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P-TRAP: a Panicle Trait Phenotyping tool

2013-08Journal article Open access
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dc.contributor.authorAl-Tam, Faroq
dc.contributor.authorAdam, Helene
dc.contributor.authorDos Anjos, António
dc.contributor.authorLorieux, Mathias
dc.contributor.authorLarmande, Pierre
dc.contributor.authorGhesquiere, Alain
dc.contributor.authorJouannic, Stefan
dc.contributor.authorShahbazkia, Hamid Reza
dc.date.accessioned2018-12-07T14:52:45Z
dc.date.available2018-12-07T14:52:45Z
dc.date.issued2013-08
dc.description.abstractBackground: In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results: This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions: P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.
dc.description.sponsorshipIRD; GRiSP; Agropolis fonudation; Cariplo foundation
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1186/1471-2229-13-122
dc.identifier.issn1471-2229
dc.identifier.urihttp://hdl.handle.net/10400.1/11193
dc.language.isoeng
dc.peerreviewedyes
dc.publisherBiomed Central Ltd
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectImage-analysis
dc.subjectAlgorithm
dc.subjectSoftware
dc.subjectShape
dc.subjectRice
dc.subjectSkeletons
dc.subjectPlatform
dc.titleP-TRAP: a Panicle Trait Phenotyping tool
dc.typejournal article
dspace.entity.typePublication
oaire.citation.startPage122
oaire.citation.titleBMC Plant Biology
oaire.citation.volume13
person.familyNameAl-Tam
person.familyNameAnjos
person.familyNameShahbazkia
person.givenNameFaroq
person.givenNameAntónio
person.givenNameHamid Reza
person.identifierR-00G-A33
person.identifier.ciencia-id2515-AFE3-525F
person.identifier.ciencia-id2D11-C8C8-D8EA
person.identifier.ciencia-id5D12-F388-568E
person.identifier.orcid0000-0001-9718-2039
person.identifier.orcid0000-0001-6521-8930
person.identifier.orcid0000-0002-5661-0612
person.identifier.ridK-7031-2016
person.identifier.ridM-7604-2013
person.identifier.scopus-author-id55246034700
person.identifier.scopus-author-id25638237700
person.identifier.scopus-author-id22735637800
rcaap.rightsopenAccess
rcaap.typearticle
relation.isAuthorOfPublication15ac97f4-a867-462d-9fc6-0a47bb2919d3
relation.isAuthorOfPublicationc525cee7-e184-4154-ab9a-23270970ca86
relation.isAuthorOfPublication11ed60f1-defe-4034-9203-633a116cf217
relation.isAuthorOfPublication.latestForDiscovery15ac97f4-a867-462d-9fc6-0a47bb2919d3

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