Plate IV.190 · Publications
OME-Zarr: a cloud-optimized bioimaging file format with international community support
Article in Histochemistry and Cell Biology, 10 July 2023.
Abstract
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.
Versions2
- PublishedHistochemistry and Cell Biology10.1007/s00418-023-02209-1
- PreprintbioRxiv10.1101/2023.02.17.528834
Cite
@article{moore2023ome,
title = {{OME-Zarr: a cloud-optimized bioimaging file format with international community support}},
author = {Moore, Josh and Basurto-Lozada, Daniela and Besson, Sébastien and Bogovic, John and Bragantini, Jordão and Brown, Eva M. and Burel, Jean-Marie and Casas Moreno, Xavier and de Medeiros, Gustavo and Diel, Erin E. and Gault, David and Ghosh, Satrajit S. and Gold, Ilan and Halchenko, Yaroslav O. and Hartley, Matthew and Horsfall, Dave and Keller, Mark S. and Kittisopikul, Mark and Kovacs, Gabor and Küpcü Yoldaş, Aybüke and Kyoda, Koji and le Tournoulx de la Villegeorges, Albane and Li, Tong and Liberali, Prisca and Lindner, Dominik and Linkert, Melissa and Lüthi, Joel and Maitin-Shepard, Jeremy and Manz, Trevor and Marconato, Luca and McCormick, Matthew and Lange, Merlin and Mohamed, Khaled and Moore, William and Norlin, Nils and Ouyang, Wei and Özdemir, Bugra and Palla, Giovanni and Pape, Constantin and Pelkmans, Lucas and Pietzsch, Tobias and Preibisch, Stephan and Prete, Martin and Rzepka, Norman and Samee, Sameeul and Schaub, Nicholas and Sidky, Hythem and Solak, Ahmet Can and Stirling, David R. and Striebel, Jonathan and Tischer, Christian and Toloudis, Daniel and Virshup, Isaac and Walczysko, Petr and Watson, Alan M. and Weisbart, Erin and Wong, Frances and Yamauchi, Kevin A. and Bayraktar, Omer and Cimini, Beth A. and Gehlenborg, Nils and Haniffa, Muzlifah and Hotaling, Nathan and Onami, Shuichi and Royer, Loic A. and Saalfeld, Stephan and Stegle, Oliver and Theis, Fabian J. and Swedlow, Jason R.},
journal = {Histochemistry and Cell Biology},
publisher = {Springer Science and Business Media LLC},
year = {2023},
month = jul,
doi = {10.1007/s00418-023-02209-1},
url = {https://doi.org/10.1007/s00418-023-02209-1},
pmid = {37428210},
pmcid = {PMC10492740}
}