Category: News

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!

[Press Release]Discovery of a new mechanism by which changes in the distance between genes regulate their expression

Drs Hiroaki Oishi, Hiroshi Ochiai, (Kyushu University, respectively) and Soya Shinkai et al. found a novel mechanism of gene expression regulation involving changes in the spatial distance between genes. Understanding the mechanisms of gene expression regulation is crucial not only for molecular biology but also for medical research, as it directly links to identifying disease causes and therapeutic targets.

Learn more about the study on Press Release by Kyushu University, RIKEN and JST. (In Japanese only)

Reference

Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H. (2024). Transcription-coupled changes in genomic region proximities during transcriptional bursting. Sci. Adv. 10, eadn0020. DOI:10.1126/sciadv.adn0020

OLSP Symposium 2025 Call for registration

OLSP Symposium 2025 -  Present and Future Perspectives of Open Life Sciences –

We are thrilled to announce that RIKEN Open Life Science Platform Project (OLSP) will hold its first open symposium, OLSP Symposium 2025 –  Present and Future Perspectives of Open Life Sciences –, on January 27, 2025 in Wako.

The symposium will feature the achievements and contributions of the OLSP. We will invite speakers from diverse fields to explore successful case studies, gaining insights into how open science can be effectively applied within the life sciences. During a poster session, participants will have an opportunity to present their research, facilitate discussions and feedback on ongoing projects related to open science, and build connections among participants from various disciplines. This will encourage collaboration and the exchange of ideas that can drive the future of open science.

General information

  • Date : January 27, 2025 (Mon）
  • Time:  13:00 – 20:00 (Tentative)
  • Venue: Okochi Hall, RIKEN Wako Campus – Saitama, Japan
  • Language: English
  • Fee: FREE

To find out more and register the symposium, please visit the OLSP Symposium 2025 website.

[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.

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

New Paper is Out

A paper by Dr. Yuki Yamagata (R-IH Life Science Data Sharing Unit, former researcher at Onami Lab ) et al. on the ontological model that organizes knowledge of cellular senescence was published in Scientific Data.

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

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