ClearedLeavesDB: an online database of cleared plant leaf images
Identifieur interne : 000343 ( Pmc/Curation ); précédent : 000342; suivant : 000344ClearedLeavesDB: an online database of cleared plant leaf images
Auteurs : Abhiram Das [États-Unis] ; Alexander Bucksch [États-Unis] ; Charles A. Price [Australie] ; Joshua S. Weitz [États-Unis]Source :
- Plant Methods [ 1746-4811 ] ; 2014.
Abstract
Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers.
The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database.
We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at
Url:
DOI: 10.1186/1746-4811-10-8
PubMed: 24678985
PubMed Central: 3986656
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ClearedLeavesDB: an online database of cleared plant leaf images</title><author><name sortKey="Das, Abhiram" sort="Das, Abhiram" uniqKey="Das A" first="Abhiram" last="Das">Abhiram Das</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author><author><name sortKey="Bucksch, Alexander" sort="Bucksch, Alexander" uniqKey="Bucksch A" first="Alexander" last="Bucksch">Alexander Bucksch</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author><author><name sortKey="Price, Charles A" sort="Price, Charles A" uniqKey="Price C" first="Charles A" last="Price">Charles A. Price</name><affiliation wicri:level="1"><nlm:aff id="I4">School of Plant Biology, University of Western Australia, Perth, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology, University of Western Australia, Perth</wicri:regionArea></affiliation></author><author><name sortKey="Weitz, Joshua S" sort="Weitz, Joshua S" uniqKey="Weitz J" first="Joshua S" last="Weitz">Joshua S. Weitz</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Physics, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24678985</idno><idno type="pmc">3986656</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986656</idno><idno type="RBID">PMC:3986656</idno><idno type="doi">10.1186/1746-4811-10-8</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000343</idno><idno type="wicri:Area/Pmc/Curation">000343</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ClearedLeavesDB: an online database of cleared plant leaf images</title><author><name sortKey="Das, Abhiram" sort="Das, Abhiram" uniqKey="Das A" first="Abhiram" last="Das">Abhiram Das</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author><author><name sortKey="Bucksch, Alexander" sort="Bucksch, Alexander" uniqKey="Bucksch A" first="Alexander" last="Bucksch">Alexander Bucksch</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author><author><name sortKey="Price, Charles A" sort="Price, Charles A" uniqKey="Price C" first="Charles A" last="Price">Charles A. Price</name><affiliation wicri:level="1"><nlm:aff id="I4">School of Plant Biology, University of Western Australia, Perth, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Plant Biology, University of Western Australia, Perth</wicri:regionArea></affiliation></author><author><name sortKey="Weitz, Joshua S" sort="Weitz, Joshua S" uniqKey="Weitz J" first="Joshua S" last="Weitz">Joshua S. Weitz</name><affiliation wicri:level="1"><nlm:aff id="I1">School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Biology, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Physics, Georgia Institute of Technology, Atlanta, Georgia</wicri:regionArea></affiliation></author></analytic><series><title level="j">Plant Methods</title><idno type="eISSN">1746-4811</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers.</p></sec><sec><title>Description</title><p>The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database.</p></sec><sec><title>Conclusions</title><p>We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at <ext-link ext-link-type="uri" xlink:href="http://clearedleavesdb.org">http://clearedleavesdb.org</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ellis, B" uniqKey="Ellis B">B Ellis</name></author><author><name sortKey="Dcd" uniqKey="Dcd">DCD</name></author><author><name sortKey="Hickey, Lj" uniqKey="Hickey L">LJ Hickey</name></author><author><name sortKey="Johnson, Kr" uniqKey="Johnson K">KR Johnson</name></author><author><name sortKey="Mitchel, Jd" uniqKey="Mitchel J">JD Mitchel</name></author><author><name sortKey="Wilf, P" uniqKey="Wilf P">P Wilf</name></author><author><name sortKey="Wing, Sl" uniqKey="Wing S">SL Wing</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sack, L" uniqKey="Sack L">L Sack</name></author><author><name sortKey="Holbrook, Nm" uniqKey="Holbrook N">NM 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Methods</journal-id><journal-id journal-id-type="iso-abbrev">Plant Methods</journal-id><journal-title-group><journal-title>Plant Methods</journal-title></journal-title-group><issn pub-type="epub">1746-4811</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24678985</article-id><article-id pub-id-type="pmc">3986656</article-id><article-id pub-id-type="publisher-id">1746-4811-10-8</article-id><article-id pub-id-type="doi">10.1186/1746-4811-10-8</article-id><article-categories><subj-group subj-group-type="heading"><subject>Database</subject></subj-group></article-categories><title-group><article-title>ClearedLeavesDB: an online database of cleared plant leaf images</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Das</surname><given-names>Abhiram</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>abhiram.das@gatech.edu</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Bucksch</surname><given-names>Alexander</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I3">3</xref><email>bucksch@gatech.edu</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Price</surname><given-names>Charles A</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>charles.price@uwa.edu.au</email></contrib><contrib contrib-type="author" corresp="yes" id="A4"><name><surname>Weitz</surname><given-names>Joshua S</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><email>jsweitz@gatech.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA</aff><aff id="I2"><label>2</label>School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA</aff><aff id="I3"><label>3</label>School of Interactive Computing, Georgia Institute of Technology, Atlanta, Georgia, USA</aff><aff id="I4"><label>4</label>School of Plant Biology, University of Western Australia, Perth, Australia</aff><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>28</day><month>3</month><year>2014</year></pub-date><volume>10</volume><fpage>8</fpage><lpage>8</lpage><history><date date-type="received"><day>10</day><month>12</month><year>2013</year></date><date date-type="accepted"><day>19</day><month>3</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Das et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Das et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><self-uri xlink:href="http://www.plantmethods.com/content/10/1/8"></self-uri><abstract><sec><title>Background</title><p>Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers.</p></sec><sec><title>Description</title><p>The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database.</p></sec><sec><title>Conclusions</title><p>We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at <ext-link ext-link-type="uri" xlink:href="http://clearedleavesdb.org">http://clearedleavesdb.org</ext-link>.</p></sec></abstract><kwd-group><kwd>Database</kwd><kwd>Images</kwd><kwd>Leaves</kwd><kwd>Digital archiving</kwd><kwd>Digital curation</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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