cross-section, stele, cortex, aerenchyma lacunae, xylem vessels, and counts of cortical cells and cell files. An increased rate of data collection allows collection of four times more variables in less time than is possible with current methods. Correlation analysis shows that RootScan data is equal or greater in accuracy than data collected with Photoshop. Conclusions Compared with currently available tools, this software offers considerable improvements in the amount and quality of data, ease of use, and time needed for data collection. RootScan permits phenotypic scoring of physiologically and agronomically important traits on a large number of genotypes.</description><subject>Agronomy</subject><subject>Agronomy. Soil science and plant productions</subject><subject>Animal, plant and microbial ecology</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Corn</subject><subject>Correlation analysis</subject><subject>Cross-sections</subject><subject>Data collection</subject><subject>Ecology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General agronomy. Plant production</subject><subject>Genotype & phenotype</subject><subject>Genotypes</subject><subject>Image analysis</subject><subject>Image contrast</subject><subject>Life Sciences</subject><subject>Phenotypic traits</subject><subject>Pixels</subject><subject>Plant Physiology</subject><subject>Plant roots</subject><subject>Plant Sciences</subject><subject>Plants</subject><subject>Regular Article</subject><subject>Root stele</subject><subject>Software</subject><subject>Soil Science & Conservation</subject><subject>Soil-plant relationships. Soil fertility</subject><subject>Soil-plant relationships. Soil fertility. Fertilization. Amendments</subject><subject>Xylem vessels</subject><issn>0032-079X</issn><issn>1573-5036</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kV1rFDEUhoNYcK3-AC-EARG8ST352GTGu1KqLRSEfoB34Wwm2c0yO1mTDNJ_b4YpVgTJRcjJ876c9xxC3jE4YwD6c2aMgaTAOGVMtJS_ICu21oKuQaiXZAUgOAXd_XhFXue8h_nN1Ipc38ZY7iyOX5q76MsvTK7xMTW7sN3Rsktx2u6OU2lwxOExh9xE36QqmQslHoLFoSkJQ8lvyInHIbu3T_cpefh6eX9xRW--f7u-OL-hdg2q0A4l2o0D5ZXthUTeytq0dgo2rO9AOK25kBsvkKN0gvXYSxSu1a2UvO824pR8WnyPKf6cXC7mELJ1w4Cji1M2rCZrO84lVPTDP-g-TqkmmSmulOYKVKXOFmqLgzNh9LEGsvX0ruaLo_Oh1s-F4pXXoq0Ctghsijkn580xhQOmx-pq5m2YZRumBjPzNgyvmo9PrWCuM_MJRxvyHyFXrONSy8rxhcv1a9y69HfL_zd_v4j2ucT0bCqFBgGd-A1i06HK</recordid><startdate>20120801</startdate><enddate>20120801</enddate><creator>Burton, Amy L.</creator><creator>Williams, Michael</creator><creator>Lynch, Jonathan P.</creator><creator>Brown, Kathleen M.</creator><general>Springer</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7ST</scope><scope>7T7</scope><scope>7X2</scope><scope>88A</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>SOI</scope><scope>7QH</scope><scope>7UA</scope><scope>F1W</scope><scope>H96</scope><scope>L.G</scope></search><sort><creationdate>20120801</creationdate><title>RootScan: Software for high-throughput analysis of root anatomical traits</title><author>Burton, Amy L. ; Williams, Michael ; Lynch, Jonathan P. ; Brown, Kathleen M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c506t-9a4acbe06f6cd34a2840127e60b1d903e77234bf3a2a4e31dad4a3e878442d9b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Agronomy</topic><topic>Agronomy. Soil science and plant productions</topic><topic>Animal, plant and microbial ecology</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Corn</topic><topic>Correlation analysis</topic><topic>Cross-sections</topic><topic>Data collection</topic><topic>Ecology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General agronomy. Plant production</topic><topic>Genotype & phenotype</topic><topic>Genotypes</topic><topic>Image analysis</topic><topic>Image contrast</topic><topic>Life Sciences</topic><topic>Phenotypic traits</topic><topic>Pixels</topic><topic>Plant Physiology</topic><topic>Plant roots</topic><topic>Plant Sciences</topic><topic>Plants</topic><topic>Regular Article</topic><topic>Root stele</topic><topic>Software</topic><topic>Soil Science & Conservation</topic><topic>Soil-plant relationships. Soil fertility</topic><topic>Soil-plant relationships. Soil fertility. Fertilization. Amendments</topic><topic>Xylem vessels</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Burton, Amy L.</creatorcontrib><creatorcontrib>Williams, Michael</creatorcontrib><creatorcontrib>Lynch, Jonathan P.</creatorcontrib><creatorcontrib>Brown, Kathleen M.</creatorcontrib><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Agricultural Science Collection</collection><collection>Biology Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>Aqualine</collection><collection>Water Resources Abstracts</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 2: Ocean Technology, Policy & Non-Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><jtitle>Plant and soil</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Burton, Amy L.</au><au>Williams, Michael</au><au>Lynch, Jonathan P.</au><au>Brown, Kathleen M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RootScan: Software for high-throughput analysis of root anatomical traits</atitle><jtitle>Plant and soil</jtitle><stitle>Plant Soil</stitle><date>2012-08-01</date><risdate>2012</risdate><volume>357</volume><issue>1-2</issue><spage>189</spage><epage>203</epage><pages>189-203</pages><issn>0032-079X</issn><eissn>1573-5036</eissn><coden>PLSOA2</coden><abstract>Background and aims RootScan is a program for semi-automated image analysis of anatomical traits in root cross-sections. Methods RootScan uses pixel thresholds to separate the cross-section from its background and to divide it into tissue regions. Area measurements and object counts are performed within various regions of interest. A graphical user interface permits the user to see which regions are selected, to edit those selections, and to rate and comment on the data. The structure of the program allows for organized workflow and increased data collection efficiency. Results The program collects data on more than 20 variables per image including areas of the cross-section, stele, cortex, aerenchyma lacunae, xylem vessels, and counts of cortical cells and cell files. An increased rate of data collection allows collection of four times more variables in less time than is possible with current methods. Correlation analysis shows that RootScan data is equal or greater in accuracy than data collected with Photoshop. Conclusions Compared with currently available tools, this software offers considerable improvements in the amount and quality of data, ease of use, and time needed for data collection. RootScan permits phenotypic scoring of physiologically and agronomically important traits on a large number of genotypes.</abstract><cop>Dordrecht</cop><pub>Springer</pub><doi>10.1007/s11104-012-1138-2</doi><tpages>15</tpages></addata></record> |
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| subjects | Agronomy Agronomy. Soil science and plant productions Animal, plant and microbial ecology Biological and medical sciences Biomedical and Life Sciences Corn Correlation analysis Cross-sections Data collection Ecology Fundamental and applied biological sciences. Psychology General agronomy. Plant production Genotype & phenotype Genotypes Image analysis Image contrast Life Sciences Phenotypic traits Pixels Plant Physiology Plant roots Plant Sciences Plants Regular Article Root stele Software Soil Science & Conservation Soil-plant relationships. Soil fertility Soil-plant relationships. Soil fertility. Fertilization. Amendments Xylem vessels |
| title | RootScan: Software for high-throughput analysis of root anatomical traits |
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