An application software development for quantitative biological image analysis

• Project/Area Number: 18K06272
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 44020:Developmental biology-related
• Research Institution: Center for Novel Science Initatives, National Institutes of Natural Sciences
• Principal Investigator: Kato Kagayaki 大学共同利用機関法人自然科学研究機構(新分野創成センター、アストロバイオロジーセンター、生命創成探究, 生命創成探究センター, 特任助教 (30391915)
• Project Period (FY): 2018-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2021)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2020: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2019: ¥260,000 (Direct Cost: ¥200,000、Indirect Cost: ¥60,000); Fiscal Year 2018: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• Keywords: 生物画像データ解析 / 生物画像解析 / 生物画像情報解析

Outline of Final Research Achievements

There is an urgent need to efficiently extract and measure biologically important features from observational images in multidimensional imaging and large-capacity biological research in recent years. Moreover, various image data are produced in the whole biological field due to the wide range of observation objects. To deal with this situation, we have developed software specializing in biological image data analysis. This software system is a foundation that enables simple expression and description of biological features in images as geometric expressions, and an application can be constructed by relatively small-scale programming. Using this system, we performed quantitative image analysis in a wide range of biological experiments, from intracellular organelles in cultured cell lines to analysis of free migration patterns in fish.

Academic Significance and Societal Importance of the Research Achievements

本研究は，生物学研究において産生される画像データについて，その観察技法の発展に伴う多次元化・高精細化と近年のデータ科学的方法論に基づく大量データの解析法の開発という要望に対応するべく，生物画像データ解析に特化したソフトウェア基盤であり，特殊な顕微鏡からビデオ撮影した動画に至るまでの多岐に渡る画像データを透過的に処理，定量的な解析までを行うことを可能とするものである．今後，本システムを適用することによって，広範な生物学実験における観察画像の定量的な解析を効率よく行う系を構築することが可能となる．

Research Products

• [Journal Article] Live imaging of avian epiblast and anterior mesendoderm grafting reveals the complexity of cell dynamics during early brain development (2022)
  • Author(s): Yoshihi Koya、Kato Kagayaki、Iida Hideaki、Teramoto Machiko、Kawamura Akihito、Watanabe Yusaku、Nunome Mitsuo、Nakano Mikiharu、Matsuda Yoichi、Sato Yuki、Mizuno Hidenobu、Iwasato Takuji、Ishii Yasuo、Kondoh Hisato
  • Journal Title: Development Volume: 149 Issue: 6
  • DOI: 10.1242/dev.199999
  • Peer Reviewed / Open Access
• [Journal Article] Neuronal Circuits That Control Rhythmic Pectoral Fin Movements in Zebrafish (2020)
  • Author(s): Uemura Yuto、Kato Kagayaki、Kawakami Koichi、Kimura Yukiko、Oda Yoichi、Higashijima Shin-ichi
  • Journal Title: The Journal of Neuroscience Volume: 40 Issue: 35 Pages: 6678-6690
  • DOI: 10.1523/jneurosci.1484-20.2020
  • Peer Reviewed
• [Journal Article] Marcksl1 modulates endothelial cell mechanoresponse to haemodynamic forces to control blood vessel shape and size (2020)
  • Author(s): Kondrychyn Igor、Kelly Douglas J.、Carretero N?ria Taberner、Nomori Akane、Kato Kagayaki、Chong Jeronica、Nakajima Hiroyuki、Okuda Satoru、Mochizuki Naoki、Phng Li-Kun
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 5476-5493
  • DOI: 10.1038/s41467-020-19308-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Polar recruitment of RLD by LAZY1-like protein during gravity signaling in root branch angle control (2020)
  • Author(s): Furutani Masahiko、Hirano Yoshinori、Nishimura Takeshi、Nakamura Moritaka、Taniguchi Masatoshi、Suzuki Kanako、Oshida Ryuichiro、Kondo Chiemi、Sun Song、Kato Kagayaki、Fukao Yoichiro、Hakoshima Toshio、Morita Miyo Terao
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 1-13
  • DOI: 10.1038/s41467-019-13729-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Endfoot regeneration restricts radial glial state and prevents translocation into the outer subventricular zone in early mammalian brain development (2019)
  • Author(s): Fujita Ikumi、Shitamukai Atsunori、Kusumoto Fumiya、Mase Shun、Suetsugu Taeko、Omori Ayaka、Kato Kagayaki、Abe Takaya、Shioi Go、Konno Daijiro、Matsuzaki Fumio
  • Journal Title: Nature Cell Biology Volume: 22 Issue: 1 Pages: 26-37
  • DOI: 10.1038/s41556-019-0436-9
  • Peer Reviewed / Open Access
• [Journal Article] イメージングデータ解析よろず相談所．大量画像解析のための自動化手法・応用編 (2019)
  • Author(s): 加藤輝
  • Journal Title: 実験医学 Volume: 37 Pages: 2346-2353
• [Journal Article] イメージングデータ解析よろず相談所．顕微観察画像の定量的情報解析とその落とし穴 (2019)
  • Author(s): 小山宏史，加藤輝
  • Journal Title: 実験医学 Volume: 37 Pages: 2772-2777
• [Journal Article] Elasticity-based boosting of neuroepithelial nukleokinesis via indirect energy transfer from mother to daughter (2018)
  • Author(s): Tomoyasu Shinoda, Arata Nagasaka, Yasuhiro Inoue, Ryo Higuchi, Yoshiaki Minami, Kagayaki Kato, Makoto Suzuki, Takefumi Kondo, Takumi Kawaue, Kanako Saito, Naoto Ueno, Yugo Fukazaawa, Masaharu Nagayama, Takashi Miura, Taiji Adachi, Takaki Miyata
  • Journal Title: PLoS Biology Volume: 16 Issue: 4 Pages: 2004426-2004426
  • DOI: 10.1371/journal.pbio.2004426
  • Peer Reviewed / Open Access
• [Journal Article] Solo and Keratin Filaments Regulate Epithelial Tubule Morphology (2018)
  • Author(s): Ryosuke Nishimura, Kagayaki Kato, Sachiko Fujiwara, Kazumasa Ohashi, Kensaku Mizuno
  • Journal Title: Cell Structure and Function Volume: 43 Issue: 1 Pages: 95-105
  • DOI: 10.1247/csf.18010
  • NAID: 130007383366
  • ISSN: 0386-7196, 1347-3700
  • Peer Reviewed
• [Journal Article] 生物画像処理・解析を加速するImageJマクロプログラミング (2018)
  • Author(s): 加藤輝
  • Journal Title: 実験医学 Volume: 36 Pages: 1513-1520
• [Presentation] 鳥類胚のライブイメージングが明らかにした、各脳領域の新しい前駆体マップと、脳形成を開始させる前部中内胚葉の作用 (2019)
  • Author(s): Hisato Kondoh, Koya Yoshihi, Hideaki Iida, Machiko Teramoto, Kagayaki Kato
  • Organizer: 第52回日本発生生物学会大会
• [Presentation] ニワトリ初期胚細胞の新しい標識法とライブイメージングによって明らかになった脳の発生の新しい機構 (2019)
  • Author(s): 近藤 寿人, 吉氷 康矢, 寺元 万智子, 飯田 英明, 加藤 輝
  • Organizer: 第42回日本分子生物学会年会
• [Presentation] Ground stateにおけるマウスES細胞の不均一性の同定とその制御機構の解明 (2019)
  • Author(s): 堀江 恭二, 渡邊 仁美, 西村 陽介, 渡邊 日佳流, 関 真秀, 清田 晃央, 加藤 輝, 若本 祐一, 瀬々 潤, 鈴木 穣, 山田 拓司, 近藤 玄, 吉田 純子
  • Organizer: 第42回日本分子生物学会年会
• [Presentation] PML bodyによる遺伝子転写制御メカニズムの解析～AP-CLaP法を用いて～ (2018)
  • Author(s): 栗原 美寿々、三宝 千秋、加藤 輝、重信 秀治、宮成 悠介
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] Ground stateにおけるマウスES細胞の不均一性の同定 (2018)
  • Author(s): 堀江 恭二、渡邊 仁美、西村 陽介、渡邊 日佳流、関 真秀、清田 晃央、加藤 輝、若本 祐一、鈴木 穣、山田 拓司、近藤 玄、吉田 純子
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] Live imaging of node graft and host cells to establish its role in head development (2018)
  • Author(s): Koya Yoshihi, Kagayaki Kato, Hisato Kondoh
  • Organizer: Joint Annual Meeting of 51st JSDB and 70th JSCB
• [Presentation] PCP factors are differentially involved in polarity establishment of ciliary orientation and cell elongation in the mouse oviduct. (2018)
  • Author(s): Fumiko Usami, Dongbo Shi, Kagayaki Kato, Toshihiko Fujimori
  • Organizer: Joint Annual Meeting of 51st JSDB and 70th JSCB
• [Presentation] Elasticity-based boosting of neuroepithelial nucleokinesis via indirect energy transfer from mother to daughter (2018)
  • Author(s): Tomoyasu Shinoda, Arata Nagasaka, Yasuhiro Inoue, Ryo Higuchi, Yoshiaki Minami, Kagayaki Kato, Makoto Suzuki, Takefumi kondo, Takumi Kawaue, Kanako Saito, Naoto Ueno, Yugo Fukazawa, Masaharu Nagayama, Takashi Miura, Taiji Adachi, Takaki Miyata
  • Organizer: Joint Annual Meeting of 51st JSDB and 70th JSCB
• [Book] 達人に訊くバイオ画像取得と定量解析Q&A (2021)
  • Author(s): 加藤 輝、小山 宏史
  • Total Pages: 220
  • Publisher: 羊土社
  • ISBN: 9784758122504