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

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 specifi...

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Detalles Bibliográficos
Autores principales: Moore, Josh, Basurto-Lozada, Daniela, Besson, Sébastien, Bogovic, John, Bragantini, Jordão, Brown, Eva M., Burel, Jean-Marie, Moreno, Xavier Casas, de Medeiros, Gustavo, Diel, Erin E., Gault, David, Ghosh, Satrajit S., Gold, Ilan, Halchenko, Yaroslav O., Hartley, Matthew, Horsfall, Dave, Keller, Mark S., Kittisopikul, Mark, Kovacs, Gabor, Yoldaş, Aybüke Küpcü, Kyoda, Koji, de la Villegeorges, Albane le Tournoulx, Li, Tong, Liberali, Prisca, Lindner, Dominik, Linkert, Melissa, Lüthi, Joel, Maitin-Shepard, Jeremy, Manz, Trevor, Marconato, Luca, McCormick, Matthew, Lange, Merlin, Mohamed, Khaled, Moore, William, Norlin, Nils, Ouyang, Wei, Özdemir, Bugra, Palla, Giovanni, Pape, Constantin, Pelkmans, Lucas, Pietzsch, Tobias, Preibisch, Stephan, Prete, Martin, Rzepka, Norman, Samee, Sameeul, Schaub, Nicholas, Sidky, Hythem, Solak, Ahmet Can, Stirling, David R., Striebel, Jonathan, Tischer, Christian, Toloudis, Daniel, Virshup, Isaac, Walczysko, Petr, Watson, Alan M., Weisbart, Erin, Wong, Frances, Yamauchi, Kevin A., Bayraktar, Omer, Cimini, Beth A., Gehlenborg, Nils, Haniffa, Muzlifah, Hotaling, Nathan, Onami, Shuichi, Royer, Loic A., Saalfeld, Stephan, Stegle, Oliver, Theis, Fabian J., Swedlow, Jason R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980008/
https://www.ncbi.nlm.nih.gov/pubmed/36865282
http://dx.doi.org/10.1101/2023.02.17.528834
Descripción
Sumario: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.