title: Phenoplant: a web resource for the exploration of large chlorophyll fluorescence image datasets.
abstract: BACKGROUND
  Image analysis is increasingly used in plant phenotyping. Among the various imaging techniques that can be used in plant phenotyping, chlorophyll fluorescence imaging allows imaging of the impact of biotic or abiotic stresses on leaves. Numerous chlorophyll fluorescence parameters may be measured or calculated, but only a few can produce a contrast in a given condition. Therefore, automated procedures that help screening chlorophyll fluorescence image datasets are needed, especially in the perspective of high-throughput plant phenotyping.
  
  
  RESULTS
  We developed an automatic procedure aiming at facilitating the identification of chlorophyll fluorescence parameters impacted on leaves by a stress. First, for each chlorophyll fluorescence parameter, the procedure provides an overview of the data by automatically creating contact sheets of images and/or histograms. Such contact sheets enable a fast comparison of the impact on leaves of various treatments, or of the contrast dynamics during the experiments. Second, based on the global intensity of each chlorophyll fluorescence parameter, the procedure automatically produces radial plots and box plots allowing the user to identify chlorophyll fluorescence parameters that discriminate between treatments. Moreover, basic statistical analysis is automatically generated. Third, for each chlorophyll fluorescence parameter the procedure automatically performs a clustering analysis based on the histograms. This analysis clusters images of plants according to their health status. We applied this procedure to monitor the impact of the inoculation of the root parasitic plant Phelipanche ramosa on Arabidopsis thaliana ecotypes Col-0 and Ler.
  
  
  CONCLUSIONS
  Using this automatic procedure, we identified eight chlorophyll fluorescence parameters discriminating between the two ecotypes of A. thaliana, and five impacted by the infection of Arabidopsis thaliana by P. ramosa. More generally, this procedure may help to identify chlorophyll fluorescence parameters impacted by various types of stresses. We implemented this procedure at http://www.phenoplant.org freely accessible to users of the plant phenotyping community.
authors: PHENOTIC, SFR 4207 QUASAV, F-49045 Angers, France.
authors: Céline
authors: C
authors: Rousseau
authors: Université d'Angers, Laboratoire d'Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, F-49045 Angers, France.
authors: Gilles
authors: G
authors: Hunault
authors: Institut de Recherche en Horticulture et Semences, UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouzé, France.
authors: Sylvain
authors: S
authors: Gaillard
authors: Institut de Recherche en Horticulture et Semences, UMR1345, AgroCampus-Ouest, SFR 4207 QUASAV, F-49045 Angers, France.
authors: Julie
authors: J
authors: Bourbeillon
authors: Université de Nantes, Laboratoire de Biologie et de Pathologie Végétales EA 1157, SFR 4207 QUASAV, F-44322 Nantes, France.
authors: Gregory
authors: G
authors: Montiel
authors: Université de Nantes, Laboratoire de Biologie et de Pathologie Végétales EA 1157, SFR 4207 QUASAV, F-44322 Nantes, France.
authors: Philippe
authors: P
authors: Simier
authors: Institut de Recherche en Horticulture et Semences, UMR1345, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
authors: Claire
authors: C
authors: Campion
authors: PHENOTIC, SFR 4207 QUASAV, F-49045 Angers, France.|Institut de Recherche en Horticulture et Semences, UMR1345, INRA, SFR 4207 QUASAV, F-49071 Beaucouzé, France.
authors: Marie-Agnès
authors: MA
authors: Jacques
authors: PHENOTIC, SFR 4207 QUASAV, F-49045 Angers, France.|Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d'Angers, F-49000 Angers, France.
authors: Etienne
authors: E
authors: Belin
authors: PHENOTIC, SFR 4207 QUASAV, F-49045 Angers, France.|Institut de Recherche en Horticulture et Semences, UMR1345, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
authors: Tristan
authors: T
authors: Boureau