Category: General

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.

foundingGIDE Community Event 2025 registration is open

We’re excited to announce that registrations are now open for the foundingGIDE Community Event 2025, taking place in Brisbane, Australia on October 17–18. Join us for 1.5 days of collaboration and engagement with the global imaging data community. More details below.

The foundingGIDE Community Event is positioned between two major data-centric conferences and offers a unique opportunity for professionals engaged in research data management, imaging, and digital infrastructure to connect with the global data research community. FoundingGIDE Community Event (October 17-18) is following International Data Week 2025 (October 13–16) and preceding eResearch Australasia 2025 (October 20–24) all at the same location, Brisbane Convention and Exhibition Centre, Australia. These three events bring together communities working toward the FAIR data principles and advancing practices in data sharing, stewardship, and interoperability across scientific domains.

To find out more about the event and to register, visit https://founding-gide.eurobioimaging.eu/community-event-2025/.

Logo of foundingGIDE

 

EU emblem and funding statement

foundingGIDE has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101130216. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Join us at GloBIAS 2025 – Registration is open!

We are delighted to invite you to join us at the GloBIAS Bioimage Analysis Conference 2025 from Oct 26, 2025 – Oct 31, 2025 in Kobe, Japan at the RIKEN Kobe Campus.

The Conference will consist of several events:

  • Training school, hackathon and taggathon from 26 October to 29 October, 
  • Symposium with poster session, Open-source Software Lounge, Call4Help sessions from 29 October to 31 October

Important dates:

  • Abstract submission deadline: 15 May 2025
  • Training school application deadline: 15 May 2025
  • Training School Trainee, Travel grants, Poster/Oral notification: 15 June 2025

More information can be found on our website: https://www.globias.org/activities/bioimage-analysis-conference-2025-in-kobe

There you can also find the link to the registration form.

We look forward to welcoming you in Kobe!

Talks at OLSP Symposium 2025 went public

We hosted an open symposium, RIKEN Symposia: OLSP Symposium 2025 – Present and Future Perspectives of Open Life Sciences – on 27th January, 2025 in Wako, Japan.

Presentations including Dr Onami’s talk are now available for public in our YouTube Channel and the symposium website.

 

OLSP Symposium 2025 Session 1 Activities in the OLSP Project

OLSP Symposium 2025 Session 2 Case Studies in Open Sciences

OLSP Symposium 2025 Session 3 Innovative Tools for Open Life Sciences

[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

[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.

[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

Protocol published

Dr Chentao Wen published a protocol in Methods in Molecular Biology. He details the challenges of cell tracking within deforming organs and moving animals and explains how to use the latest version of 3DeeCellTracker to accurately track cells, thereby enhancing our understanding of various organ dynamics and biological processes.

Reference

Wen, C. (2024). Deep Learning-Based Cell Tracking in Deforming Organs and Moving Animals. In: Wuelfing, C., Murphy, R.F. (eds) Imaging Cell Signaling. Methods in Molecular Biology, vol 2800. Humana, New York, NY. doi: 10.1007/978-1-0716-3834-7_14