Category: Uncategorized

New Paper is out

New paper by Dr Yamagata is published.

This study presents an ontology-driven framework for the SSBD that enhances metadata management and interoperability in bioimaging, promoting a FAIR (Findable, Accessible, Interoperable, Reusable) data ecosystem.

Reference

Yamagata, Y., Kyoda, K., Itoga, H., Fujisawa, E., Onami, S. (2026). SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata. In: Garijo, D., et al. The Semantic Web – ISWC 2025. ISWC 2025. Lecture Notes in Computer Science, vol 16141. Springer, Cham. https://doi.org/10.1007/978-3-032-09530-5_19
Published 29 October 2025

Last call for GloBIAS2025

GloBIAS is an international society for bioimage analysts, and its 1st annual conference will be held in Kobe, Japan, in October 2025. Around 150 researchers worldwide have already confirmed their participation, and we are still accepting participants to join the symposium. Be there, and get to know all the people interested in bioimage analysis!

Here is the program of the symposium:

GloBIAS2025 schedule Draft
https://lnkd.in/dDimrtsm

Attention: If you come to the symposium, you can submit and present your issue at the Call4Help session (“How can I analyze this image data?”), where you can get direct and valuable feedback from experts in the audience. If you are interested, please check out the website dedicated to this session, where you can also submit your issue:

https://lnkd.in/dNvtF6Th

The deadline for the GloBIAS symposium registration is September 15th, 2025. Please find the link to the registration form on the following page.

The conference website:
https://lnkd.in/dHCFYtCR

Last call for foundingGIDE 2025 in Brisbane

Join us in Brisbane, Australia, on October 17-18, 2025, for the foundingGIDE Community Event 2025. This event will bring together the global imaging community to explore key challenges such as interoperability and standardization of biological and preclinical imaging data. This year’s theme Image Data Ecosystems:Towards Shared Solutions, highlights foundingGIDE’s commitment to building a collaborative and interoperable global image data ecosystem. 

The event will feature engaging discussions, interactive sessions, and networking opportunities, all designed to address critical challenges in biological and preclinical imaging data interoperability.Read more and register at: https://founding-gide.eurobioimaging.eu/community-event-2025/

New Publication Available

The foundingGIDE Deliverable D6.1 report is now available on Zenodo.


This report defines requirements for metadata harmonization across major bioimaging data resources—BIA, IDR, and SSBD—to improve data interoperability and reuse. It analyzes current metadata models, identifies key overlaps and gaps, and proposes steps toward global metadata alignment for bioimaging data sharing.
Read more: https://doi.org/10.5281/zenodo.16794787


Onami, S., Kyoda, K., Yamagata, Y., & Itoga, H. (2025). foundingGIDE Deliverable D6.1: Report in metadata model overlap and gaps. Zenodo. https://doi.org/10.5281/zenodo.16794787

Link to foundingGIDE website

EU emblem and funding statement

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