학술논문

OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Document Type
Academic Journal
Author
Moore J; German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany. josh@openmicroscopy.org.; 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, USA.; 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.; Casas Moreno X; 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.; Küpcü Yoldaş A; European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.; Kyoda K; RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.; le Tournoulx de la Villegeorges A; 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; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.; McCormick M; Kitware, Inc, Carrboro, NC, USA.; Lange M; Chan Zuckerberg Biohub, San Francisco, CA, USA.; 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, Göttingen, Germany.; Pelkmans L; University of Zürich, Zürich, 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, Rockville, USA.; Schaub N; Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA.; Sidky H; Axle Research and Technology, Rockville, USA.; Solak AC; Chan Zuckerberg Biohub, San Francisco, CA, USA.; Stirling DR; Glencoe Software Inc., Seattle, WA, USA.; Striebel J; scalable minds GmbH, Potsdam, Germany.; Tischer C; EMBL, Heidelberg, Germany.; Toloudis D; Allen Institute for Cell Science, Seattle, WA, USA.; Virshup I; Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.; Walczysko P; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.; Watson AM; University of Pittsburgh, Pittsburgh, PA, USA.; Weisbart E; Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Wong F; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.; Yamauchi KA; Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland.; Bayraktar O; Wellcome Sanger Institute, Hinxton, UK.; Cimini BA; Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Gehlenborg N; Harvard Medical School, Boston, MA, USA.; Haniffa M; Wellcome Sanger Institute, Hinxton, UK.; Hotaling N; Information Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA.; Onami S; RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.; Royer LA; Chan Zuckerberg Biohub, San Francisco, CA, USA.; Saalfeld S; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.; Stegle O; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.; Theis FJ; Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.; Swedlow JR; Divisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
Source
Publisher: Springer Country of Publication: Germany NLM ID: 9506663 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-119X (Electronic) Linking ISSN: 09486143 NLM ISO Abbreviation: Histochem Cell Biol Subsets: MEDLINE
Subject
Language
English
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.
(© 2023. The Author(s).)