Laboratory for Developmental Dynamics, RIKEN BDR
We welcomed Ms Xiaohan Ding from Shanghai Jiao Tong University as an intern.
She is learning about developmental biology and three-dimensional cell tracking techniques using in the latest AI technology through projects such as the analysis of mouse embryo tracking data using ELEPHANT.
Good luck!
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.
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.
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.
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.
embryonic development / single-cell tracking / SPIM microscope / trans-scale / live-imaging @sonamix @BDR_RIKEN @RIKEN_en https://t.co/YNBUV1KaaB pic.twitter.com/rsp89XJaIy
— LifeScienceAlliance (@LSAjournal) January 16, 2025
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
"Mesoscale heterogeneity is a critical determinant for spiral pattern formation in…"https://t.co/RXNrBzHo5O has been published in @SciReports
Congrats! @Lab_Nagai sensei
SSBD:repository shares the original trans-scale scope images of the paper,https://t.co/mBQ0rBt7Gq
— SSBD:database / SSBD:repository (@ssbd_en) January 10, 2025
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)
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
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.
To find out more and register the symposium, please visit the OLSP Symposium 2025 website.
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)
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
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.
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
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.
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.
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.
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.