Laboratory for Developmental Dynamics, RIKEN BDR
Our TL Dr Onami joined discussions on metadata standards in biological image data sharing with an international bioimaging community lead by EMBL-EBI. They propose global metadata guidelines, REMBI: Recommended Metadata for Biological Images.
https://doi.org/10.1038/s41592-021-01166-8
TL Dr Shuichi Onami and Prof. Jason Swedlow (University of Dundee, UK) along with Global Bioimaging, an international consortium of the leading experts in bioimaging communities, released recommendations for bioimage data format standards and open access image data repositories. These recommendations contribute to accelerating the development of the bioimaging field through data sharing.
Read the full press release article on the RIKEN website (in Japanese).
Swedlow, J.R., Kankaanpää, P., Sarkans, U. et al. A global view of standards for open image data formats and repositories. Nat Methods (2021). https://doi.org/10.1038/s41592-021-01113-7
A new paper by Momoko Imakubo, Student Trainee in the Onami lab, was published in the BMC Bioinformatics.
In this paper, we quantified age-associated changes in oocyte appearance in the nematode Caenorhabditis elegans by statistical image processing. We showed that the oocyte cytoplasmic texture in Nomarski differential interference contrast images significantly changes with aging.
Dr. Yuki Yamagata, Research Scientist in the Onami lab, co-authored a review paper with Dr. Hiroshi Masuya, RIKEN BRC, et al. The paper was published in the January issue of Laboratory Animal Research.
The RIKEN BioResource Research Center released an integrated database of bioresources including, experimental mouse strains, Arabidopsis thaliana as a laboratory plant, cell lines, microorganisms, and genetic materials using Resource Description Framework-related technologies in 2020. This review summarizes the features of current version of databases related to mouse strain resources in RIKEN BioResource Research Center and discusses future views.
Team Leader Dr. Onami attended an online open symposium “
Prospects for next-generation integrated bioimaging and mathematical collaboration” which was organized by the Science Council of Japan in October. His presentation is now available online.
This symposium was aimed to discuss a theme: ” Will the advanced fusion of imaging technology and mathematical/ information science lead to a paradigm shift in life science? ” in Japan with not only researchers in the field of advanced bioimaging measurement but also researchers in a wide range of fields such as mathematics, physics, and information science.
To watch his talk visit our multimedia page.
Other presentations and discussions are available on the symposium website. The website and all videos were only in Japanese.
Dr. Yuki Yamagata, a research scientist in Onami lab, gave a presentation regarding “Extending existing Ontologies for COVID-19” in a virtual workshop, WCO-2020: Workshop on COVID-19 Ontologies.
To watch her talk, please visit our MULTIMEDIA page.
Or visit the website of the workshop.
Our Team Leader Dr. Onami joined an international virtual workshop on “Pre-publication image management and processing” by the Global BioImaging, The Exchange of Experience Ⅴ (EoE V), in September.
His presentations as well as other experts’ in the bio-imaging data sharing field and discussions are available to watch online at the EoE V website.
Or visit our multimedia page.
One month has already gone by since the #EoE_V workshop… but if you want to watch its great presentations again, the videos of all the sessions are available on our website https://t.co/068RS9Rvvu. Enjoy!! pic.twitter.com/oycvAqmR6p
— Global BioImaging (@GlobalBioImage) October 9, 2020
Dr. Soya Shinkai wrote his essay in a series of articles by RIKEN in THE SANKEI SHINBUN .
To read the article, visit the SANKEI NEWS website (in Japanese only).
We are pleased to announce that a new paper by Koji Kyoda, a Research Scientist in Onami lab, et al. was published in PLOS ONE.
In this paper, we developed the BD5, a new binary data format based on HDF5. It can be used to represent quantitative data of biological dynamics obtained from bioimage informatics techniques and mechanobiological simulations. BD5 allows fast access to quantitative data and fast transfer of files containing large quantitative data.
A press release introducing the PHi-C, an original simulation method of the Hi-C data analysis by Dr. Soya Shinkai, has been issued.
We have discovered a formula that links the contact probability in Hi-C matrix data and the interaction parameter of the polymer network model. Using Hi-C matrix data as input, the PHi-C method allows for the simulation of the dynamic 3D genome in living cells.
Read the full press release article regarding PHi-C in Japanese on RIKEN website.
Soya Shinkai, et al. (2020) PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genom. Bioinform. doi: 10.1093/nargab/lqaa020