Improvement in image quality via the pseudo confocal effect in multidirectional digital scanned laser light-sheet microscopy

Our TL Onami and DR Kaneshiro (Laboratory for Comprehensive Bioimaging, RIKEN BDR) et al. proposed a new pseudo confocal system that combines multiline scanning for light-sheet illumination combined and simple image construction.  By further combining our method with multidirectional digital scanned laser light-sheet microscopy (mDSLM), we demonstrated improvement of image quality in biological samples.

Texture-Based Screening to Identify Genes Involved in Reproductive Aging in C. elegans

Dr Momoko Imakubo et al.’s study on analysis of genes involved in reproductive aging in C. elegans oocytes by using an image database of RNAi embryos and image processing has been published online at

Congratulations to our former student trainee Momoko Imakubo who earned her PhD from Kobe University in March 2021 on her achievement. We wish you all the best in your future endeavour!

[For Students] Join BDR Lecture Program.

Our TL is going to hold a talk session in the BDR Lecture Programs in August. Graduate students outside the joined graduate universities of BDR can join and have a chance to talk with PIs directly.

If you are interested in the program, register at the BDR website by June 12.

Details and lectures will be given in Japanese but English is available in the talk session.

[Press Release] Launch of “NeuroGT Database”, a brain atlas of neurogenic tagging CreER mouse drivers

Drs. Yukako Tohsato and Hiroya Itoga in our SSBD team, together with Prof. Tatsumi Hirata (NIG) and colleagues, developed the “NeuroGT database,” which contains whole-brain image data of tagged neurons based on time of neurogenesis. Through NeuroGT, researchers can find suitable neurogenic tagging driver lines for their research.

Learn more about Neuro GT on the National Institute of Genetics Press Release.


Hirata, T., Tohsato, Y., Itoga, H. et al. NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons. Cell Rep. Methods 1, 100012 (2021).

REMBI: Recommended Metadata for Biological Images

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.

[Press Release] Recommendations for global standards of open image data formats and repositories.

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).

New Paper by Momoko Imakubo

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.

Paper Published by Dr. Yamagata

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.

TL’s talk in Symposium went public

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.