Author: Aiko Sekiguchi

[Press Release] Development of life sciences by sharing image data

Drs Koji Kyoda, Hitoya Itoga, Yuki Yamagata (RIKEN R-IH), et al. developed and published a public repository and high-value database that facilitates the sharing and re-using of image data in the life sciences. In this paper, we describe the international positioning and functions of the SSBD.

The SSBD is positioned as one of the core ecosystems of the international consortium ‘foundingGIDE’, which aims to promote the standardisation and sharing of FAIR image data, and is expected to enhance the transparency and reliability of science and contribute to the development of science throughout society through the advancement of open science. The project is expected to contribute to the development of science in society as a whole through the advancement of open science.

Learn more about the study on Press Release by RIKEN. (In Japanese only)

Reference

Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., Onami, S.(2024) SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Res. gkae860. https://doi.org/10.1093/nar/gkae860

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

[Registration open] foundingGIDE community event 2024 and BioImage Hackathon

We are exciting to announce the foudingGIDE first community event in Okazaki and first technical event, the BioImage Hackathon in Kobe. We look forward your participation.

foundingGIDE community event 2024

A key step towards creating a global image data ecosystem is to connect the community. We invite you to the first foundingGIDE community event that will bring together various stakeholders from the global imaging data community to Okazaki, Japan.

foundingGIDE BioImage Hackathon

Join us for an exciting 4 days where we will work together with experts on imaging ontologies and metadata. The event will focus on practical next steps to make these key components of image data management useful to scientists and software developers. There will be a limited number of selected participants.

AJACS Call for Registration

Dr Ko Sugawara will lecture at the Integrated Database Workshop: AJACS, organised by the JST – NBDC. You can learn how to think about your first foray into biological image analysis and how to use the main image analysis tools in a practical way.

The registration is now open on their website.

AJACS ‘Know, Learn and Use BioImage Analysis’

We look forward to your participation.

Behind the Paper “Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective”

Dr. Yuki 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. We published a video to introduce our study on YouTube.

We developed the HoIP ontology to organize cellular senescence knowledge from a homeostasis disturbance perspective. HoIP was assessed, and relationships between cellular senescence, COVID-19, and diabetes were inferred. This framework elucidates mechanisms linking cellular and organismal aging. Lean more about the study at https://go.nature.com/3yLP0QO.

Reference

Yamagata, Y., Fukuyama, T., Onami, S. et al. Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Sci Data 11, 485 (2024). https://doi.org/10.1038/s41597-024-03331-y

[Press Release] Development and publication of the zebrafish brain gene expression database

Dr Towako Hiraki-Kajiyama(Assistant professor at Graduate School of Life Science, Tohoku University, former researcher at RIKEN CBS) and Yoshihiro Yoshihara (TL at Riken CBS) et al. with Drs Hiroya Itoga and Shuichi Onami established the database for scanned data of brain sections of zebrafish.

The database uses SSBD (https://ssbd.riken.jp/) and OMERO (https://openmicroscopy.org) as infrastructures.The database and anatomical findings will contribute to future neuroscience research using zebrafish.

Learn more about the study on Press Release from RIKEN. (In Japanese only)

Reference

Hiraki-Kajiyama, T., Miyasaka, N., Ando, R., Wakisaka, N., Itoga, H., Onami, H. I. S., & Yoshihara, Y. (2024). An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. Journal of Comparative Neurology, 532, e25619. https://doi.org/10.1002/cne.25619

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