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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
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; Yoldas, 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.
Afiliación
  • Moore J; German BioImaging - Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany.
  • Basurto-Lozada D; Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
  • Besson S; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Bogovic J; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
  • Bragantini J; Chan Zuckerberg Biohub, San Francisco, CA, United States.
  • Brown EM; Allen Institute for Cell Science, Seattle, WA, USA.
  • Burel JM; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Moreno XC; Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
  • de Medeiros G; Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.
  • Diel EE; Glencoe Software Inc., Seattle, WA, USA.
  • Gault D; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Ghosh SS; Massachusetts Institute of Technology: Cambridge, MA, USA.
  • Gold I; Harvard Medical School, Boston, MA, USA.
  • Halchenko YO; Dartmouth College, Hanover, NH, USA.
  • Hartley M; European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.
  • Horsfall D; Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
  • Keller MS; Harvard Medical School, Boston, MA, USA.
  • Kittisopikul M; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
  • Kovacs G; Allen Institute for Neural Dynamics, Seattle, WA, USA.
  • Yoldas AK; European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.
  • Kyoda K; RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
  • de la Villegeorges ALT; scalable minds GmbH, Potsdam, Germany.
  • Li T; Wellcome Sanger Institute, Hinxton, UK.
  • Liberali P; Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.
  • Lindner D; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Linkert M; Glencoe Software Inc., Seattle, WA, USA.
  • Lüthi J; Friedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.
  • Maitin-Shepard J; Google Research, Mountain View, CA, USA.
  • Manz T; Harvard Medical School, Boston, MA, USA.
  • Marconato L; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
  • McCormick M; Kitware, Inc, Carrboro, NC, USA.
  • Lange M; Chan Zuckerberg Biohub, San Francisco, CA, United States.
  • Mohamed K; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Moore W; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
  • Norlin N; Department of Experimental Medical Science & Lund Bioimaging Centre, Lund University, Lund, Sweden.
  • Ouyang W; Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
  • Özdemir B; Euro-BioImaging Bio-Hub, EMBL Heidelberg, Germany.
  • Palla G; Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
  • Pape C; Georg-August Universität Göttingen, Germany.
  • Pelkmans L; University of Zurich, Zurich, Switzerland.
  • Pietzsch T; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
  • Preibisch S; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
  • Prete M; Wellcome Sanger Institute, Hinxton, UK.
  • Rzepka N; scalable minds GmbH, Potsdam, Germany.
  • Samee S; Axle Research and Technology.
  • Schaub N; Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health.
  • Sidky H; Axle Research and Technology.
  • Solak AC; Chan Zuckerberg Biohub, San Francisco, CA, United States.
  • Stirling DR; Glencoe Software Inc., Seattle, WA, USA.
  • Striebel J; scalable minds GmbH, Potsdam, Germany.
bioRxiv ; 2023 May 07.
Article en En | MEDLINE | ID: mdl-36865282
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.
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Texto completo: 1 Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article
Texto completo
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Texto completo: 1 Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article