SSBD:database

Publications

SSBD

• Koji Kyoda, Hiroya Itoga, Yuki Yamagata, Emi Fujisawa, Fangfang Wang, Miguel Miranda-Miranda, Haruna Yamamoto, Yasue Nakano, Yukako Tohsato, Shuichi Onami (2024)
  SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data,
  Nucleic Acids Research, gkae860,
  https://doi.org/10.1093/nar/gkae860
• Yukako Tohsato, Kenneth H. L. Ho, Koji Kyoda, Shuichi Onami (2016)
  SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena,
  Bioinformatics, Volume 32, Issue 22, 15 November 2016, Pages 3471–3479,
  https://doi.org/10.1093/bioinformatics/btw417

BDML (Biological Dynamics Markup Language), BD5

• Koji Kyoda, Kenneth H. L. Ho, Yukako Tohsato, Hiroya Itoga, Shuichi Onami (2020)
  BD5: An open HDF5-based data format to represent quantitative biological dynamics data,
  PLOS ONE, Volume 15, Issue 8, August 2020, Pages e0237468,
  https://doi.org/10.1371/journal.pone.0237468.
• Koji Kyoda, Yukako Tohsato, Kenneth H. L. Ho, Shuichi Onami (2015)
  Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data ,
  Bioinformatics, Volume 31, Issue 7, 1 April 2015, Pages 1044–1052,
  https://doi.org/10.1093/bioinformatics/btu767

Global Standards

• Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M. Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E. Diel, David Gault, Satrajit S. Ghosh, Ilan Gold, Yaroslav O. Halchenko, Matthew Hartley, Dave Horsfall, Mark S. Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Bugra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas Schaub, Hythem Sidky, Ahmet Can Solak, David R. Stirling, Jonathan Striebel, Christian Tischer, Daniel Toloudis, Isaac Virshup, Petr Walczysko, Alan M. Watson, Erin Weisbart, Frances Wong, Kevin A. Yamauchi, Omer Bayraktar, Beth A. Cimini, Nils Gehlenborg, Muzlifah Haniffa, Nathan Hotaling, Shuichi Onami, Loic A. Royer, Stephan Saalfeld, Oliver Stegle, Fabian J. Theis & Jason R. Swedlow (2023)
  OME-Zarr: a cloud-optimized bioimaging file format with international community support.
  Histochemistry and Cell Biology, Volume 160, Pages 223-251.
  https://doi.org/10.1007/s00418-023-02209-1
• Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, Ian M. Dobbie, John E. Eriksson, Orestis Faklaris, Julia Fernandez-Rodriguez, Alexia Ferrand, Laurent Gelman, Ali Gheisari, Hella Hartmann, Christian Kukat, Alex Laude, Miso Mitkovski, Sebastian Munck, Alison J. North, Tobias M. Rasse, Ute Resch-Genger, Lucas C. Schuetz, Arne Seitz, Caterina Strambio-De-Castillia, Jason R. Swedlow, Ioannis Alexopoulos, Karin Aumayr, Sergiy Avilov, Gert-Jan Bakker, Rodrigo R. Bammann, Andrea Bassi, Hannes Beckert, Sebastian Beer, Yury Belyaev, Jakob Bierwagen, Konstantin A. Birngruber, Manel Bosch, Juergen Breitlow, Lisa A. Cameron, Joe Chalfoun, James J. Chambers, Chieh-Li Chen, Eduardo Conde-Sousa, Alexander D. Corbett, Fabrice P. Cordelieres, Elaine Del Nery, Ralf Dietzel, Frank Eismann, Elnaz Fazeli, Andreas Felscher, Hans Fried, Nathalie Gaudreault, Wah Ing Goh, Thomas Guilbert, Roland Hadleigh, Peter Hemmerich, Gerhard A. Holst, Michelle S. Itano, Claudia B. Jaffe, Helena K. Jambor, Stuart C. Jarvis, Antje Keppler, David Kirchenbuechler, Marcel Kirchner, Norio Kobayashi, Gabriel Krens, Susanne Kunis, Judith Lacoste, Marco Marcello, Gabriel G. Martins, Daniel J. Metcalf, Claire A. Mitchell, Joshua Moore, Tobias Mueller, Michael S. Nelson, Stephen Ogg, Shuichi Onami, Alexandra L. Palmer, Perrine Paul-Gilloteaux, Jaime A. Pimentel, Laure Plantard, Santosh Podder, Elton Rexhepaj, Arnaud Royon, Markku A. Saari, Damien Schapman, Vincent Schoonderwoert, Britta Schroth-Diez, Stanley Schwartz, Michael Shaw, Martin Spitaler, Martin T. Stoeckl, Damir Sudar, Jeremie Teillon, Stefan Terjung, Roland Thuenauer, Christian D. Wilms, Graham D. Wright, Roland Nitschke (2021)
  QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.
  Journal of Microscopy, Volume 284, Issue 1, pp. 56–73.
  https://doi.org/10.1111/jmi.13041
• Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C Darrow, Jan Ellenberg, David Grunwald, Jean-Karim Hériché, Andrii Iudin, Gabriel G Martins, Terry Meehan, Kedar Narayan, Ardan Patwardhan, Matthew Robert Geoffrey Russell, Helen R Saibil, Caterina Strambio-De-Castillia, Jason R Swedlow, Christian Tischer, Virginie Uhlmann, Paul Verkade, Mary Barlow, Omer Bayraktar, Ewan Birney, Cesare Catavitello, Christopher Cawthorne, Stephan Wagner-Conrad, Elizabeth Duke, Perrine Paul-Gilloteaux, Emmanuel Gustin, Maria Harkiolaki, Pasi Kankaanpää, Thomas Lemberger, Jo McEntyre, Josh Moore, Andrew W Nicholls, Shuichi Onami, Helen Parkinson, Maddy Parsons, Marina Romanchikova, Nicholas Sofroniew, Jim Swoger, Nadine Utz, Lenard M Voortman, Frances Wong, Peijun Zhang, Gerard J Kleywegt, Alvis Brazma (2021)
  REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
  Nature methods, 10.1038/s41592-021-01166-8. Advance online publication.
  https://doi.org/10.1038/s41592-021-01166-8
• Jason R. Swedlow, Pasi Kankaanpää, Ugis Sarkans, Wojtek Goscinski, Graham Galloway, Leonel Malacrida, Ryan P. Sullivan, Steffen Härtel, Claire M. Brown, Christopher Wood, Antje Keppler, Federica Paina, Ben Loos, Sara Zullino, Dario Livio Longo, Silvio Aime, Shuichi Onami (2021)
  A global view of standards for open image data formats and repositories.
  Nature methods, 10.1038/s41592-021-01113-7. Advance online publication.
  https://doi.org/10.1038/s41592-021-01113-7

Sister databases (Powered by SSBD)

NeuroGT database

• Tatsumi Hirata, Yukako Tohsato, Hiroya Itoga, Go Shioi, Hiroshi Kiyonari, Sanae Oka, Toshihiko Fujimori, Shuichi Onami (2021)
  NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons,
  Cell Reports Methods, 100012, ISSN 2667-2375,
  https://doi.org/10.1016/j.crmeth.2021.100012

Azebex database

• Towako Hiraki-Kajiyama, Nobuhiko Miyasaka, Reiko Ando, Noriko Wakisaka, Hiroya Itoga, Shuichi Onami, Yoshihiro Yoshihara (2024)
  An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain ,
  The Journal of Comparative Neurology, Volume 532, Issue 6, e25619,
  https://doi.org/10.1002/cne.25619

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