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Development of Informatics technologies for identification and analysis of singularity cells

Planned Research

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

Onami Shuichi  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 Completed (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 / バイオイメージ・インフォマティクス / 画像認識 / ライブイメージング
Outline of Final Research Achievements

We have achieved the following research results: a systematic analysis of cell morphodynamics in C. elegans early embryogenesis, quantification of changes in cytoplasmic texture associated with aging in C. elegans oocytes, global recommendations for bioimaging data format standards and data sharing systems, development of BD5, an open HDF5-based data format to represent quantitative biological dynamics data, development of NeuroGT, a brain atlas of neurogenic tagging CreER mouse drivers, development of PHi-C, a method for deciphering Hi-C data into polymer dynamics, implementation of BDML format output plug-in for Nikon Corporation's image analysis software, and development of a data platform for singularity biology.

Academic Significance and Societal Importance of the Research Achievements

バイオイメージ・インフォマティクス技術により、組織や個体等の様々な生命現象について様々な細胞特徴量についての全細胞ダイナミクス解析が可能になった。これにより、それぞれの生命現象において、従来の方法では不可能であったシンギュラリティ現象の解析が可能になった。更に、全細胞ダイナミクス解析により、細胞分化や組織のホメオスタシスに関与する、シンギュラリティ現象とは異なる、新たなメカニズムの発見も可能になった。加えて、バイオイメージデータのグローバルな共有に向けての世界連携組織の構築に成功し、生命科学分野の持続的な発展に向けての大きな一歩を日本が主導権を持つ形で踏み出すことに成功した。

Report

(6 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (217 results)

All 2023 2022 2021 2020 2019 2018 Other

All Int'l Joint Research (12 results) Journal Article (26 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 26 results,  Open Access: 22 results) Presentation (152 results) (of which Int'l Joint Research: 64 results,  Invited: 53 results) Book (4 results) Remarks (19 results) Patent(Industrial Property Rights) (1 results) Funded Workshop (3 results)

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

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] EMBL/Global BioImaging(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Dundee/EMBL-EBI(英国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] EMBL(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [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] Systematic analysis of cell morphodynamics in C. elegans early embryogenesis2023

    • Author(s)
      Azuma Yusuke、Okada Hatsumi、Onami Shuichi
    • Journal Title

      Frontiers in Bioinformatics

      Volume: 3

    • DOI

      10.3389/fbinf.2023.1082531

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Homeostasis Imbalance Process Ontology: a Study on COVID-19 Infectious Processes2023

    • Author(s)
      Yamagata Yuki、Kushida Tatsuya、Onami Shuichi、 Masuya Hiroshi
    • Journal Title

      BMC bioinformatics

      Volume: -

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Ontology for Cellular Senescence Mechanisms2023

    • Author(s)
      Yamagata Yuki、Fukuyama Tsubasa、Onami Shuichi、Masuya Hiroshi
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2023.03.09.531883

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] PHi-C2: interpreting Hi-C data as the dynamic 3D genome state2022

    • Author(s)
      Shinkai Soya、Itoga Hiroya、Kyoda Koji、Onami Shuichi
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: 21 Pages: 4984-4986

    • DOI

      10.1093/bioinformatics/btac613

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phenotype Anomaly Detection for Biological Dynamics Data Using a Deep Generative Model2022

    • Author(s)
      Ito Eisuke、Ueda Takaya、Takano Ryo、Tohsato Yukako、Kyoda Koji、Onami Shuichi、Nishikawa Ikuko
    • Journal Title

      Proceedings of the 31st International Conference on Artificial Neural Networks (ICANN 2022)

      Volume: - Pages: 432-444

    • DOI

      10.1007/978-3-031-15931-2_36

    • ISBN
      9783031159305, 9783031159312
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells2022

    • Author(s)
      Iida Shiori、Shinkai Soya、Itoh Yuji、Tamura Sachiko、Kanemaki Masato T.、Onami Shuichi、Maeshima Kazuhiro
    • Journal Title

      Science Advances

      Volume: 8 Issue: 22

    • DOI

      10.1126/sciadv.abn5626

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The PAF1 complex cell autonomously promotes oogenesis in Caenorhabditis elegans2022

    • Author(s)
      Kubota Yukihiro、Ota Natsumi、Takatsuka Hisashi、Unno Takuma、Onami Shuichi、Sugimoto Asako、Ito Masahiro
    • Journal Title

      Genes to Cells

      Volume: 27 Issue: 6 Pages: 409-420

    • DOI

      10.1111/gtc.12938

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain2022

    • Author(s)
      Towako Hiraki-Kajiyama, Nobuhiko Miyasaka, Reiko Ando, Noriko Wakisaka, Hiroya Itoga, Shuichi Onami, Yoshihiro Yoshihara
    • Journal Title

      bioRxiv

      Volume: N/A

    • DOI

      10.1101/2023.03.29.534505

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The centromere/kinetochore is assembled through CENP-C oligomerization2022

    • Author(s)
      Hara Masatoshi、Ariyoshi Mariko、Sano Tomoki、Nozawa Ryu-suke、Shinkai Soya、Onami Shuichi、Jansen Isabelle、Hirota Toru、Fukagawa Tatsuo
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2022.08.17.504347

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single-molecule tracking of Nanog and Oct4 in mouse embryonic stem cells2022

    • Author(s)
      Okamoto Kazuko、Fujita Hideaki、Okada Yasushi、Shinkai Soya、Onami Shuichi、Abe Kuniya、Fujimoto Kenta、Watanabe Tomonobu M
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/2022.08.08.503148

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Improvement in image quality via the pseudo confocal effect in multidirectional digital scanned laser light-sheet microscopy2021

    • Author(s)
      Kaneshiro Junichi、Shioi Go、Okamoto Kazuko、Onami Shuichi、Watanabe Tomonobu M.
    • Journal Title

      Optics Express

      Volume: 29 Issue: 15 Pages: 24278-24278

    • DOI

      10.1364/oe.423783

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy2021

    • Author(s)
      Nelson Glyn、et al.
    • Journal Title

      Journal of Microscopy

      Volume: 284 Issue: 1 Pages: 56-73

    • DOI

      10.1111/jmi.13041

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Texture-based screening to identify genes involved in reproductive aging in Caenorhabditis elegans2021

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

      International Journal of Bioscience, Biochemistry and Bioinformatics

      Volume: 11 Issue: 3 Pages: 40-49

    • DOI

      10.17706/ijbbb.2021.11.3.40-49

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons2021

    • Author(s)
      Hirata Tatsumi、Tohsato Yukako、Itoga Hiroya、Shioi Go、Kiyonari Hiroshi、Oka Sanae、Fujimori Toshihiko、Onami Shuichi
    • Journal Title

      Cell Reports Methods

      Volume: 1 Issue: 3 Pages: 100012-100012

    • DOI

      10.1016/j.crmeth.2021.100012

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology2021

    • Author(s)
      Sarkans Ugis、et al.
    • Journal Title

      Nature Methods

      Volume: 18 Issue: 12 Pages: 1418-1422

    • DOI

      10.1038/s41592-021-01166-8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A global view of standards for open image data formats and repositories2021

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

      Nature Methods

      Volume: 18 Issue: 12 Pages: 1440-1446

    • DOI

      10.1038/s41592-021-01113-7

    • Related Report
      2021 Annual Research 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 Issue: 1 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 Issue: 8 Pages: e0237468-e0237468

    • 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 Issue: 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

      Biophysical Journal

      Volume: 118 Issue: 9 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] SSBD:database / SSBD:repository - global sharing of bioimaging data2023

    • Author(s)
      糸賀裕弥, 王放放, 山縣友紀, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      日本生理学会第100回記念大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 理研オープンライフサイエンスプラットフォームの紹介および活動報告2023

    • Author(s)
      大浪修一
    • Organizer
      理研シンポジウム: 理研オープンライフサイエンスプラットフォーム 研究課題成果報告会
    • Related Report
      2022 Annual Research Report
  • [Presentation] SSBD:repository/database:バイオイメージングデータのグローバルなデータ共有2023

    • Author(s)
      京田耕司, 糸賀裕弥, 王放放, 山縣友紀, 遠里由佳子, 大浪修一
    • Organizer
      第64回日本植物生理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] SSBD:database, SSBD:repository, Data platform and Data portal for Singularity Biology - シンギュラリティ生物学のためのSSBD、データプラットフォーム、データポータルの取り組み2023

    • Author(s)
      糸賀裕弥, 王放放, 山縣友紀, 京田耕司, Miranda Miguel Miranda., 山本春菜, 遠里由佳子, 大浪修一
    • Organizer
      新学術領域「シンギュラリティ生物学」成果報告シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] バイオイメージングデータの次世代フォーマット開発と解析ワー クフロー基盤の開発構想2023

    • Author(s)
      京田耕司, 糸賀裕弥, 大浪修一
    • Organizer
      新学術領域「シンギュラリティ生物学」成果報告シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] 画像処理による細胞動態の定量解析2023

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      新学術領域研究「シンギュラリティ生物学」 成果報告シンポジウム・領域会議
    • Related Report
      2022 Annual Research Report
  • [Presentation] シンギュラリティ生物学のためのデータサイエンスプラットフォーム:現状と今後の展望2023

    • Author(s)
      大浪修一
    • Organizer
      新学術領域「シンギュラリティ生物学」成果報告シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] SSBD:database and SSBD:repository - Global sharing of bioimaging data -2023

    • Author(s)
      Itoga Hiroya, Wang Fangfang, Yamagata Yuki, Kyoda Koji, Tohsato Yukako, Onami Shuichi
    • Organizer
      RIKEN BDR Symposium 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Ontology Development for Knowledge Organization of Cellular Senescence Processes.2023

    • Author(s)
      Yamagata Yuki, Masuya Hiroshi, Onami Shuichi
    • Organizer
      RIKEN BDR Symposium 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Image data-driven modeling of developmental systems and open bioimaging DX2023

    • Author(s)
      Onami Shuichi
    • Organizer
      IPR x RIKEN (BDR) Symposium 2023 Dive into Data of Life
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SSBD:database / SSBD:repository バイオイメージングデータのグローバルなデータ共有2023

    • Author(s)
      糸賀裕弥, 王放放, 山縣友紀, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      第14回光塾
    • Related Report
      2022 Annual Research Report
  • [Presentation] Functions of the eggshell in C.elegans development: Effects on starvation resistance and body-surface structure2023

    • Author(s)
      Hatakeyama Akiko, Onami Shuichi
    • Organizer
      RIKEN BDR Symposium 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] データ駆動型および仮説検証型アプローチによる細胞形態変化の定量解析2022

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Single nucleosome imaging reveals “steady-state” motion of interphase chromatin in living human cells2022

    • Author(s)
      Iida Shiori, Shinkai Soya, Itoh Yuji, Tamura Sachiko, Kanemaki Masato, Onami Shuichi, Maeshima Kazuhiro
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 線虫の行動個体差を生み出すメカニズムの解明2022

    • Author(s)
      尾上詩織, 京田耕司, 大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] SSBD:database/repository: バイオイメージングデータのグローバルなデータ共有2022

    • Author(s)
      京田耕司, 糸賀裕弥, 王放放, 山縣友紀, 遠里由佳子, 大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] CENP-Cの自己多量体化はセントロメアクロマチンおよびキネトコアの形成に必須である2022

    • Author(s)
      原昌稔, 有吉眞理子, 佐野智基, 野澤竜介, 新海創也, 大浪修一, Isabelle Jansen, 広田亨, 深川竜郎
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] バイオイメージングデータの解析、管理、公開に関する情報科学技術の現状と将来展望2022

    • Author(s)
      大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] SSBDデータベースによるグローバルなバイオイメージングデータの共有2022

    • Author(s)
      大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] オントロジーに基づく細胞老化プロセスの知識記述モデリング2022

    • Author(s)
      山縣友紀, 大浪修一, 桝屋啓志
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 流体力学的相互作用が駆動する3次元ゲノム組織化2022

    • Author(s)
      新海創也, 大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Polymer physics for Hi-C data reveals rheological features of chromatin2022

    • Author(s)
      Shinkai Soya, Onami Shuichi
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 次世代SPIM:マウス胚まるごとのライブイメージングと全細胞トラッキングに向けて2022

    • Author(s)
      塩井剛, 渡邉朋信, 金城純一, 東裕介, 大浪修一
    • Organizer
      第45回日本分子生物学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 細胞のセグメンテーションデータ作成と公開2022

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第25回情報論的学習理論ワークショップ
    • Related Report
      2022 Annual Research Report
  • [Presentation] データベースSSBD、データ共有プラットフォームOMEROが開くオープンサイエンス2022

    • Author(s)
      大浪修一
    • Organizer
      日本学術会議 公開シンポジウム「異なるモダリティを統合するバイオ計測の最前線と展望」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] SSBD:database/repository バイオイメージングデータのグローバルなデータ共有2022

    • Author(s)
      糸賀裕弥, 王放放, 山縣友紀, 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2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] BD-zarr: 生命現象の時空間動態データを記述するための次世代フォーマットの開発2022

    • Author(s)
      京田耕司, 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2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] バイオイメージングデータのグローバルなデータ共有システムの構築2022

    • Author(s)
      大浪修一
    • Organizer
      トーゴーの日シンポジウム2022
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] ヒト生細胞の局所クロマチン動態は細胞周期を通して一定である2022

    • Author(s)
      Iida Shiori, Shinkai Soya, Itoh Yuji, Tamura Sachiko, Kanemaki Masato, Onami Shuichi, Maeshima Kazuhiro
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 長期間ライブイメージングを可能にする光損傷を軽減する撮影条件の最適化2022

    • Author(s)
      塩井剛, 渡邉朋信, 金城純一, 東裕介, 大浪修一
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Polymer physics for Hi-C data reveals dynamic viscoelastic features of chromatin controlled by SMC proteins2022

    • Author(s)
      Shinkai Soya
    • Organizer
      Genome organisation by SMC complexes
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Knowledge Systematization for Cellular Senescence Processes by Homeostasis Imbalance Process Ontology2022

    • Author(s)
      山縣友紀, 大浪修一, 桝屋啓志
    • Organizer
      ICBO 2022: International Conference on Biomedical Ontology
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] General overview of Image Data Management WG2022

    • Author(s)
      Onami Shuichi
    • Organizer
      Exchange of Experience VII
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Phenotype anomaly detection for biological dynamics data using a deep generative model2022

    • Author(s)
      Ito Eisuke, Ueda Takaya, Takano RYo, Yukako Tohsato, Kyoda Koji, Onami Shuichi, Nishikawa Ikuko
    • Organizer
      The 31st International Conference on Artificial Neural Networks
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD:database/repository バイオイメージングデータのグローバルなデータ共有2022

    • Author(s)
      糸賀裕弥, 王放放, 山縣友紀, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      第31回日本バイオイメージング学会学術集会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 先端バイオイメージングデータのデータ駆動解析とオープンサイエンス2022

    • Author(s)
      大浪修一
    • Organizer
      第31回日本バイオイメージング学会学術集会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Individual behavioral differences in C. elegans2022

    • Author(s)
      Onoue Shiori, Kyoda Koji, Onami Shuichi
    • Organizer
      C. elegans Topic Meeting: neuronal development, synaptic function and behavior
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Role of the Eggshell in Starvation Resistance during L1 arrest in Caenorhabditis elegans2022

    • Author(s)
      Hatakeyama Akiko, Onami Shuichi
    • Organizer
      2022 International C. elegans Topic Meeting on Metabolism, Aging, Pathogenesis, Stress, and Small RNAs
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Comparative analysis of cellular dynamics of C. inopinata and C. elegans zygotes2022

    • Author(s)
      Oomura Shun, Onami Shuichi, Kyoda Koji, Haruta Nami, Sugimoto Asako
    • Organizer
      Evolutionary Biology of Caenorhabditis and Other Nematodes
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] BD5: an open data format for representing quantitative biological dynamics data2022

    • Author(s)
      Kyoda Koji, Ho Kenneth H.L. ., Itoga Hiroya, Tohsato Yukako, Onami Shuichi
    • Organizer
      2022 European HDF5 Users Group (HUG)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Next Generation SPIM towards live imaging and all-cells tracking of a whole mouse embryo2022

    • Author(s)
      塩井剛, 渡邉朋信, 金城純一, 東裕介, 大浪修一
    • Organizer
      日本発生生物学会第55回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] An image processing and deep learning-based pipeline for quantitative analysis of cellular (morpho)dynamics2022

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      日本発生生物学会第55回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] BD-zarr: a zarr-based format for representing quantitative data of biosystems dynamics2022

    • Author(s)
      Kyoda Koji, Ho Kenneth H.L.., Itoga Hiroya, Onami Shuichi
    • Organizer
      I2K 2022 From Images to Knowledge
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 線虫初期胚において胚性致死遺伝子が示す時空間的発現パターンの分類2022

    • Author(s)
      岡田初美、古島理恵、京田耕司、大浪修一
    • Organizer
      線虫研究の未来をつくる会2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] 先端バイオイメージングのオープンサイエンスとDXプラットフォーム2022

    • Author(s)
      大浪修一
    • Organizer
      第127回日本解剖学会総会・全国学術集会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Data-driven modeling of animal embryogenesis2022

    • Author(s)
      Shuichi Onami
    • Organizer
      BDR Symposium 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] SSBD:database and SSBD:repository - Open Resources for Bioimages and Quantitative Data for Biosystems Dynamics2022

    • Author(s)
      Hiroya Itoga, Fangfang Wang, Koji Kyoda, Yukako Tohsato, Shuichi Onami
    • Organizer
      BDR Symposium 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] イメージングデータ解析が拓く生命科学の新時代2022

    • Author(s)
      大浪修一
    • Organizer
      ソニー先端技術講演会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] バイオイメージングデータの標準化・共有化の国際情勢2022

    • Author(s)
      大浪修一
    • Organizer
      ABiS Symposium イメージングデータ解析が拓く生命科学の新時代
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] A global view of standards for open image data formats and repositories2022

    • Author(s)
      Shuichi Onami
    • Organizer
      The BINA January Community Conversation
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 画像関連データの公開と共有について2022

    • Author(s)
      大浪修一
    • Organizer
      CREST多細胞領域 第3回領域会議
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] イメージングデータ駆動型生命科学と理研のオープンライフサイエンス2021

    • Author(s)
      大浪修一
    • Organizer
      CSRSインフォマティクス・データ科学推進プログラム成果報告会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 流体力学的相互作用化の動的3次元ゲノム組織化2021

    • Author(s)
      新海創也, 大浪修一
    • Organizer
      第39回染色体ワークショップ・第19回核ダイナミクス研究会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Development of bioimage informatics methods for Singularity Biology2021

    • Author(s)
      Shuichi Onami
    • Organizer
      Pacifichem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] データ駆動型モデリングによる生命動態の理解と予測2021

    • Author(s)
      大浪修一
    • Organizer
      理化学研究所・熊本大学合同生命科学領域DXシンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Single molecule measurement of core-transcription factors for pluripotency maintenance, Nanog and Oct4, in living nuclei of mouse embryonic stem cells2021

    • Author(s)
      Kazuko Okamoto, Hideaki Fujita, Soya Shinkai, Shuichi Onami, Yasushi Okada, Kuniya Abe, Tomonobu M. Watanabe
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] NeuroGT:神経細胞の誕生日タグづけ用CreERドライバーマウスの脳アトラス2021

    • Author(s)
      平田たつみ, 遠里由佳子, 糸賀裕弥, 塩井剛, 清成寛, 岡早苗, 藤森俊彦, 大浪修一
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 線虫C. elegansの胚発生における細胞形態変化の定量解析2021

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 線虫の行動個体差を生み出すメカニズムの解明2021

    • Author(s)
      尾上詩織, 大浪修一
    • Organizer
      第44回日本分子生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Quantitative analysis of cell morphology dynamics in C. elegans embryogenesis2021

    • Author(s)
      Yusuke Azuma, Shuichi Onami
    • Organizer
      Bioimage Informatics 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] バイオDXを推進する生命現象の時空間動態データを解析する基盤の構築2021

    • Author(s)
      京田耕司,糸賀裕弥,遠里由佳子,大浪修一
    • Organizer
      バイオDXの最前線 - JST戦略的創造研究推進事業 CREST「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」キックオフシンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] SBD:databaseとSSBD:repositoryを核とした生命画像と生命動態のオープンデータ駆動による研究ライフサイクルの実現2021

    • Author(s)
      糸賀裕弥, 王放放, 京田耕司, 遠里由佳子, 大浪修一
    • Organizer
      バイオDXの最前線 - JST戦略的創造研究推進事業 CREST「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」キックオフシンポジウム
    • Related Report
      2021 Annual Research Report
  • [Presentation] Launching NeuroGT: a brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons2021

    • Author(s)
      Tasumi Hirata, Yukako Tohsato, Hiroya Itoga, Go Shioi, Hiroshi Kiyonari, Sanae Oka, Toshihiko Fujimori, Shuichi Onami
    • Organizer
      Neuroscience 2021, 50th Annual Meeting
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD:database/repository 生命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2021

    • Author(s)
      糸賀裕弥, 王放放, 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2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] Homeostasis Imbalance Process Ontology: a Study on COVID-19 Infectious Processes2021

    • Author(s)
      Yuki Yamagata, Tatsuya Kushida, Shuichi Onami, Hiroshi Masuya
    • Organizer
      10th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] シンギュラリティ生物学を実現する大量データの解析・保存・標準化2021

    • Author(s)
      大浪修一
    • Organizer
      新学術三領域合同勉強会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Comparative analysis of cellular dynamics of C. elegans and C. inopinata zygotes2021

    • Author(s)
      大村駿, 大浪修一, 京田耕司, 春田奈美, 杉本亜砂子
    • Organizer
      線虫研究の未来を創る会2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] 胚発生における細胞形態変化の定量解析2021

    • Author(s)
      東裕介, 大浪修一
    • Organizer
      線虫研究の未来を創る会2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] Worm Developmental Dynamics Database 2 - an open database with visualization for biological dynamics of large-scale RNAi experiments on C. elegans embryos2021

    • Author(s)
      糸賀裕弥, 京田耕司, 大浪修一
    • Organizer
      線虫研究の未来を創る会2021
    • Related Report
      2021 Annual Research Report
  • [Presentation] NeuroGT:神経細胞の誕生日タグづけ用CreERドライバーマウスの脳アトラス2021

    • Author(s)
      平田たつみ, 遠里由佳子, 糸賀裕弥, 塩井剛, 清成寛, 岡早苗, 藤森俊彦, 大浪修一
    • Organizer
      第44回日本神経科学大会 / CJK第1回国際会議
    • Related Report
      2021 Annual Research Report
  • [Presentation] 生命科学領域知識統合に向けたオントロジー開発とCOVID-19機序解明に向けた取り組み2021

    • Author(s)
      山縣友紀, 櫛田達矢, 大浪修一, 桝屋啓志
    • Organizer
      2021年度人工知能学会全国大会(第35回)
    • Related Report
      2021 Annual Research Report
  • [Presentation] Comparative analysis of cellular dynamics of C. inopinata and C. elegans zygotes2021

    • Author(s)
      Shun Oomura, Shuichi Onami, Koji Kyoda, Nami Haruta, Asako Sugimoto
    • Organizer
      The 23rd International C. elegans Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Worm Developmental Dynamics Database 2 - an open database with visualization for biological dynamics of large-scale RNAi experiments on C. elegans embryos2021

    • Author(s)
      Hiroya Itoga, Koji Kyoda, Shuichi Onami
    • Organizer
      The 23rd International C. elegans Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Individual behavioral differences in C. elegans2021

    • Author(s)
      Shiori Onoue, Shuichi Onami
    • Organizer
      The 23rd International C. elegans Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons2021

    • Author(s)
      平田たつみ, 遠里由佳子, 糸賀裕弥, 塩井剛, 清成寛, 岡早苗, 藤森俊彦, 大浪修一
    • Organizer
      第54回日本発生生物学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] BDZ: Zarr-based format of quantitative biological dynamics data for object storage and cloud computing2021

    • Author(s)
      Koji Kyoda, Ho Kenneth HL, Hiroya Itoga, Yukako Tohsato, Shuichi Onami
    • Organizer
      OME 2021 Community Meeting
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] SSBD:database and SSBD:repository - an added-value database and archive service for bioimages and quantitative data of biological dynamics -2021

    • Author(s)
      Hiroya Itoga, Fangfang Wang, Koji Kyoda, Yukako Tohsato, Shuichi Onami
    • Organizer
      OME 2021 Community Meeting
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [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] 実験医学別冊 最強のステップUPシリーズ 空間オミクス解析スタートアップ実践ガイド2022

    • Author(s)
      京田耕司、大浪修一
    • Total Pages
      6
    • Publisher
      羊土社
    • ISBN
      9784758122610
    • Related Report
      2022 Annual Research Report
  • [Book] 実験医学2021年12月号 Vol.39 No.192021

    • Author(s)
      大浪修一
    • Total Pages
      6
    • Publisher
      羊土社
    • ISBN
      9784758125505
    • Related Report
      2021 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] 細胞が成長する過程におけるDNAの「ゆらぎ」をとらえた!

    • URL

      https://www.nig.ac.jp/nig/ja/2022/06/research-highlights_ja/pr20220604.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] Homeostasis imbalance process ontology (HoIP)

    • URL

      https://bioportal.bioontology.org/ontologies/HOIP

    • Related Report
      2022 Annual Research Report
  • [Remarks] Chronic cellular senescence course- HoIPをNEDxに公開

    • URL

      https://doi.org/10.18119/N9KS4H

    • Related Report
      2022 Annual Research Report
  • [Remarks] “誕生日タグづけ”マウスの脳画像データベース「NeuroGT」を公開

    • URL

      https://www.nig.ac.jp/nig/ja/2021/05/research-highlights_ja/pr20210525.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] 生命科学画像のデータ形式の標準化とデータ共有リポジトリの整備に向けた国際提言

    • URL

      https://www.riken.jp/pr/news/2021/20210511_2/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] データの「共有」で生命科学研究のレベルをジャンプアップ!

    • URL

      https://www.riken.jp/pr/closeup/2021/20211026_1/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] 人工知能学会受賞者【全国大会優秀賞】

    • URL

      https://www.ai-gakkai.or.jp/about/award/jsai_award-conf/

    • Related Report
      2021 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
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    • 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
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Published: 2018-07-20   Modified: 2024-01-30  

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