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

Authors :
Moore J
Basurto-Lozada D
Besson S
Bogovic J
Bragantini J
Brown EM
Burel JM
Casas Moreno X
de Medeiros G
Diel EE
Gault D
Ghosh SS
Gold I
Halchenko YO
Hartley M
Horsfall D
Keller MS
Kittisopikul M
Kovacs G
Küpcü Yoldaş A
Kyoda K
le Tournoulx de la Villegeorges A
Li T
Liberali P
Lindner D
Linkert M
Lüthi J
Maitin-Shepard J
Manz T
Marconato L
McCormick M
Lange M
Mohamed K
Moore W
Norlin N
Ouyang W
Özdemir B
Palla G
Pape C
Pelkmans L
Pietzsch T
Preibisch S
Prete M
Rzepka N
Samee S
Schaub N
Sidky H
Solak AC
Stirling DR
Striebel J
Tischer C
Toloudis D
Virshup I
Walczysko P
Watson AM
Weisbart E
Wong F
Yamauchi KA
Bayraktar O
Cimini BA
Gehlenborg N
Haniffa M
Hotaling N
Onami S
Royer LA
Saalfeld S
Stegle O
Theis FJ
Swedlow JR
Source :
Histochemistry and cell biology [Histochem Cell Biol] 2023 Sep; Vol. 160 (3), pp. 223-251. Date of Electronic Publication: 2023 Jul 10.
Publication Year :
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.<br /> (© 2023. The Author(s).)

Details

Language :
English
ISSN :
1432-119X
Volume :
160
Issue :
3
Database :
MEDLINE
Journal :
Histochemistry and cell biology
Publication Type :
Academic Journal
Accession number :
37428210
Full Text :
https://doi.org/10.1007/s00418-023-02209-1