A robot-assisted imaging pipeline for tracking the growths of maize ear and silks in a high-throughput phenotyping platform

Nicolas Brichet 1 Christian Fournier 1, 2 Olivier Turc 1 Olivier Strauss 3 Simon Artzet 1, 2 Christophe Pradal 2, 4 Claude Welcker 1 Francois Tardieu 1 Llorenç Cabrera-Bosquet 1
2 VIRTUAL PLANTS - Modeling plant morphogenesis at different scales, from genes to phenotype
CRISAM - Inria Sophia Antipolis - Méditerranée , INRA - Institut National de la Recherche Agronomique, Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR51
3 ICAR - Image & Interaction
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Background: In maize, silks are hundreds of filaments that simultaneously emerge from the ear for collecting pollen over a period of 1–7 days, which largely determines grain number especially under water deficit. Silk growth is a major trait for drought tolerance in maize, but its phenotyping is difficult at throughputs needed for genetic analyses. Results: We have developed a reproducible pipeline that follows ear and silk growths every day for hundreds of plants, based on an ear detection algorithm that drives a robotized camera for obtaining detailed images of ears and silks. We first select, among 12 whole ‑plant side views, those best suited for detecting ear position. Images are seg‑ mented, the stem pixels are labelled and the ear position is identified based on changes in width along the stem. A mobile camera is then automatically positioned in real time at 30 cm from the ear, for a detailed picture in which silks are identified based on texture and colour. This allows analysis of the time course of ear and silk growths of thousands of plants. The pipeline was tested on a panel of 60 maize hybrids in the PHENOARCH phenotyping platform. Over 360 plants, ear position was correctly estimated in 86% of cases, before it could be visually assessed. Silk growth rate, estimated on all plants, decreased with time consistent with literature. The pipeline allowed clear identification of the effects of genotypes and water deficit on the rate and duration of silk growth. Conclusions: The pipeline presented here, which combines computer vision, machine learning and robotics, provides a powerful tool for large ‑scale genetic analyses of the control of reproductive growth to changes in environ‑ mental conditions in a non ‑invasive and automatized way. It is available as Open Source software in the OpenAlea platform.
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Plant Methods, BioMed Central, 2017, 13 (1), pp.12. 〈10.1186/s13007-017-0246-7〉
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Nicolas Brichet, Christian Fournier, Olivier Turc, Olivier Strauss, Simon Artzet, et al.. A robot-assisted imaging pipeline for tracking the growths of maize ear and silks in a high-throughput phenotyping platform. Plant Methods, BioMed Central, 2017, 13 (1), pp.12. 〈10.1186/s13007-017-0246-7〉. 〈hal-01631186〉

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