A new paper on SSBD has been published. It describes the two-tier ecosystem of SSBD:repository and database and the Global Image Data Ecosystem (GIDE), based on a global collaboration.
Koji Kyoda, Hiroya Itoga, Yuki Yamagata, Emi Fujisawa, Fangfang Wang, Miguel Miranda-Miranda, Haruna Yamamoto, Yasue Nakano, Yukako Tohsato, Shuichi Onami, "SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data," Nucleic Acids Research, 10.1093/nar/gkae860
DOI: https://doi.org/10.1093/nar/gkae860
PubMed: https://pubmed.ncbi.nlm.nih.gov/39479781/
Paper: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae860/7824603
News release from RIKEN (in Japanese): https://www.riken.jp/press/2024/20241031_1/index.html
News release from JST (in Japanese): https://www.jst.go.jp/pr/announce/20241031-3/index.html
SSBD has revised its data storage policy as follows to ensure proper data collection, metadata annotation, publication, and reuse.
- From SSBD:repository, all original data will be stored and published, and the download and API service will be unified via SSBD:repository
- From SSBD:database, we promote data publication in highly reusable data formats (OME-Zarr, BDML/BD5, etc.), and store original data file in SSBD:repository
Due to urgent system maintenance, SSBD might be unavailable from 10:00 to 12:00, Friday 20 October 2023. Sorry for the inconvenience.
We are pleased to announce the SSBD:database 2023 update,
We released 29 projects, which include 2030 image datasets (1.7TB) and 168 quantitative datasets (100GB).
The added datasets have already been released and announced on http://x.com/ssbd_en
The projects are
214-Arata-BehavioralActivity, 219-Konishi-CalciumIonDyn, 220-Imanishi-ROCKActivity,
231-Asakura-ERKactivation, 237-Jin-CellDynamics, 244-Tokuoka-Embryogenesis,
245-Hirasawa-OR-PAM, 246-Hung-CircadianRhythm, 247-Adhitama-Embryogenesis,
253-Shimauchi-CalciumIonDyn, 254-Seita-GrowthDyn, 257-Kubota-ERKActivity,
258-Oginuma-EmbryoDev, 259-Lu-TemperatureDyn, 267-Sugiura-CellDyn,
268-Oishi-VesselClassification, 269-Wang-CellPhysicalDyn, 271-Tanaka-FilamentDev,
272-Yoshida-EGFRSignalingDyn, 274-Aini-MitochondrialDyn, 275-Sasaki-HistonDyn,
277-Matsuura-Suzuki-CryoEM, 279-Suzuki-CaspaseActivity, 281-Kogure-EmbryoDev,
283-Kanadome-CellAdhesion, 291-Deguchi-SARS-CoV2, 294-Asamitsu-DNAPTP6Dyn,
295-Katoh-CiliumDyn, 296-Kawabata-MouseBrainShape
We present an upgrade of the QtBD5Viewer software. This new version offers:
- Visualize track paths described in the BD5 format.
- Show objects and label names as a hierarchical tree. With this tree, the user can turn on/off individual objects. It also lets to define individual colors for labels. The software interface assigns an individual color to every biological entity marked with a label for its easy differentiation.
- Support for Xbox-compatible controllers. By default, the interaction is performed with the mouse and keyboard. Now, the user has the option of more friendly interaction with the support of an Xbox-compatible controller.
- Improve mouse interaction and fix bugs when reading BD5 files.
Try QtBD5Viewer at https://github.com/openssbd/QTBD5Viewer
Due to urgent maintenance of SSBD OMERO, there are problems viewing images. We are working to resolve the problem.
QTBD5Viewer https://github.com/openssbd/QTBD5Viewer - a visualizer for BD5-format files - is now available. It runs on Windows, macOS, and Ubuntu Linux. BD5-format is a unified file format for quantitative biodynamics data and SSBD:database provides various types of such data in BD5-format.
Due to system maintenance, the SSBD database, SSBD repository, and related databases will be unavailable from January 20, 17:00, to January 21, 17:00. Sorry for the inconvenience.
Due to system maintenance, SSBD might be unavailable between 9:00 am and 5:00 pm on Wednesday, December 7, 2022. Sorry for the inconvenience.
We are pleased to announce the SSBD:database 2022.11 update, which includes 1123 image datasets (6.5TB).
Added datasets are 163-Wang-MitochondrialDyn, 186-Tsuboi-TumorDyn, 187-Tsuboi-TumorDyn, 197-Bannai-CalciumIonSignaling, 199-Ichimura-MulticellularDyn, 209-Kimura-SkinMorphology, 210-Takeo-HFregeneration, 218-Tanaka-CellSignallingDyn, 222-Dodo-RamanImaging, 224-Kamada-MitosisDyn, 225-Seiriki-WholeBrainDev, 226-Matsumura-WholeBrainDev, 227-Egoshi-RamanImaging, 228-Kanadome-CellInteration, 229-Yamada-GeneExpression, 233-Nishiyama-CellDyn, 234-Kobayashi-ChemotaxisDyn, 235-Hattori-SmartphoneBioImaging, 239-Miyamoto-MitochondrialDyn, 240-Yoshizawa-MitosisDyn, 241-Vu-TemperatureDyn, 242-Wazawa-CellDyn.
We are pleased to announce the second half of the SSBD 2021 update in the cherry blossom season in Japan. The update includes 755 image datasets (569 GB) and one quantitative dataset (13MB).
The added datasets are 131-Wen-NeuronalNucDyn, 138-Ito-SPBDyn, 164-Ono-NeuPMCA, 170-Tsutsui-HookBM, 172-Yoshida-ERKTracheaDev, 177-Kinjo-cAMPsignalingDyn, 178-konagaya-CellMigration, 179-Kobachi-BLVRAactivity, 180-Watabe-Biosensoractivity, 183-Iwasaki-SpineDyn, 184-Tanaka-SpineDyn, 185-Hoshino-MyotubeCa2Signal, 188-Ipponjima-NHEKsCornification, 189-Kobayashi-NSCsDyn, 190-Iguchi-SpineDyn, 192-Hiroshima-SingleMolDyn, 194-Obashi-SpineDyn, 196-Sueda-GeneExpReg, 202-Miyagawa-ChemotaxisDyn, 203-Tanabe-SingleDyn, 205-Shen-CellPatterning, 206-Miyamoto-CiliaryMorphology, 207-Kuroda-FinMorphology, 211-Hiroshima-EGFRTracking, 212-Kajikawa-GeckoEmbryos, 213-Yoshida-SpindleDyn, 217-Sakai-iRFPactivity.
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.
SSBD is now rebranded as SSBD:database with a new logo.
MATLAB wrapper for connecting to SSBD API is now available at Github. https://github.com/openssbd/MATLAB_SSBDapi
4D Cell Nuclear Tracking - training course material is now available on Github
https://github.com/openssbd/4D-cell-nuclear-tracking
All the visualization data for quantitative data have been updated.
Error on Keller et al. 2010 had been reported and a new version of BDML/BD5 files have been updated.
Due to system maintenance, SSBD database will not be available between. 14:00 - 17:00 on 24 July 2019,
Due to system maintenance, SSBD database will not be available between Jan. 25, 17:00 to Jan 28, 09:00 (JST)
453 sets of images and 103 sets of quantitative data were added. Please visit the Resources page http://ssbd.qbic.riken.jp/resources/ for more details.
OMERO Open Workshop in Kobe 2018
Click here for more details
http://ssbd.qbic.riken.jp/event/omero2018/
We are migrating to a new server. Some of the services are not available during this period. We hope to provide full service asap.
Due to system maintenance, SSBD database will be unavailable on Monday 4 December 2017
A new REST API v3 has been released to support SSBD 3.0. Manual of the REST API has been updated.
BDML schema version 3.0, PDPML schema version 1.0, and OMICSBDML version 1.0 have been released. All BDML-files have been updated. 23 BDML-files and 280 image-sets have been added. SSBD database system was updated.
SSBD will not be available on 10 July 2017 due to unscheduled maintenance
SSBD REST API full service is now available.
SSBD REST API coordsXYZ is currently unavailable due to recent system maintenance. The service will resume shortly. Please check back later.
Due to system maintenance, SSBD database will be unavailable Feb. 20 to 28 (About 9 days, JST).
Due to system maintenance, SSBD database will be unavailable Jan. 27, 5:00 pm to 28, 05:00 pm (About 1 day, JST).
SSBD REST API "coordinates" is now available to retrieve data for both BDML ver0.15 and 0.18 files. "coordsXYZ" API is also available for backward compatibility, but it will be phased out in the future.
14 BDML-files in C. elegans have been updated and 123 BDML-files in C. elegans, D. discoideum, PC-12 cell, and so on have been added.
SSBD REST API coordsXYZ is currently under maintenance and is unavailable due to recent update. The service will resume shortly after the updates. Please check back later.
Due to system maintenance, SSBD database will be unavailable Oct. 4, 2016 13:00 pm to 18:00 pm (About 5 hours, JST).
14 BDML-files and the corresponding microscopy images in C. elegans have been added.
OpenSSBD, an open-source version of SSBD, has been released. Viewer and RESTful API have been updated.
2 BDML-files in M. musculus and microscopy images in M. musculus, R. norvegicus, and D. discoideum have been added.
Phenochar has been updated (version 3 and 2 for BDML schema 0.15 and 0.18, respectively). Manuals about SSBD-RDF data have been added.
1 BDML-file in D. discoideum has been added.
Viewer and RESTful API have been updated.
Due to system maintenance, SSBD database will be unavailable Mar. 19, 13:00 pm to 18:00 pm (About 5 hours, JST).
Due to system maintenance, SSBD database will be unavailable Jan. 30, 09:00 pm to 31, 09:00 pm (About 1 day, JST).
Our BDML paper is published online (http://bioinformatics.oxfordjournals.org/content/early/2014/11/19/bioinformatics)
OmicsBDML schema version 0.18 have been released. 20 BDML-files in M. musculus and C. elegans have been added.
Due to system maintenance, SSBD database will be unavailable Oct. 1, 2014 11:00 am to 12:00 am (About 1 hour, JST).
BDML schema version 0.2 has been released. All software have been updated.
BDML schema version 0.18 have been released. All BDML-files and software have been updated.
Due to system maintenance, SSBD database will be unavailable Mar. 19, 2014 10:00 am to 13:00 pm (About 4 hours, JST).
Due to system maintenance, SSBD database will be unavailable Mar. 8, 2014 09:00 am to 13:00 pm (About 4 hours, JST).
Visit us at MBSJ 2013 (booth: BioDB6)
94 BDML-files in Zebrafish, and C. elegans have been added.
Due to system maintenance, SSBD database will be unavailable Nov. 27, 2013 02:00 pm to 04:00 pm (About 2 hours, JST).
Due to system maintenance, SSBD database will be unavailable Nov. 21, 2013 10:00 am to 01:00 pm (About 3 hours, JST).
Due to system maintenance, SSBD database will be unavailable Nov. 12, 2013 04:00 pm to 07:00 pm (About 3 hours, JST).
17 BDML-files in Zebrafish, D. melanogaster, and C. elegans have been added.
Due to system maintenance, SSBD database will be unavailable Oct. 9, 2013 10:00 am to 01:00 pm (About 3 hours, JST).
SSBD database was opened. BDML schema version 0.15 and PDPML schema version 0.05 have been finalized and released.