Laboratory for Developmental Dynamics, RIKEN BDR
JST and RIKEN BDR host an online symposium “JST CREST “BioDX” Kickoff Symposium” on November 21 – 22. This symposium provides presentation and discussion on the current status and future prospects of bio- DX from researchers working at the forefront.
For more information, visit the symposium website.
The symposium will only be in Japanese.
We are currently looking for a data annotator as either a full time or part-time worker.
This position’s main role is data annotation in SSBD, such as selecting data from papers in life science research, extracting their metadata, requesting other laboratories inside/ outside the RIKEN to provide their research data, and registering them into SSBD.
The successful candidate must be able to understand papers in English as well as have excellent writing skills in Japanese.
Job Descriptions are posted on the RIKEN’s official website. (In Japanese only)
Technical Staff: テクニカルスタッフ募集（DD2101）
Research Part-timer: 研究パートタイマー募集（DD2102）
If you are interested in the position, please contact Dr Onami in advance of your application.
We look forward to your application!
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.
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 https://doi.org/10.17706/ijbbb.2021.11.3.40-49.
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!
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.
理研BDRの連携大学院集中レクチャー「発生・再生・進化のダイナミクス」を8月4-5日に開催！
— 理研BDR(生命機能科学研究センター) (@RIKEN_BDR) June 28, 2021
BDRの最先端研究を講義形式で紹介します。
連携大学院の講義として企画されていますが、それ以外の方も聴講可能です。
希望するPIとディスカッションできる時間もあります！
詳細は?https://t.co/wBUvl9eeeK
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). https://doi.org/10.1016/j.crmeth.2021.100012
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.