Category: Uncategorized

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