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

Histochemistry and cell biology

Authors	Josh Moore Daniela Basurto-Lozada Sébastien Besson John Bogovic Jordão Bragantini Eva Brown Jean-Marie Burel Xavier Moreno Gustavo de Medeiros Erin Diel David Gault Satrajit Ghosh Ilan Gold Yaroslav Halchenko Matthew Hartley Dave Horsfall Mark Keller Mark Kittisopikul Gabor Kovacs Aybüke Yoldaş Koji Kyoda Albane 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 Solak David Stirling Jonathan Striebel Christian Tischer Daniel Toloudis Isaac Virshup Petr Walczysko Alan Watson Erin Weisbart Frances Wong Kevin Yamauchi Omer Bayraktar Beth Cimini Nils Gehlenborg Muzlifah Haniffa Nathan Hotaling Shuichi Onami Loic Royer Stephan Saalfeld Oliver Stegle Fabian Theis Jason Swedlow
Keywords	Bioimaging Cloud Community Data FAIR Format
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.
Year of Publication	2023
Journal	Histochemistry and cell biology
Date Published	07/2023
ISSN	1432-119X
DOI	10.1007/s00418-023-02209-1
PubMed ID	37428210
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