Category: Uncategorized

Released a new video about SSBD

We have released a new video introducing and explaining SSBD.

This video will help you better understand what SSBD is and how it works.
For more details, please refer to the related publication:

  • Koji Kyoda, Hiroya Itoga, Yuki Yamagata, Emi Fujisawa, Fangfang Wang, Miguel Miranda-Miranda, Haruna Yamamoto, Yasue Nakano, Yukako Tohsato, Shuichi Onami, SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1716–D1723, https://doi.org/10.1093/nar/gkae860

We encourage you to explore how SSBD can be utilized in your research!

Please note that the video is in Japanese only.

Received RIKEN BAIHO Award

We received RIKEN BAIHO Award, which go to work that is unique and has an impact both inside and outside RIKEN.

Awardees: Koji Kyota, Yuya Itoga (BDR Development Dynamics Research Team), Yuki Yamagata (R-IH Life Sciences Data Sharing Development Unit), Shuichi Onami (BDR Development Dynamics Research Team)
Achievement Title: Building a Global Ecosystem to Promote the Sharing and Reuse of Imaging Data in Life Sciences
Reference: RIKEN EIHO Award, RIKEN BAIHO Award, and RIKEN OUBU Award Presentation (March 14, 2025, RIKEN) in Japanese

foundingGIDE Community Event 2024 Highlights

Check out the video highlights of the foundingGIDE Community Event 2024.

Talks at the community event is also available on the youtube and slides are on Zenodo.

Take a look at the GIDE24 Survey plots.

foundingGIDE Community Event 2025

The upcoming community event is taking place in Brisbane, Australia, from October 17 – 18th. Get a notification so that you won’t miss this exciting event.

Community Event 2025

New Paper is out

We are thrilled to share our newly developed incubator-type biaxial light-sheet microscope in collaboration with the Tomonobu Watanabe Lab. The system allows in toto single-cell observation in a whole hemisphere of an E5.5 embryo for 12h.

Reference

Shioi G, Watanabe TM, Kaneshiro J, Azuma Y, Onami S. Trans-scale live-imaging of an E5.5 mouse embryo using incubator-type biaxial light-sheet microscopy. Life Sci. Alliance. 2025 Jan 15;8(3):e202402839. doi: 10.26508/lsa.202402839.

New Paper is out

A collaborative research paper with Dr Horikawa (Tokushima University) and Dr Nagai (Osaka University) et al. has been published.

Kakizuka, T., Nakaoka, H., Hara, Y. et al. Mesoscale heterogeneity is a critical determinant for spiral pattern formation in developing social amoeba. Sci Rep 15, 1422 (2025). doi: 10.1038/s41598-025-85759-9

New Paper is Out

Dr. Shinkai et al. published a paper in Physical Review E. In this study, we derived that the motion of an individual bead in the linear elastic network model—a polymer model used in our genome modeling approach, “PHi-C”—can be rigorously described by generalized Langevin equations.

Reference

Shinkai, S., Onami, S., Miyaguchi. Generalized Langevin dynamics for single beads in linear elastic networks. Phys. Rev. E 110, 044136 (2024). doi: 10.1103/PhysRevE.110.044136

ilastik Workshop in Kobe (Nov 5, 2024)

As a part of the foundingGIDE BioImage Hackathon and Workshops, we will host an ilastik workshop at RIKEN BDR, Kobe on Nov 5, 2024.


ilastik is a free, open-source, and user-friendly image analysis tool that can help you leverage machine learning algorithms to easily segment, classify, track, and count your cells or other experimental data.
Dominik Kutra at the ilastik team in Anna Kreshuk’s lab at EMBL will provide tutorials and hands-on exercises in this workshop.
For more information, please see the following URL:
https://bioimaging.riken.jp/workshop/20241105/

The deadline for registration is Oct 4, 2024.
We look forward to your participation.

ilastik_workshop_posterDownload

RIKEN Symposium Call for registration

We are delighted to announce to host RIKEN Symposium Challenges in Bioimaging: beyond the scales and beyond the borders together with Laboratory for Comprehensive Bioimaging, RIKEN BDR.

  • Date: June 26, Wednesday, 2024
  • Place: Kobe
  • Venue: Kobe: DB Bldg. Auditorium C1F
  • Organizers: Shuichi Onami and Tomonobu Watanabe
  • URL: http://bioimaging.riken.jp/sympo/20240626/
  • Advance registration is required for participation.
  • Fees
    • Participation: free
    • Mixer: JPY 4,000-
    • Lunch box (prepared on request): JPY 1,000-
  • Due dates
    • Talk session: 25th June
    • Mixer: 10th June
    • Lunch box request: 10th June
  • Contact: Symposium Office rikensymposium[at]ml.riken.jp
Poster RIKEN Symposium Challenges in Bioimaging: beyond the scales and beyond the borders. Date June 26th, 2024 Venue Auditorium, Developmental Biology Building “C” 1st floor, Riken BDR (Kobe Campus West Area) Speakers Oluwaseun F. Gakenou (Stellenbosch University, South Africa) Tokuko Haraguchi (Osaka University, Japan) Ioanna Mela (University of Cambridge, UK) Josh Moore (German BioImaging, Germany) Shuichi Onami (RIKEN BDR, Japan) Shotaro Otsuka (Max Perutz Labs, Austria) Timothy Stasevich (Colorado State University, USA) Caterina Strambio-De-Castillia (The University of Massachusetts Medical School, USA) Tomonobu Watanabe (RIKEN BDR, Japan)Guan-Yu Zhuo (China Medical University, Taiwan)

New Paper is Out

Dr. Yamagata (R-IH Life Science Data Sharing Unit) et al. published a paper in BMC Medical Informatics and Decision Making on the development of an otology related to COVID-19 infectious processes.

Reference

Yamagata, Y., Kushida, T., Onami, S. et al. Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. BMC Med Inform Decis Mak 23 (Suppl 4), 301 (2024). doi: 10.1186/s12911-024-02516-0