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OME-Zarr: a cloud-optimized bioimaging file format with international community support.

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.

SUBMITTER: Moore J 

PROVIDER: S-EPMC10492740 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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OME-Zarr: a cloud-optimized bioimaging file format with international community support.

Moore Josh J   Basurto-Lozada Daniela D   Besson Sébastien S   Bogovic John J   Bragantini Jordão J   Brown Eva M EM   Burel Jean-Marie JM   Casas Moreno Xavier X   de Medeiros Gustavo G   Diel Erin E EE   Gault David D   Ghosh Satrajit S SS   Gold Ilan I   Halchenko Yaroslav O YO   Hartley Matthew M   Horsfall Dave D   Keller Mark S MS   Kittisopikul Mark M   Kovacs Gabor G   Küpcü Yoldaş Aybüke A   Kyoda Koji K   le Tournoulx de la Villegeorges Albane A   Li Tong T   Liberali Prisca P   Lindner Dominik D   Linkert Melissa M   Lüthi Joel J   Maitin-Shepard Jeremy J   Manz Trevor T   Marconato Luca L   McCormick Matthew M   Lange Merlin M   Mohamed Khaled K   Moore William W   Norlin Nils N   Ouyang Wei W   Özdemir Bugra B   Palla Giovanni G   Pape Constantin C   Pelkmans Lucas L   Pietzsch Tobias T   Preibisch Stephan S   Prete Martin M   Rzepka Norman N   Samee Sameeul S   Schaub Nicholas N   Sidky Hythem H   Solak Ahmet Can AC   Stirling David R DR   Striebel Jonathan J   Tischer Christian C   Toloudis Daniel D   Virshup Isaac I   Walczysko Petr P   Watson Alan M AM   Weisbart Erin E   Wong Frances F   Yamauchi Kevin A KA   Bayraktar Omer O   Cimini Beth A BA   Gehlenborg Nils N   Haniffa Muzlifah M   Hotaling Nathan N   Onami Shuichi S   Royer Loic A LA   Saalfeld Stephan S   Stegle Oliver O   Theis Fabian J FJ   Swedlow Jason R JR  

Histochemistry and cell biology 20230710 3

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 re  ...[more]

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