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

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bioRxiv. 2023 Feb 25;. doi: 10.1101/2023.02.17.528834

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

Moore Josh, Basurto-Lozada Daniela, Besson Sébastien, Bogovic John, Brown Eva, Burel Jean-Marie, de Medeiros Gustavo, Diel Erin, Gault David, Ghosh Satrajit, Gold Ilan, Halchenko Yaroslav, Hartley Matthew, Horsfall Dave, Keller Mark, Kittisopikul Mark, Kovacs Gabor, Yoldaş Aybüke, de la Villegeorges Albane, Li Tong, Liberali Prisca, Linkert Melissa, Lindner Dominik, Lüthi Joel, Maitin-Shepard Jeremy, Manz Trevor, McCormick Matthew, Mohamed Khaled, Moore William, Özdemir Bugra, Pape Constantin, Pelkmans Lucas, Prete Martin, Pietzsch Tobias, Preibisch Stephan, Rzepka Norman, Stirling David, Striebel Jonathan, Tischer Christian, Toloudis Daniel, Walczysko Petr, Watson Alan, Wong Frances, Yamauchi Kevin, Bayraktar Omer, Haniffa Muzlifah, Saalfeld Stephan, Swedlow Jason

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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 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.

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bioRxiv PrePrint https://doi.org/10.1101/2023.02.17.528834

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

Abstract

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