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3D morphological benchmark datasets for accelerating plant phenotyping studies

Research Project

Project/Area Number 19K15946
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 41040:Agricultural environmental engineering and agricultural information engineering-related
Research InstitutionKyushu University

Principal Investigator

Noshita Koji  九州大学, 理学研究院, 助教 (10758494)

Project Period (FY) 2019-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2019: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords植物フェノタイピング / 数理モデル / 形態測定学 / 画像解析 / 3次元計測
Outline of Research at the Start

植物フェノタイピング(plant phenotyping)による表現型データ収集の加速を目指す.表現型データの収集は労働集約的な場合が多く,多様性をもった農作物生産技術開発上のボトルネックとなっている.このボトルネック解消に向けて植物フェノタイピングへの取り組みが世界的に盛んになってきたが,各手法の定量的比較のための基盤となるベンチマークデータセットが殆ど存在しない.また,革新的な成果を挙げつつある深層学習などの成果を農作物生産の現場へも応用するには,分野に合わせた訓練データが必要である.本提案では,植物3次元形態データに注目し,データの収集とメタデータの付与をおこない,その基盤を整備する.

Outline of Final Research Achievements

I worked on the creation of a 3D morphological dataset of plant structure. I acquired multi-view images by using a photogrammetry studio with multiple digital cameras, created annotation data for the obtained multi-view images, reconstructed the 3D images using the multi-view images, estimated phenotypic values by analyzing the reconstructed point cloud data, and developed a method for properties that have been difficult to quantify. As a result, we created a 3D plant morphological dataset, especially for traits related mainly to leaves of soybean. In addition, we were able to demonstrate the value of the dataset in the development of a novel mathematical model-based measurement method and a model.

Academic Significance and Societal Importance of the Research Achievements

植物地上部の3次元形態データセットの作成に取り組んだ.これにより,新規に開発する計測方法の評価や機械学習モデルの訓練データとしての活用が見込める.また,従来計測が困難であった性質の評価手法の開発にもつながった.すなわち,詳細な計測データ,アノテーションデータ,形質データを組み合わせたデータセットを作成することで,新規に提案される計測手法の有用性を検証できる基盤の構築や新しい手法の開発の支援をおこなうことが可能になると考えられる.

Report

(3 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • Research Products

    (12 results)

All 2021 2020 2019 Other

All Int'l Joint Research (1 results) Journal Article (5 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results) Presentation (6 results) (of which Int'l Joint Research: 2 results)

  • [Int'l Joint Research] University of Georgia(米国)

    • Related Report
      2019 Research-status Report
  • [Journal Article] Climate-smart crops: key root anatomical traits that confer flooding tolerance2021

    • Author(s)
      Yamauchi Takaki、Noshita Koji、Tsutsumi Nobuhiro
    • Journal Title

      Breeding Science

      Volume: 71 Issue: 1 Pages: 51-61

    • DOI

      10.1270/jsbbs.20119

    • NAID

      130007991329

    • ISSN
      1344-7610, 1347-3735
    • Related Report
      2020 Annual Research Report
  • [Journal Article] Field‐based individual plant phenotyping of herbaceous species by unmanned aerial vehicle2020

    • Author(s)
      Guo Wei、Fukano Yuya、Noshita Koji、Ninomiya Seishi
    • Journal Title

      Ecology and Evolution

      Volume: 10 Issue: 21 Pages: 12318-12326

    • DOI

      10.1002/ece3.6861

    • Related Report
      2020 Annual Research Report
  • [Journal Article] A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea)2020

    • Author(s)
      Kirie Shiryu、Iwasaki Hideo、Noshita Koji、Iwata Hiroyoshi
    • Journal Title

      PLOS ONE

      Volume: 15 Issue: 10 Pages: e0239781-e0239781

    • DOI

      10.1371/journal.pone.0239781

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 植物科学の「人工知能」との関わり方を考える2020

    • Author(s)
      大倉 史生、水谷 未耶、野下 浩司、戸田 陽介
    • Journal Title

      BSJ-Review

      Volume: 11 Issue: C Pages: 185-206

    • DOI

      10.24480/bsj-review.11c2.00191

    • ISSN
      2432-9819
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 深層学習の利活用による植物表現型解析技術の展望2019

    • Author(s)
      大倉 史生, 野下 浩司, 木下 俊則, 戸田 陽介.
    • Journal Title

      BSJ-Review

      Volume: 10 Issue: B Pages: 99-107

    • DOI

      10.24480/bsj-review.10b7.00160

    • ISSN
      2432-9819
    • Related Report
      2019 Research-status Report
    • Open Access
  • [Presentation] 3次元空間における植物葉面再構築と輪郭形状解析2021

    • Author(s)
      野下 浩司
    • Organizer
      日本生態学会第68回全国大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Quantitative Representation of Plant Style as Spacial Pattern of Foliage for Morphometrics on ill-defined Homology2020

    • Author(s)
      Noshita, K.
    • Organizer
      Phenome2020
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 葉群の空間パターンとしての草姿・草型の定量的表現:相同性が自明でない場合の形態測定学に向けて2020

    • Author(s)
      野下 浩司
    • Organizer
      第16回 生物数学の理論とその応用 ~生命現象の定量的理解に向けて~
    • Related Report
      2019 Research-status Report
  • [Presentation] A unified framework for image-based plant phenotyping under controlled growth environment: From image acquisition to phenotype interpretation.2019

    • Author(s)
      Toda, Y., Noshita, K., Fujita, M., Nakamichi, N., Okura, F., Kinoshita, T., Shinozaki, K.
    • Organizer
      IPPS2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] 植物形態の計測とモデル化2019

    • Author(s)
      野下 浩司
    • Organizer
      2019年度日本数理生物学会年会
    • Related Report
      2019 Research-status Report
  • [Presentation] 植物フェノタイピング向け仮想データセットの生成と解析2019

    • Author(s)
      野下 浩司
    • Organizer
      定量生物学の会 北海道キャラバン 2019
    • Related Report
      2019 Research-status Report

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Published: 2019-04-18   Modified: 2022-01-27  

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