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
Author: Aiko Sekiguchi
New paper is out.
A paper by Drs Koji Kyoda and Shuichi Onami as co-authors has been published.
Reference
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
Summer internship
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!
QuPath extension SAM v0.3 is released
Dr Ko Sugawra has released QuPath extension for Segment Anything Model (SAM) v0.3.
Lean about more, please visit Ko’s annoucement on Image-sc, a scientific image community forum.
Get to know about QTBD5Viewer
An article featuring QTBD5Viewer and SSBD:database is published on NBDC blog.
Seminar Information
Onami lab hosts the BDR Seminar by Dr. Matthew Hartley from EMBL-EBI, Wellcome Genome Campus, Hinxton, UK on July 10, 2023 in Kobe and Online.
Title: The BioImage Archive: Accelerating AI for bioimaging
The seminar is open for public with a registration. Please visit the BDR Seminar website to find more information.
New paper is out.
A paper written by Drs Soya Shinkai and Shuichi Onami as co-authors has been published.
Reference
Hara, M., Ariyoshi, M., Sano, T., Nozawa, R., Shinkai, S., Onami, S., Jansen, I., Hirota, T., Fukagawa, T.: Centromere/kinetochore is assembled through CENP-C oligomerization. Mol. Cell 83. (2023).
doi:10.1016/j.molcel.2023.05.023
New Paper by Dr Chentao Wen
Our SPDR, Dr Chentao Wen published a new paper on “Seg2Link” in Scientific Reports.
Nagoya City University, his former affiliation, issued a press release on his research: Seg2Link: an efficient and versatile solution for semi-automatic cell segmentation in 3D image
stacks (May 22, 2023. In Japanese Only.)
Reference
Wen, C., Matsumoto, M., Sawada, M. et al. Seg2Link: an efficient and versatile solution for semi-automatic cell segmentation in 3D image stacks. Sci Rep 13, 7109 (2023). https://doi.org/10.1038/s41598-023-34232-6
We are hiring.
We are currently seeking a data curator as Technical Staff. Please visit job opportunities to get more details.
If you are interested, please contact Dr Onami.
We look forward to you joining our laboratory!
[Press Release]Euchromatin forms condensed chromatin domain.
Tadasu Nozaki (Former Graduate Student at NIG)and Prof. Kazuhiro Maeshima (NIG) et. al. together with Drs Soya Shinkai and Shuichi Onami have found euchromatin forms condensed chromatin domains. This finding suggests an innovative model that condensed structure is the default state of chromatin.
Learn more about the study on Press Release from the National Institute of Genetics.
Reference
Nozaki, T., Shinkai, S., Ide, S., Higashi, K., Tamura, S., Shimazoe, M. A., Nakagawa, M., Suzuki, Y., Okada, Y., Sasai, M., Onami, S., Kurokawa, K., Iida, S., Maeshima, K. (2023). Condensed but liquid-like domain organization of active chromatin regions in living human cells. Sci. Adv. 9, eadf1488.
https://doi.org/10.1126/sciadv.adf1488
Excited to share our new paper @ScienceAdvances:https://t.co/0LVVQy2dbF
Dual-color imaging of two neighbor nucleosomes reveals that nucleosomes in euchromatin form condensed domains with ~150 nm diameter. Nucleosomes locally fluctuate in the condensed domain like a liquid. 1/ pic.twitter.com/4SLE0YLeXG— Kazuhiro Maeshima (@kazu_maeshima) April 5, 2023