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Development of Deep Learning-based Nuclear Detection Algorithm for Mouse Embryo

Research Project

Project/Area Number 16H04731
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field System genome science
Research InstitutionKeio University

Principal Investigator

Funahashi Akira  慶應義塾大学, 理工学部(矢上), 准教授 (70324548)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥16,380,000 (Direct Cost: ¥12,600,000、Indirect Cost: ¥3,780,000)
Fiscal Year 2019: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Fiscal Year 2018: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2017: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2016: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Keywords画像解析 / 機械学習 / 深層学習 / 発生・分化
Outline of Final Research Achievements

Using deep learning, we developed an image processing algorithm to identify nuclei from the 4-dimensional fluorescence microscopic images of mouse embryo development. The existing analysis of cell dynamics in mouse embryogenesis has a problem that the accuracy of nuclear identification after 16 cell stages is very low for the 4D microscopy images. In this research, we developed a nuclear identification algorithm using deep learning, which has recently attracted attention as a powerful technique in image analysis. Our algorithm performed accurate nuclear identification up to the 50 cell stage to obtain quantitative criteria that can evaluate the quality of embryos.

Academic Significance and Societal Importance of the Research Achievements

学術的意義として、当研究課題で開発したQCANetは、極体を除いた細胞核のセグメンテーションを行うことに成功し、初期マウス発生過程における胚ごとの違いを定量的に比較することが可能であることが示された点が挙げられる。
社会的意義としては、今後QCANetを用いて初期胚を定量的に評価するための最適な指標の探索を行うことで、経験的に定められた指標に代わる、産仔作出能との関連性が高い「胚の質を評価し得る指標」の確立が期待される点が挙げられる。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (44 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (8 results) Journal Article (3 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 3 results,  Open Access: 3 results) Presentation (32 results) (of which Int'l Joint Research: 14 results,  Invited: 19 results) Remarks (1 results)

  • [Int'l Joint Research] University of Nottingham(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Kazan Federal University(ロシア連邦)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] University of Nottingham(英国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Kazan Federal University(ロシア連邦)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Linkoping University(スウェーデン)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of Nottingham(英国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Kazan Federal University(ロシア連邦)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Linkoping University(スウェーデン)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Predicting the future direction of cell movement with convolutional neural networks2019

    • Author(s)
      Nishimoto Shori、Tokuoka Yuta、Yamada Takahiro G.、Hiroi Noriko F.、Funahashi Akira
    • Journal Title

      PLOS ONE

      Volume: 14 Issue: 9 Pages: e0221245-e0221245

    • DOI

      10.1371/journal.pone.0221245

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep Learning for Non-Invasive Determination of the Differentiation Status of Human Neuronal Cells by Using Phase-Contrast Photomicrographs2019

    • Author(s)
      Ooka Maya、Tokuoka Yuta、Nishimoto Shori、Hiroi Noriko F.、Yamada Takahiro G.、Funahashi Akira
    • Journal Title

      Applied Sciences

      Volume: 9 Issue: 24 Pages: 5503-5503

    • DOI

      10.3390/app9245503

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Quantitative Biology: Dynamics of Living Systems2016

    • Author(s)
      N Hiroi, VM Draviam, A Funahashi
    • Journal Title

      Frontiers in Physiology

      Volume: 7

    • DOI

      10.3389/fphys.2016.00196

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 機械学習による細胞動態解析2020

    • Author(s)
      西本 勝利, 徳岡 雄大, 山田 貴大, 広井 賀子, 舟橋 啓
    • Organizer
      第67回応用物理学会春季学術講演会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 不妊治療に資する深層学習を用いた初期胚定量評価手法の開発2019

    • Author(s)
      舟橋 啓
    • Organizer
      Cardiovascular Meeting
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 畳み込みニューラルネットワークを用いた神経分化判別および特徴量解析2019

    • Author(s)
      舟橋 啓
    • Organizer
      山口大学 AIシステム医学医療研究教育センター セミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] CellDesigner: A modeling tool for biochemical networks2019

    • Author(s)
      Funahashi, A.
    • Organizer
      COMBINE 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 機械学習による画像分類2019

    • Author(s)
      舟橋 啓, 徳岡 雄大
    • Organizer
      AIによる生物画像解析トレーニングコース
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 腫瘍内不均一性を考慮した予後の予測に向けた深層学習ベースの組織画像解析2019

    • Author(s)
      舟橋 啓
    • Organizer
      群馬大学数理データ科学教育研究センター主催第1回レギュラトリー サイエンスセミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 人工知能と医学研究2019

    • Author(s)
      舟橋 啓
    • Organizer
      群馬大学総合外科学講座 Translational Researchセミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] CellDesigner2019

    • Author(s)
      Funahashi, A.
    • Organizer
      COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 一細胞系譜解析による低グルコース培養下大腸菌集団のATP 濃度多様性生成機構の解明2019

    • Author(s)
      中谷 諒, 板橋 正寛, 山田 貴大, 広井 賀子, 舟橋 啓
    • Organizer
      定量生物学の会 北海道キャラバン 2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Deep Learning-based quantitative evaluation of early embryo in infertility treatments2019

    • Author(s)
      Tokuoka, Y., Yamada, T. G., Hiroi, N. F., Kobayashi, T. J., Yamagata, K., Funahashi, A.
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 画像解析による不妊治療応用を目指した深層学習アルゴリズムの提案: 非染色マウス初期胚の細胞核セグメンテーションおよび多様な生物種へのアルゴリズムの適応2019

    • Author(s)
      徳岡 雄大, 山田 貴大, 小林 徹也, 山縣 一夫, 舟橋 啓
    • Organizer
      定量生物学の会 北海道キャラバン 2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Deep Learning Based Tissue Analysis for Predicting Cancer Outcomes Accounting for Intratumoral Heterogeneity2019

    • Author(s)
      Nishimoto, S
    • Organizer
      Seminar at University of Nottingham
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development2019

    • Author(s)
      Funahashi, A.
    • Organizer
      Seminar at University of Nottingham
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 不妊治療に資する深層学習を用いた初期胚定量評価手法の開発2019

    • Author(s)
      徳岡雄大, 山田貴大, 広井賀子, 小林徹也, 山縣一夫, 舟橋啓
    • Organizer
      第18回日本再生医療学会総会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Mechanical Modeling of Cell Migration During the Early Embryogenesis of C. elegans to Reveal the Mechanism for Controlling Cell Arrangement2019

    • Author(s)
      Motomuro, M., Yamamoto, K., Yamada, T. G., Hiroi, N. F., Kimura, A. and Funahashi, A.
    • Organizer
      The Seventh Annual Winter Q-Bio Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 生命現象の定量解析に資するConvolutional Neural Networksを基盤とした顕微鏡画像解析手法の開発2019

    • Author(s)
      徳岡雄大, 山田貴大, 広井賀子, 小林徹也, 山縣一夫, Cornette Richard, 黄川田隆洋, 舟橋啓
    • Organizer
      定量生物学の会 第九回年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ディープラーニングを用いたマウス発生過程における定量的指標の獲得2018

    • Author(s)
      舟橋 啓
    • Organizer
      第36回 日本受精着床学会総会・学術講演会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] CellDesigner - Modeling Tool for Biochemical Networks2018

    • Author(s)
      Funahashi, A.
    • Organizer
      COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Predicting the future direction of cell movement with convolutional neural networks2018

    • Author(s)
      Shori Nishimoto, Yuta Tokuoka, Takahiro G Yamada, Noriko Hiroi, Akira Funahashi
    • Organizer
      19th International Conference on Systems Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development2018

    • Author(s)
      Tokuoka, Y., Yamada, TG., Hiroi, NF., Kobayashi, TJ., Yamagata, K. and Funahashi, A.
    • Organizer
      19th International Conference on Systems Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 深層学習が明らかにする細胞顕微鏡画像解析の新展開2018

    • Author(s)
      舟橋 啓
    • Organizer
      自然科学研究機構 新分野創成センター合同シンポジウム「分野横断・分野融合研究による生命創成を探究する新しい科学の創成」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] リアルタイム制御が導く定量生物学の未来2017

    • Author(s)
      舟橋 啓
    • Organizer
      定量生物学のNEXT CHALLENGE
    • Place of Presentation
      ホテルたつき会議室 (愛知県・蒲郡市)
    • Year and Date
      2017-01-09
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 細胞シミュレーションライブラリLibSBMLSim-v2の設計と実装2017

    • Author(s)
      舟橋 啓
    • Organizer
      定量生物学の会 第8回年会
    • Place of Presentation
      自然科学研究機構 岡崎カンファレンスセンター (愛知県・岡崎市)
    • Year and Date
      2017-01-08
    • Related Report
      2016 Annual Research Report
  • [Presentation] 細胞質流動に着目した細胞質分裂位置決定モデルの構築2017

    • Author(s)
      吉見 祐亮
    • Organizer
      定量生物学の会 第8回年会
    • Place of Presentation
      自然科学研究機構 岡崎カンファレンスセンター (愛知県・岡崎市)
    • Year and Date
      2017-01-08
    • Related Report
      2016 Annual Research Report
  • [Presentation] 深層学習を用いた3次元蛍光顕微鏡画像セグメンテーションアルゴリズムの提案2017

    • Author(s)
      徳岡 雄大
    • Organizer
      定量生物学の会 第8回年会
    • Place of Presentation
      自然科学研究機構 岡崎カンファレンスセンター (愛知県・岡崎市)
    • Year and Date
      2017-01-08
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Requirement of spatiotemporal resolution for imaging intracellular temperature distribution2017

    • Author(s)
      N Hiroi
    • Organizer
      SPIE Technologies and Applications of Structured Light
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Segmenting four-dimensional fluorescence microscopic image using Convolutional Neural Network2017

    • Author(s)
      Y Tokuoka
    • Organizer
      International Conference on Systems Biology 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Segmenting Four-dimensional Fluorescence Microscopic Image using Convolutional Neural Network2017

    • Author(s)
      A Funahashi
    • Organizer
      Life of Genomes 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Segmenting Four-dimensional Fluorescence Microscopic Image using Convolutional Neural Network2017

    • Author(s)
      A Funahashi
    • Organizer
      Integrated Open Systems Unit Seminar
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Design and Implementation of High Performance Biochemical Simulator2016

    • Author(s)
      Akira Funahashi
    • Organizer
      LibSBMLSim & Flint Hackathon
    • Place of Presentation
      沖縄科学技術大学院大学 (沖縄県・恩納村)
    • Year and Date
      2016-11-21
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 4次元画像解析による核同定アルゴリズムの構築2016

    • Author(s)
      舟橋 啓
    • Organizer
      ネムリユスリカワークショップ2016
    • Place of Presentation
      東京大学検見川セミナーハウス (千葉県・千葉市)
    • Year and Date
      2016-07-28
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] CellDesigner: Modeling Tool for Biochemical Networks2016

    • Author(s)
      Akira Funahashi
    • Organizer
      COMBINE Tutorial Modelling and Simulation Tools in Systems Biology
    • Place of Presentation
      Barcelona (Spain)
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] QCANet: Quantitative Criterion Acquisition Network

    • URL

      https://github.com/funalab/QCANet

    • Related Report
      2019 Annual Research Report

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Published: 2016-04-21   Modified: 2022-07-19  

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