Category: General

[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

[For Students] BDR Summer School

BDR are holding a summer school for students.

This is an excellent opportunity for students who are interested in life science research and want to become researchers in the future, interested in entering the RIKEN Collaborative Graduate School to join cutting-edge research laboratories. In the Onami lab, students will work on the mathematical and computational science of genomic 3D structural data.

For more information, please visit the BDR Summer School 2024 website.

GBI_EoE 2024

Global BioImaging Exchange of Experience (EoE) workshops are a unique open forum for discussion and generation of new ideas, where imaging facility managers and technical staff, scientists, science policy officers and funders from around the globe, come together to build the interpersonal relations necessary for the success of the Global BioImaging network.

This year, EoE is coming to Okazaki, Japan. We are co-organizing #GBI_EoE2024 with ABiS and Global BioImaging. Save the data and see you in Okazaki.

Global BioImaging Exchange of Experience IX

  • DATES: 29th to 31st of October of 2024
  • LOCATION: Okazaki Conference Centre, Okazaki – Japan
  • TOPIC: Image Data Horizons – Global Strategies for Accessible Knowle
  • WEBSITE

Travel Grant for Exchange of Experience IX

foundingGIDE – Laying the foundations of a Global Image Data Ecosystem

We are very excited to announce the launch of foundingGIDE project funded by Horizon Europe.

Led by Euro-BioImaging, the foundingGIDE project is a global consortium with 7 partners including our SSBD that aim to found of a Global Image Data Ecosystem (GIDE).

To find more about the foundingGIDE project, read “foundingGIDE – Laying the foundations of a Global Image Data Ecosystem“, published by Euro-BioImaging.

Follow us on social media to keep updated!

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.