We are pleased to announce the first half of the SSBD 2021 update, which includes 1799 image datasets (8TB) and four quantitative datasets (6MB). We have a plan for the second half of the 2021 update until next spring. Added datasets are 70-Yoshida-KTMTDyn, 72-Kyogoku-CytoplasmNucDyn, 120-Ding-CentromericDyn, 126-Imanishi-CellMorNuCyM, 127-Konishi-ERKDyn, 128-Muta-IECsERKDync, 129-Komatsu-ERKBiosensorActivity, 130-Sano-CellMigrationDyn, 161-Tanaka-MEFMitochondrial, 165-Kinjo-ERKactivity, 166-Takubo-ECsTrajectory, 171-Ochi-Hes1DynNPCs.
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.
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://so.riken.jp/2021/05/24/rembi-recommended-metadata-for-biological-images/
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.
https://so.riken.jp/2021/05/11/sharing-global-standards-of-open-image-date/
Due to network maintenance, the SSBD:database, SSBD:repository, and the sister databases will not be accessible from 00:00 a.m. to 01:30 a.m. JST (GMT-9) on May 6 (Thu) 2021. Sorry for the inconvenience.
Due to network maintenance, the SSBD:database/repository will not be accessible intermittently on Mar 23 afternoon. Sorry for the inconvenience.
Some BD5 APIs are not available now cause of the technical issue. We're working on a fix.
Due to system maintenance, the 4D visualizer and APIs will not be available on Feb 9, 9:00-16:00. Sorry for the inconvenience.
Due to system maintenance, SSBD:database/repository will not be available from Jan 22 17:00 to Jan 23 17:00. Sorry for inconvenience.
SSBD 2020 update, the metadata database fully renewed, and 77 image datasets (7GB) and 4 quantitative datasets are added. We are plaining next database update in a half year for COVID-19 situation.
We will be performing some maintenance work on the SSBD:database this week (2020-11-25). You may experience some service outage from time to time.
A new paper "BD5: an open HDF5-based data format to represent quantitative biological dynamics data" is now published in PLOS ONE. https://doi.org/10.1371/journal.pone.0237468
BD5 manual was updated. http://ssbd.qbic.riken.jp/bdml/bd5.html
Shuichi Onami presented SSBD:database and SSBD:repository at the online 2020 OME Community Meeting. You can watch it here https://downloads.openmicroscopy.org/presentations/2020/Dundee/main-talks/Shuichi_Onami.mp4
A preprint paper on "BD5: an open HDF5-based data format to represent quantitative biological dynamics data" is available in bioarivx. doi: https://doi.org/10.1101/2020.04.26.062976
REST API service is now returned to normal operation.
We have opened SSBD:repository page. You can find it here http://ssbd.qbic.riken.jp/repository.
We have made some minor updates to the system correcting some errors on past datasets and allowing more quantitative datasets to be accessed by REST API. We have also revised our Japanese page. For more details http://ssbd.qbic.riken.jp/update
*Note: REST API is temporary unavailable (2020-02-03), we shall try to return it to service as soon as possible.
The system will be under maintenance on 3 February 2019. SSBD database will not be available between 14:00~17:00 JST
In 2019 there are now 687 BDML files which include 810,685,686 entries, and 4,162 image sets. Please visit the Resources page http://ssbd.qbic.riken.jp/resources/ for more details.
The system will be updated on 20 November 2019. SSBD database will not be available on that day.