OME-Zarr: a cloud-optimized bioimaging file format with international community support
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Published:2023-07-10
Issue:3
Volume:160
Page:223-251
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ISSN:0948-6143
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Container-title:Histochemistry and Cell Biology
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language:en
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Short-container-title:Histochem Cell Biol
Author:
Moore JoshORCID, Basurto-Lozada DanielaORCID, Besson SébastienORCID, Bogovic JohnORCID, Bragantini JordãoORCID, Brown Eva M.ORCID, Burel Jean-MarieORCID, Casas Moreno XavierORCID, de Medeiros GustavoORCID, Diel Erin E.ORCID, Gault David, Ghosh Satrajit S.ORCID, Gold IlanORCID, Halchenko Yaroslav O.ORCID, Hartley MatthewORCID, Horsfall DaveORCID, Keller Mark S.ORCID, Kittisopikul MarkORCID, Kovacs GaborORCID, Küpcü Yoldaş AybükeORCID, Kyoda KojiORCID, le Tournoulx de la Villegeorges AlbaneORCID, Li TongORCID, Liberali PriscaORCID, Lindner DominikORCID, Linkert Melissa, Lüthi JoelORCID, Maitin-Shepard JeremyORCID, Manz TrevorORCID, Marconato LucaORCID, McCormick MatthewORCID, Lange MerlinORCID, Mohamed KhaledORCID, Moore WilliamORCID, Norlin NilsORCID, Ouyang WeiORCID, Özdemir BugraORCID, Palla GiovanniORCID, Pape ConstantinORCID, Pelkmans LucasORCID, Pietzsch TobiasORCID, Preibisch StephanORCID, Prete MartinORCID, Rzepka NormanORCID, Samee SameeulORCID, Schaub NicholasORCID, Sidky HythemORCID, Solak Ahmet CanORCID, Stirling David R.ORCID, Striebel JonathanORCID, Tischer ChristianORCID, Toloudis DanielORCID, Virshup IsaacORCID, Walczysko PetrORCID, Watson Alan M.ORCID, Weisbart ErinORCID, Wong FrancesORCID, Yamauchi Kevin A.ORCID, Bayraktar OmerORCID, Cimini Beth A.ORCID, Gehlenborg NilsORCID, Haniffa MuzlifahORCID, Hotaling NathanORCID, Onami ShuichiORCID, Royer Loic A.ORCID, Saalfeld StephanORCID, Stegle OliverORCID, Theis Fabian J.ORCID, Swedlow Jason R.ORCID
Abstract
AbstractA 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.
Funder
Chan Zuckerberg Initiative Deutsche Forschungsgemeinschaft National Institutes of Health Wellcome Trust UK Research and Innovation National Human Genome Research Institute NSF Graduate Research Fellowship European Molecular Biology Laboratory VINNOVA Science for Life Laboratory EOSC-Life National Institutes of Health,United States Wellcome National Bioscience Database Center Japan Science and Technology Agency
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Medical Laboratory Technology,Molecular Biology,Histology
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