LAMINA: a tool for rapid quantification of leaf size and shape parameters.
Identifieur interne : 003876 ( Main/Exploration ); précédent : 003875; suivant : 003877LAMINA: a tool for rapid quantification of leaf size and shape parameters.
Auteurs : Max Bylesjö [Suède] ; Vincent Segura ; Raju Y. Soolanayakanahally ; Anne M. Rae ; Johan Trygg ; Petter Gustafsson ; Stefan Jansson ; Nathaniel R. StreetSource :
- BMC plant biology [ 1471-2229 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
- anatomie et histologie : Feuilles de plante, Populus.
- méthodes : Traitement d'image par ordinateur.
- Analyse en composantes principales, Validation de logiciel.
English descriptors
- KwdEn :
- MESH :
- anatomy & histology : Plant Leaves, Populus.
- methods : Image Processing, Computer-Assisted.
- Principal Component Analysis, Software Validation.
Abstract
BACKGROUND
An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.
RESULTS
We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.
CONCLUSION
We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.
DOI: 10.1186/1471-2229-8-82
PubMed: 18647399
PubMed Central: PMC2500018
Affiliations:
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Soolanayakanahally</name></author><author><name sortKey="Rae, Anne M" sort="Rae, Anne M" uniqKey="Rae A" first="Anne M" last="Rae">Anne M. Rae</name></author><author><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></author><author><name sortKey="Gustafsson, Petter" sort="Gustafsson, Petter" uniqKey="Gustafsson P" first="Petter" last="Gustafsson">Petter Gustafsson</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. 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Soolanayakanahally</name></author><author><name sortKey="Rae, Anne M" sort="Rae, Anne M" uniqKey="Rae A" first="Anne M" last="Rae">Anne M. Rae</name></author><author><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></author><author><name sortKey="Gustafsson, Petter" sort="Gustafsson, Petter" uniqKey="Gustafsson P" first="Petter" last="Gustafsson">Petter Gustafsson</name></author><author><name sortKey="Jansson, Stefan" sort="Jansson, Stefan" uniqKey="Jansson S" first="Stefan" last="Jansson">Stefan Jansson</name></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Image Processing, Computer-Assisted (methods)</term><term>Plant Leaves (anatomy & histology)</term><term>Populus (anatomy & histology)</term><term>Principal Component Analysis (MeSH)</term><term>Software Validation (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse en composantes principales (MeSH)</term><term>Feuilles de plante (anatomie et histologie)</term><term>Populus (anatomie et histologie)</term><term>Traitement d'image par ordinateur (méthodes)</term><term>Validation de logiciel (MeSH)</term></keywords><keywords scheme="MESH" qualifier="anatomie et histologie" xml:lang="fr"><term>Feuilles de plante</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="anatomy & histology" xml:lang="en"><term>Plant Leaves</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Image Processing, Computer-Assisted</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Traitement d'image par ordinateur</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Principal Component Analysis</term><term>Software Validation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse en composantes principales</term><term>Validation de logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18647399</PMID><DateCompleted><Year>2008</Year><Month>08</Month><Day>14</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><PubDate><Year>2008</Year><Month>Jul</Month><Day>22</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>LAMINA: a tool for rapid quantification of leaf size and shape parameters.</ArticleTitle><Pagination><MedlinePgn>82</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-8-82</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. 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In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bylesjö</LastName><ForeName>Max</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Research Group for Chemometrics, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden. max.bylesjo@chem.umu.se</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Segura</LastName><ForeName>Vincent</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Soolanayakanahally</LastName><ForeName>Raju Y</ForeName><Initials>RY</Initials></Author><Author ValidYN="Y"><LastName>Rae</LastName><ForeName>Anne M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Trygg</LastName><ForeName>Johan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Gustafsson</LastName><ForeName>Petter</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Stefan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D023361">Validation Study</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>07</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant 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Rae</name><name sortKey="Segura, Vincent" sort="Segura, Vincent" uniqKey="Segura V" first="Vincent" last="Segura">Vincent Segura</name><name sortKey="Soolanayakanahally, Raju Y" sort="Soolanayakanahally, Raju Y" uniqKey="Soolanayakanahally R" first="Raju Y" last="Soolanayakanahally">Raju Y. Soolanayakanahally</name><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></noCountry><country name="Suède"><noRegion><name sortKey="Bylesjo, Max" sort="Bylesjo, Max" uniqKey="Bylesjo M" first="Max" last="Bylesjö">Max Bylesjö</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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