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Development of Informatics technologies for identification and analysis of singularity cells

Planned

Project AreaSingularity biology
Project/Area Number 18H05412
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

大浪 修一  国立研究開発法人理化学研究所, 生命機能科学研究センター, チームリーダー (50348843)

Project Period (FY) 2018-06-29 – 2023-03-31
Project Status Granted (Fiscal Year 2022)
Budget Amount *help
¥98,020,000 (Direct Cost: ¥75,400,000、Indirect Cost: ¥22,620,000)
Fiscal Year 2022: ¥16,770,000 (Direct Cost: ¥12,900,000、Indirect Cost: ¥3,870,000)
Fiscal Year 2021: ¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2020: ¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2019: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2018: ¥26,650,000 (Direct Cost: ¥20,500,000、Indirect Cost: ¥6,150,000)
Keywordsバイオイメージ・インフォマティクス / データプラットフォーム / 深層学習 / ビッグデータ / データ統合 / 画像認識 / ライブイメージング
Outline of Annual Research Achievements

1.シンギュラリティ細胞を同定するインフォマティクス技術の開発
「1-1. オブジェクト認識依存型のシンギュラリティ細胞同定法の開発」として、前年度に引き続きA03-2堀川班の粘菌、およびA03-4岡崎班のT細胞の遊走の2次元タイムラプス蛍光顕微鏡画像に対して、細胞の移動を自動計測するソフトウェアを開発した。これらの計測データを用いてT細胞とB細胞の相互作用と遊走様式、およびそれに対するLAG-3発現の影響に関するデータ解析を行なった。。また、堀川班の粘菌の遊走解析で使用してきた(株)ニコン製の画像解析ソフトウェアについて、当該ソフトウェアを用いた解析結果をオープンフォーマットBDML形式で出力するソフトウェアプラグインをニコンと協力して開発した。当該プラグインは、(株)ニコン製の画像ソフトウェアの最新バージョンに標準装備された。「1-2. オブジェクト認識非依存型のシンギュラリティ細胞同定法の開発」として、前年度に引き続き、老化に伴う卵母細胞の細胞質の外観の変化を検出する画像認識手法の開発を行なった。老化に伴う卵母細胞の外観の特徴を検出する画像特徴としてMm ValueとGLCM-CORを見出し、各々の特徴が細胞質のどのような特徴を認識しているのかを解析した。その結果、老化に伴い、卵母細胞の細胞質顆粒の大きさが増加していることを見出した。
2.シンギュラリティ生物学のためのデータプラットフォームの開発
「2-1. データ保管プラットフォームの開発」として、前年度開発した1.0ペタバイトのネットワークストレージシステムを運用した。「2-2. データ活用プラットフォームの開発」として、シンギュラリティ生物学用データポータルのシステムを開発した。更に、前年度に開発したオープンデータフォーマットBD5をGalaxy等のワークフローで活用するためのライブラリを開発し、公開した。

Current Status of Research Progress
Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

当初の計画通り、「1.シンギュラリティ細胞を同定するインフォマティクス技術の開発」に関しては、A03生物班が対象とする複数の細胞種に対する自動認識ソフトウェアの開発が順調に進んでおり、プロトタイプ版を活用したデータ計測が始まっている。また、これらのソフトウェアを用いて計測したデータを用いた解析に関しても共同研究が進んでおり、A03生物班の具体的な研究課題に関する解析研究が順調に進んでいる。また、大浪班が独自に行っている、線虫胚を対象にした研究も進展している。
「2.シンギュラリティ生物学のためのデータプラットフォームの開発」に関しても、当初の計画のとおり、領域全体で研究データを共有し利活用するデータプラットフォームの初期版の構築は完了しており、計画班とAMATERASプロトタイプ機利用者を中心に実際の活用が始まっている。また、画像認識により定量化した生命動態データを高速かつ効率的に取り扱うデータフォーマットBD5を開発し、更に、クラウド環境における次世代の生命科学イメージングデータの解析に使用する、次世代ファイルフォーマットの確立に向けて国際的な会議に参加し議論を進めている。
これらの理由から、当研究課題はおおむね順調に進展していると判断している。

Strategy for Future Research Activity

当初の計画通り研究開発を進める。2021年度については下記を進める。
1.シンギュラリティ細胞を同定するインフォマティクス技術の開発: 「1-1.オブジェクト認識依存型のシンギュラリティ細胞同定法の開発」としては、引き続きA03-2堀川班の粘菌、およびA03-4岡崎班のT細胞の遊走の2次元タイムラプス顕微鏡画像に対する自動計測ソフトウェアの開発を継続する。更に、これらの計測データを用いた粘菌/T細胞のシンギュラリティ現象の解明を、各班と協力して進める。また、公募班の高里班について、細胞自動認識ソフトウェアの開発を開始する。公募班の蛭田班とプローブ開発の共同研究を実施する。「1-2.オブジェクト認識非依存型のシンギュラリティ細胞同定法の開発」としては、引き続き、AMATERASプロトタイプ機で取得したA03-2堀川班の粘菌遊走の2次元タイムラプス顕微鏡画像を対象に手法の開発を継続する。また、公募班も含めたその他の班の研究対象について、オブジェクト認識被依存型手法の適用可能性について検討する。
2.シンギュラリティ生物学のためのデータプラットフォームの開発: 「2-1.データ保管プラットフォームの開発」としては、引き続き、内外の多様な公開データを統合的に管理するシステムを開発し整備する。「2-2.データ活用プラットフォームの開発」としては、引き続きSSBDデータベースで得られた定量データの表現・可視化技術を用いて、ROIデータ、細胞特徴量データ、1細胞網羅的遺伝子発現解析データなどを迅速かつ容易に可視化、解析可能なシステムを開発する。
3.シンギュラリティ現象を解析するインフォマティクス技術の開発: 引き続き取得したデータより個々の現象の発現に関する因果関係ネットワークを推定し、推定結果を用いて目的のシンギュラリティ現象を解明する。

Report

(3 results)
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report

Research Products

(112 results)

All 2021 2020 2019 2018 Other

All Int'l Joint Research (8 results) Journal Article (11 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 11 results,  Open Access: 10 results) Presentation (75 results) (of which Int'l Joint Research: 39 results,  Invited: 35 results) Book (2 results) Remarks (12 results) Patent(Industrial Property Rights) (1 results) Funded Workshop (3 results)

  • [Int'l Joint Research] University of Dundee/EMBL-EBI(英国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] EMBL(ドイツ)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Dundee/EMBL-EBI(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] University of British Columbia(カナダ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] EMBL(ドイツ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Uppsala University(スウェーデン)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] UMass Medical School(米国)

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

    • Related Report
      2018 Annual Research Report
  • [Journal Article] A global view of standards for open image data formats and repositories2021

    • Author(s)
      Jason R. Swedlow, Pasi Kankaanpaa, Ugis Sarkans, Wojtek Goscinski, Graham Galloway, Leonel Malacrida, Ryan P. Sullivan, Steffen Hartel, Claire M. Brown, Christopher Wood, Antje Keppler, Federica Paina, Ben Loos, Sara Zullino, Dario Livio Longo, Silvio Aime, Shuichi Onami
    • Journal Title

      Nature Methods

      Volume: -

    • DOI

      10.1038/s41592-021-01113-7

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Texture-based screening of genes involved in reproductive aging in Caenorhabditis elegans2021

    • Author(s)
      Momoko Imakubo, Koji Kyoda, Hiroya Itoga, Jun Takatama, Shuichi Onami
    • Journal Title

      International Journal of Bioscience, Biochemistry and Bioinformatics

      Volume: -

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] C. elegans spermatozoa lacking spe-45 are incapable of fusing with the oocyte plasma membrane2021

    • Author(s)
      Jun Takayama, Tasuya Tajima, Shuichi Onami, Htoshi Nishimura
    • Journal Title

      microPublication Biology

      Volume: -

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes2021

    • Author(s)
      Momoko Imakubo, Jun Takayama, Hastumi Okada, Shuichi Onami
    • Journal Title

      BMC Bioinformatics

      Volume: 22 Pages: 73-73

    • DOI

      10.1186/s12859-021-03990-3

    • NAID

      120007006688

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Toward understanding the dynamic state of 3D genome2020

    • Author(s)
      Shinkai S, Onami S, Nakato R.
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 18 Pages: 2259-2269

    • DOI

      10.1016/j.csbj.2020.08.014

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] BD5: An open HDF5-based data format to represent quantitative biological dynamics data2020

    • Author(s)
      Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami
    • Journal Title

      PLOS ONE

      Volume: 15

    • DOI

      10.1371/journal.pone.0237468

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] PHi-C: deciphering Hi-C data into polymer dynamics2020

    • Author(s)
      Shinkai Soya、Nakagawa Masaki、Sugawara Takeshi、Togashi Yuichi、Ochiai Hiroshi、Nakato Ryuichiro、Taniguchi Yuichi、Onami Shuichi
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 2

    • DOI

      10.1093/nargab/lqaa020

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization2020

    • Author(s)
      Soya Shinkai, Takeshi Sugawara, Hisashi Miura, Ichiro Hiratani, Shuichi Onami
    • Journal Title

      Biophys J.

      Volume: 118 Pages: 2220-2228

    • DOI

      10.1016/j.bpj.2020.02.020

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] On Bringing Bioimaging Data into the Open(-World)2019

    • Author(s)
      Josh Moore, Norio Kobayashi, Susanne Kunis, Shuichi Onami and Jason R. Swedlow
    • Journal Title

      Proceedings of the 12th International SWAT4HCLS Conference

      Volume: -

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Improvement and Evaluation of a Mathematical Model for Fertilization Calcium Waves in <i>Caenorhabditis Elegans</i>2018

    • Author(s)
      Imakubo Momoko、Takayama Jun、Onami Shuichi
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: 11 Issue: 0 Pages: 24-30

    • DOI

      10.2197/ipsjtbio.11.24

    • NAID

      130007402844

    • ISSN
      1882-6679
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of an Integrated Visualization System for Phenotypic Character Networks2018

    • Author(s)
      Onoue Yosuke、Kyoda Koji、Kioka Miki、Baba Kazutaka、Onami Shuichi、Koyamada Koji
    • Journal Title

      IEEE Pacific Visualization Symposium (PacificVis 2018)

      Volume: - Pages: 21-25

    • DOI

      10.1109/pacificvis.2018.00012

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] 理研オープンライフサイエンスプラットフォーム2021

    • Author(s)
      大浪修一, 粕川雄也, 桝屋啓志
    • Organizer
      理研ハッカソン オープンシンポジウム ―理研が進めるオープンサイエンスの実践―
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 時空間レジストレーションに基づく分子間相互作用の自動抽出2021

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      2020年度AIPチャレンジ成果報告会
    • Related Report
      2020 Annual Research Report
  • [Presentation] SBD:database and SSBD:repository - Online open resources for bioimages and quantitative data for biosystems dynamics2021

    • Author(s)
      Hiroya Itoga, Ho Kenneth Hunglit, Koji Kyoda, Yukako Tohsato, Shuichi Onami
    • Organizer
      RIKEN BDR Symposium 2021 - Structuring Biosystems: Functions Emerging from Molecules -
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Data-driven analysis of the mechanism of animal development2021

    • Author(s)
      Shuichi Onami
    • Organizer
      ERCIM-JST Joint Symposium on Big Data and Artificial Intelligence
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven analysis of the mechanism of animal development2021

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Toward understanding the dynamic state of 3D genome by polymer modeling of Hi-C data2020

    • Author(s)
      Soya Shinkai, Ryuichiro Nakato, Shuichi Onami
    • Organizer
      Cell Bio Virtual 2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Texture-based screening to identify genes involved in reproductive aging in Caenorhabditis elegans.2020

    • Author(s)
      Momoko Imakubo, Koji Kyoda, Hiroya Itoga, Jun Takayama, Shuichi Onami
    • Organizer
      The 2020 Asia Digital Image Processing Conference (ADIP2020)
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD:database and SSBD:repository - Online open resources for bioimages and quantitative data for biosystems dynamics2020

    • Author(s)
      Hiroya Itoga, Ho Kenneth Hunglit, Koji Kyoda, Yukako Tohsato, Shuichi Onami
    • Organizer
      Biological Data Science
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] バイオ計測と画像解析技術2020

    • Author(s)
      大浪修一
    • Organizer
      公開シンポジウム 「次世代統合バイオイメージングと数理の協働の展望」
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] SSBD:細胞・発生画像情報と生命動態情報の統合データベース・レポジトリ2020

    • Author(s)
      糸賀裕弥, ホーケネス, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      トーゴーの日シンポジウム2020
    • Related Report
      2020 Annual Research Report
  • [Presentation] 大規模イメージングデータを用いた生命システムのデータ駆動モデリング2020

    • Author(s)
      大浪修一
    • Organizer
      ゲノム創薬・創発フォーラム 第4回シンポジウム
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Toward a physical understanding of the dynamic 3D genome organization2020

    • Author(s)
      Soya Shinkai, Shuichi Onami, Nakato Ryuichiro
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Global BioImaging: Scope, planned activities and its work on image data2020

    • Author(s)
      Federica Paina, Jason Swedlow, Shuichi Onami
    • Organizer
      Global Bioimaging Exchange of Experience V
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Pre-publication image data: Management and processing in Japan2020

    • Author(s)
      Shuichi Onami
    • Organizer
      Global Bioimaging Exchange of Experience V
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SBD:database and SSBD:repository for sharing quantitative biosystems dynamics data and bioimaging data2020

    • Author(s)
      Shuichi Onami
    • Organizer
      2020 OME Community Meeting
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] シンギュラリティ細胞の同定と解析のためのインフォマティクス技術2020

    • Author(s)
      大浪修一
    • Organizer
      シンギュラリティ生物学×細胞ダイバース 合同ワークショップ
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] RIKEN Open Life Science Platform2020

    • Author(s)
      Shuichi Onami
    • Organizer
      RIKEN Hackathon FY2019 Open Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Deep learning based image restoration with efficient training data acquisition2020

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      ABiS Symposium Forefront and Future of Electron Microscopic Imaging
    • Related Report
      2019 Annual Research Report
  • [Presentation] 線虫C. elegans の発生動態の定量解析2020

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      CREST「ビッグデータ応用」第7回若手研究者合宿
    • Related Report
      2019 Annual Research Report
  • [Presentation] Data-driven modeling of animal development2020

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST International Symposium of Big Data Application
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven analysis of the mechanism of animal development2020

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST Big Data Joint Research Area-NSF-DATAIA Joint Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ゲノム構造データから読み解く階層的でダイナミックなゲノムレオロジー特性2019

    • Author(s)
      新海創也, 菅原武志, 三浦尚, 平谷伊智朗, 大浪修一
    • Organizer
      第37回染色体ワークショップ・第18回核ダイナミクス研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] On Bringing Bioimaging Data into the Open(-World)2019

    • Author(s)
      Josh Moore, Norio Kobayashi, Susanne Kunis, Shuichi Onami, Jason R. Swedlow
    • Organizer
      12th International SWAT4HCLS Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Microrheology for Hi-C data reveals a spectrum of dynamic 3D genome organization2019

    • Author(s)
      Soya Shinkai
    • Organizer
      Chromosome Dynamics 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] OME Core Ontology: An OWL-based Life Science Imaging Data Model2019

    • Author(s)
      Norio Kobayashi, Josh Moore, Shuichi Onami, Jason R. Swedlow
    • Organizer
      12th International SWAT4HCLS Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] バイアスフリーライフサイエンスに関して思うこと2019

    • Author(s)
      大浪修一
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] The 4DN-OME Ontology: an OME-OWL Extension with Emphasis on Usability, Minimum Information Guidelines and Quality Control for Super-Resolution Fluorescence Microscopy2019

    • Author(s)
      Mathias Hammer, Maximiliaan Huisman, Norio Kobayashi, Josh Moore, Alessandro Rigano, Shuichi Onami, Jason Swedlow, David Grunwald, Caterina Strambio-De-Castillia
    • Organizer
      The 2019 4DN-ASCB Satellite Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 線虫C. elegans の胚発生における細胞体積の定量解析2019

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 表現型特徴-遺伝子ネットワークの横断的探索を支援する可視化ツール2019

    • Author(s)
      夏川浩明, 石野隼伍、尾上洋介、京田耕司、大浪修一、小山田耕二
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] スケーリングを中心としたゲノム構造・動態の時空間階層性2019

    • Author(s)
      新海創也
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Microrheology of 3D genome organization by polymer modeling2019

    • Author(s)
      新海創也, 菅原武志、大浪修一
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 顕微鏡画像の自動取得と深層学習による画像修復2019

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第22回情報論的学習理論ワークショップ (IBIS 2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 線虫の胚発生画像を対象としたSeq-VAEに基づく時間的超解像2019

    • Author(s)
      田村壮, 河合新, 延原肇, 東裕介, 大浪修一
    • Organizer
      第22回情報論的学習理論ワークショップ (IBIS 2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] 線虫C. elegans胚発生後期における卵殻の機械的機能と性質2019

    • Author(s)
      畠山明子, 佐藤麻子, 田中陽, 大浪修一
    • Organizer
      第十一回光塾
    • Related Report
      2019 Annual Research Report
  • [Presentation] SSBD:database バイオイメージングデータベースの使い方2019

    • Author(s)
      京田耕司, ホー・ケネス, 糸賀裕弥, 遠里由佳子, 大浪修一
    • Organizer
      第十一回光塾
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 先人に学べ?!~科学者として生きてきた中での、出会い、決断、失敗、たまに成功~2019

    • Author(s)
      大浪修一
    • Organizer
      第十一回光塾
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 画像処理による線虫C. elegans の発生動態の定量解析2019

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第十一回光塾
    • Related Report
      2019 Annual Research Report
  • [Presentation] ゲノム構造データから読み解く階層的でダイナミックなゲノムレオロジー特性2019

    • Author(s)
      新海創也, 菅原武志, 三浦尚, 平谷伊智朗, 大浪修一
    • Organizer
      第十一回光塾
    • Related Report
      2019 Annual Research Report
  • [Presentation] RIKEN Open Life Science Platform2019

    • Author(s)
      Shuichi Onami
    • Organizer
      The 6th RIKEN-KI SciLifeLab Symposium: Biomedical Data for Artificial Intelligence
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SSBD: an open public database of microscopy images and quantitative data of biological dynamics facilitating the reuse and reanalyze of biological data.2019

    • Author(s)
      Ho Kenneth H.L., Yukako Tohsato, Koji Kyoda, Hiroya Itoga, Shuichi Onami
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Quantitative analysis of cellular dynamics in C. elegans embryos2019

    • Author(s)
      Yusuke Azuma, Shuichi Onami
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of bioimage informatics technologies for singularity biology2019

    • Author(s)
      Shuichi Onami
    • Organizer
      The 20th International Conference on Systems Biology (ICSB2019), Workshop “Singularity Biology: small elements change the function of the whole systems”
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Explorative Visualization for Phenotypic-Genotypic Network2019

    • Author(s)
      Hiroaki Natsukawa, Shungo Ishino, Yosuke Onoue, Koji Kyoda, Shuichi Onami and Koji Koyamda
    • Organizer
      IEEE VIS 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ゲノム構造データから読み解く階層的でダイナミックなゲノムレオロジー特性2019

    • Author(s)
      新海創也
    • Organizer
      令和元年度遺伝研研究会「クロマチン・細胞核の形成とダイナミクスによるゲノム制御」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Microrheology for Hi-C data reveals the spectrum of the dynamic 3D genome organization2019

    • Author(s)
      新海創也, 菅原武志, 三浦尚, 平谷伊智朗, 大浪修一
    • Organizer
      研究会「理論と実験」2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] SSBD: 細胞・発生画像情報と生命動態情報の統合データベース2019

    • Author(s)
      糸賀裕弥, ホーケネス, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      トーゴーの日シンポジウム2019~バイオデータベース:つないで使う~;
    • Related Report
      2019 Annual Research Report
  • [Presentation] Deep learning based image restoration with efficient training data acquisition2019

    • Author(s)
      Yusuke Azuma, Shuichi Onami
    • Organizer
      BioImage Informatics 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD: an open database for sharing quantitative data and microscopy images of biosystems dynamics2019

    • Author(s)
      Koji Kyoda, Kenneth Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami
    • Organizer
      BioImage Informatics 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mathematical modeling of chromatin and chromosome dynamics2019

    • Author(s)
      Soya Shinkai
    • Organizer
      The 78th Annual Meeting of the Japanese Cancer Association
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Deciphering genome organization and dynamics by mathematical modeling and simulation2019

    • Author(s)
      Soya Shinkai
    • Organizer
      The 57th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven analysis of the mechanism of animal development2019

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST Big Data Application Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Public Data Resources for the Global Bioimaging Community2019

    • Author(s)
      Jason Swedlow, Shuichi Onami
    • Organizer
      Global Bioimaging Exchange of Experience IV
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 胚発生における細胞動態の定量解析2019

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      線虫研究の未来を創る会 2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] 表現型特徴―遺伝子ネットワークの横断的探索を支援する視覚的分析2019

    • Author(s)
      夏川浩明, 石野隼伍, 尾上洋介, 京田耕司, 大浪修一, 小山田耕二
    • Organizer
      可視化情報シンポジウム2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Deciphering chromatin dynamics and structure by polymer modeling2019

    • Author(s)
      Soya Shinkai
    • Organizer
      International Congress on Industrial and Applied Mathematics (ICIAM2019)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 顕微鏡ビッグデータを用いた胚発生のデータ駆動モデリング2019

    • Author(s)
      大浪修一
    • Organizer
      第44回レーザ顕微鏡研究会&シンポジウム
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] シンギュラリティ細胞の同定と解析のためのインフォマティクス技術の開発2019

    • Author(s)
      大浪修一
    • Organizer
      第19回日本蛋白質科学会年会第71回日本細胞生物学会大会 合同年次大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Data-driven analysis of female pronuclear migration by image-processing embryonic movies in Phenobank2019

    • Author(s)
      Yukako Tohsato, Hatsumi Okada, Koji Kyoda, Shuichi Onami
    • Organizer
      22nd International C. elegans Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Mechanical functions of eggshell in C. elegans development.2019

    • Author(s)
      Akiko Hatakeyama, Asako Sato, Yo Tanaka, Shuichi Onami
    • Organizer
      22nd International C.elegans Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] New design and Improvement of Worm Developmental Dynamics Database (WDDD).2019

    • Author(s)
      Hiroya Itoga, Koji Kyoda, Shuichi Onami
    • Organizer
      22nd International C. elegans Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD: an open public database of microscopy images and quantitative data of biological dynamics2019

    • Author(s)
      Kenneth Ho, Yukako Tohsato, Koji Kyoda, Hiroya Itoga, Shuichi Onami
    • Organizer
      The 52nd Annual Meeting of the Japanese Society of Developmental Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Quantitative analysis of cell shape features in C. elegans embryos2019

    • Author(s)
      Yusuke Azuma, Shuichi Onami
    • Organizer
      52nd Annual Meeting of JSDB
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] データベース→データ駆動→AI駆動2019

    • Author(s)
      大浪修一
    • Organizer
      勉強会「人類の健康と生存圏拡大のためのAI駆動型生命科学~自律的に知識を発見するロボットでノーベル賞級の発見を目指す~」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Deciphering Hi-C data into polymer dynamics. Biophysical Society Thematic Meetings, Multiscale Modeling of Chromatin2019

    • Author(s)
      Soya Shinka, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, Shuichi Onami
    • Organizer
      Biophysical Society Thematic Meetings, Multiscale Modeling of Chromatin: Bridging Experiment with Theory
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD: an open database for sharing quantitative data and microsccopy images of biosystems dynamics2019

    • Author(s)
      Koji Kyoda, Ho Kenneth H.L., Yukako Tohsato, Hiroya Itoga, Shuichi Onami
    • Organizer
      International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Data-driven modeling of C. elegans development2019

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST International Symposium on Big Data Application
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Quantitative analysis of cell shape dynamics in C. elegans embryogenesis2018

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第56回日本生物物理学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Quantitative analysis of cellular dynamics in C. elegans embryo2018

    • Author(s)
      Shuichi Onami
    • Organizer
      The 56th Annual Meeting of The Biophysical Society of Japan
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 公共データベースの顕微鏡画像を用いた細胞核分裂の定量計測と表現型解析2018

    • Author(s)
      遠里由佳子, 岡田初美, 京田耕司, 大浪修一
    • Organizer
      生命医薬情報学連合大会(IIBMP2018)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Integration of big image and omics data for modeling of animal development2018

    • Author(s)
      Shuichi Onami
    • Organizer
      The 5th RIKEN-KI/SciLifeLab Joint Symposium Artificial Intelligence Meets Life Sciences
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Data-driven analysis of the mechanism of animal development2018

    • Author(s)
      Shuichi Onami
    • Organizer
      CREST「Big Data Application」Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SSBD: 細胞・発生画像情報と生命動態情報の統合データベース2018

    • Author(s)
      京田耕司、遠里由佳子、ホーケネス、糸賀裕弥、大浪修一
    • Organizer
      トーゴーの日シンポジウム2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] 受精と胚発生のシステムバイオロジーからオルガノイドの4Dデザイン・プラットフォームの構築へ2018

    • Author(s)
      大浪修一
    • Organizer
      理研―農研機構連携キックオフワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] SSBD: 細胞・発生画像情報と生命動態情報の統合データベース2018

    • Author(s)
      ホーケネス,遠里由佳子,京田耕司,糸賀裕弥,大浪修一
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Quantitative analysis of cell shape dynamics in C. elegans embryogenesis2018

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Book] 可視化学会学会誌 Vol.40, No.1562020

    • Author(s)
      京田耕司, ホーケネス, 糸賀裕弥, 遠里由佳子, 大浪修一
    • Total Pages
      3
    • Publisher
      社団法人 可視化情報学会
    • Related Report
      2019 Annual Research Report
  • [Book] イメージングの選び方・使い方100+2018

    • Author(s)
      大浪修一(分担執筆)
    • Total Pages
      2
    • Publisher
      羊土社
    • ISBN
      9784758103756
    • Related Report
      2018 Annual Research Report
  • [Remarks] ゲノムの動きをシミュレーションする新手法 -Hi-Cデータ解析パイプライン「PHi-C法」の開発-

    • URL

      https://www.riken.jp/press/2020/20200807_3/index.html

    • Related Report
      2020 Annual Research Report
  • [Remarks] TL’s talk in Symposium went public

    • URL

      https://so.riken.jp/2020/11/18/tls-talk-in-symposium-went-public/

    • Related Report
      2020 Annual Research Report
  • [Remarks] Watch TL’s Talk in GBI EoE V.

    • URL

      https://so.riken.jp/2020/10/21/watch-tls-talk-in-eoev-v/

    • Related Report
      2020 Annual Research Report
  • [Remarks] Watch TL’s Talk on Public Image Data Online.

    • URL

      https://so.riken.jp/2020/05/27/watch-tls-talk-on-public-image-data-online/

    • Related Report
      2020 Annual Research Report
  • [Remarks] SSBD was highlighted in Nature

    • URL

      https://so.riken.jp/2020/03/05/ssbd-was-appeared-in-nature/

    • Related Report
      2019 Annual Research Report
  • [Remarks] データドリブン・ライフサイエンス

    • URL

      https://bdrtimes.riken.jp/2019/10/01/kkyoda/

    • Related Report
      2019 Annual Research Report
  • [Remarks] TIFF image ROI contours written to BDML/BD5 format

    • URL

      https://so.riken.jp/2020/02/

    • Related Report
      2019 Annual Research Report
  • [Remarks] Watch TL's Talk on Public Image Data online

    • URL

      https://so.riken.jp/2020/05/

    • Related Report
      2019 Annual Research Report
  • [Remarks] The Onami Laboratory

    • URL

      https://so.riken.jp

    • Related Report
      2018 Annual Research Report
  • [Remarks] 発生動態研究チーム

    • URL

      http://www.riken.jp/research/labs/bdr/dev_dyn/

    • Related Report
      2018 Annual Research Report
  • [Remarks] 発生動態研究チーム

    • URL

      http://www.bdr.riken.jp/jp/research/labs/onami-s/index.html

    • Related Report
      2018 Annual Research Report
  • [Remarks] OMERO Open Workshop in Kobe

    • URL

      http://ssbd.qbic.riken.jp/event/omero2018/

    • Related Report
      2018 Annual Research Report
  • [Patent(Industrial Property Rights)] 光シート照射装置、光シート顕微鏡、光シート照射方法、および光シート照射プログラム2020

    • Inventor(s)
      渡邉朋信, 金城純一, 大浪修一
    • Industrial Property Rights Holder
      渡邉朋信, 金城純一, 大浪修一
    • Industrial Property Rights Type
      特許
    • Filing Date
      2020
    • Related Report
      2020 Annual Research Report
  • [Funded Workshop] シンギュラリティ生物学第1回国際トレーニング2019

    • Related Report
      2019 Annual Research Report
  • [Funded Workshop] Singularity Biology: small elements change the function of the whole systems2019

    • Related Report
      2019 Annual Research Report
  • [Funded Workshop] OMERO Open Workshop in Kobe 20182018

    • Related Report
      2018 Annual Research Report

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Published: 2018-07-20   Modified: 2022-07-01  

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