Laboratory for Developmental Dynamics, RIKEN BDR
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 delighted to announce to host RIKEN Symposium Challenges in Bioimaging: beyond the scales and beyond the borders together with Laboratory for Comprehensive Bioimaging, RIKEN BDR.
Dr. 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.
Yamagata, Y., Kushida, T., Onami, S. et al. Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. BMC Med Inform Decis Mak 23 (Suppl 4), 301 (2024). doi: 10.1186/s12911-024-02516-0
Onami Lab is going to join a BDR affiliated graduate school programs virtual open lab program on April 13, 2024.
This is a great opportunity to learn how your students life will be at RIKEN and you can expand your career as a scientist.
If you are interested in the event, please visit at the website for BDR joint graduate school laboratory tour (in Japanese only).
We have new job openings. Please see job opportunities to get more details.
If you are interested, please contact Dr Onami.
We look forward to you joining our laboratory.
A new position is open!
We are seeking a researcher who works for the CREST Bio-DX project led by Dr Soya Shinkai. Please see job opportunities to get more details.
If you are interested, please contact Dr Shinkai.
We look forward to you joining our laboratory
An article featured open-source software published in Nature, which Dr Onami was interviewed.
Read the article online:
How open-source software could finally get the world’s microscopes speaking the same language
A paper by Drs Koji Kyoda and Shuichi Onami as co-authors has been published.
Moore, J., Basurto-Lozada, D., Besson, S. et al. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem Cell Biol (2023).
doi: 10.1007/s00418-023-02209-1
Out now! “#OMEZarr: a #CloudOptimized #BioImaging #FileFormat with Int’l #Community Support” 😍
Huge thanks to the 68 co-authors, across 32 institutions (see the quoted tweet) 🙌
If you use #OMEZarr & weren’t involved, let’s start the next report! 📝https://t.co/iSFOr3RYYU https://t.co/vnUMdlGcUW
— Josh Moore (@notjustmoore) July 17, 2023
We welcomed Junbo Xia from Shanghai Jiao Tong University as an intern this summer.
He is working on a project, Development of deep learning program to identify cells from bioimaging data.
Good luck!