ArticlebioRxiv : the preprint server for biology2023
OME-Zarr: a cloud-optimized bioimaging file format with international community support.
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Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1citing papers in PubMed
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1 citing paper in PubMed.
- Multiplex protein imaging in tumour biology.Nature reviews. Cancer · 2024Review
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Authors and funding
69 authors.
Josh MooreGerman BioImaging - Gesellschaft für Mikroskopie und Bildanalyse e.V., Konstanz, Germany.ORCID 0000-0003-4028-811X
Daniela Basurto-LozadaBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0003-3943-8424
Sébastien BessonDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0001-8783-1429
John BogovicJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID 0000-0002-4829-9457
Jordão BragantiniChan Zuckerberg Biohub, San Francisco, CA, United States.ORCID 0000-0001-7652-2735
Eva M BrownAllen Institute for Cell Science, Seattle, WA, USA.ORCID 0000-0003-2564-0373
Jean-Marie BurelDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0002-1789-1861
Xavier Casas MorenoScience for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID 0000-0002-9583-9022
Gustavo de MedeirosFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID 0000-0001-5877-3012
Erin E DielGlencoe Software Inc., Seattle, WA, USA.ORCID 0000-0003-2526-3512
David GaultDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.
Satrajit S GhoshMassachusetts Institute of Technology: Cambridge, MA, USA.ORCID 0000-0002-5312-6729
Ilan GoldHarvard Medical School, Boston, MA, USA.ORCID 0000-0002-5823-1026
Yaroslav O HalchenkoDartmouth College, Hanover, NH, USA.ORCID 0000-0003-3456-2493
Matthew HartleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.ORCID 0000-0001-6178-2884
Dave HorsfallBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0002-8086-812X
Mark S KellerHarvard Medical School, Boston, MA, USA.ORCID 0000-0003-3003-874X
Mark KittisopikulJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID 0000-0002-9558-6248
Gabor KovacsAllen Institute for Neural Dynamics, Seattle, WA, USA.ORCID 0000-0003-1779-775X
Aybüke Küpcü YoldaşEuropean Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.ORCID 0000-0001-6191-5069
Koji KyodaRIKEN Center for Biosystems Dynamics Research, Kobe, Japan.ORCID 0000-0001-9455-2153
Albane le Tournoulx de la Villegeorgesscalable minds GmbH, Potsdam, Germany.ORCID 0000-0001-7394-8941
Tong LiWellcome Sanger Institute, Hinxton, UK.ORCID 0000-0002-8240-4476
Prisca LiberaliFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID 0000-0003-0695-6081
Dominik LindnerDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0001-8038-1250
Melissa LinkertGlencoe Software Inc., Seattle, WA, USA.
Joel LüthiFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID 0000-0003-3023-170X
Jeremy Maitin-ShepardGoogle Research, Mountain View, CA, USA.ORCID 0000-0001-8453-7961
Trevor ManzHarvard Medical School, Boston, MA, USA.ORCID 0000-0001-7694-5164
Luca MarconatoEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.ORCID 0000-0003-3198-1326
Matthew McCormickKitware, Inc, Carrboro, NC, USA.ORCID 0000-0001-9475-3756
Merlin LangeChan Zuckerberg Biohub, San Francisco, CA, United States.ORCID 0000-0003-0534-4374
Khaled MohamedDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0003-1480-8695
William MooreDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0002-7264-8338
Nils NorlinDepartment of Experimental Medical Science & Lund Bioimaging Centre, Lund University, Lund, Sweden.ORCID 0000-0003-1970-3198
Wei OuyangScience for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID 0000-0002-0291-926X
Bugra ÖzdemirEuro-BioImaging Bio-Hub, EMBL Heidelberg, Germany.ORCID 0000-0001-9823-0581
Giovanni PallaInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID 0000-0002-8004-4462
Constantin PapeGeorg-August Universität Göttingen, Germany.ORCID 0000-0001-6562-7187
Lucas PelkmansUniversity of Zurich, Zurich, Switzerland.ORCID 0000-0002-6754-9730
Tobias PietzschJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID 0000-0002-9477-3957
Stephan PreibischJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID 0000-0002-0276-494X
Martin PreteWellcome Sanger Institute, Hinxton, UK.ORCID 0000-0002-5946-821X
Norman Rzepkascalable minds GmbH, Potsdam, Germany.ORCID 0000-0002-8168-7929
Sameeul SameeAxle Research and Technology.ORCID 0009-0006-9305-7146
Nicholas SchaubInformation Technology Branch, National Center for Advancing Translational Science, National Institutes of Health.ORCID 0000-0001-6581-7191
Hythem SidkyAxle Research and Technology.ORCID 0000-0003-3532-4809
Ahmet Can SolakChan Zuckerberg Biohub, San Francisco, CA, United States.ORCID 0000-0002-1381-8309
David R StirlingGlencoe Software Inc., Seattle, WA, USA.ORCID 0000-0001-6802-4103
Jonathan Striebelscalable minds GmbH, Potsdam, Germany.ORCID 0000-0002-5547-5973
Christian TischerEMBL Heidelberg, Germany.ORCID 0000-0003-4105-1990
Daniel ToloudisAllen Institute for Cell Science, Seattle, WA, USA.ORCID 0000-0003-2620-1233
Isaac VirshupInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID 0000-0002-1710-8945
Petr WalczyskoDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0003-0302-8247
Alan M WatsonUniversity of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0003-0632-8296
Erin WeisbartImaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0002-6437-2458
Frances WongDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0001-7397-8251
Kevin A YamauchiDepartment of Biosystems Science and Engineering, ETH Zürich, Switzerland.ORCID 0000-0002-7818-1388
Omer BayraktarWellcome Sanger Institute, Hinxton, UK.ORCID 0000-0001-6055-277X
Beth A CiminiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0001-9640-9318
Nils GehlenborgHarvard Medical School, Boston, MA, USA.ORCID 0000-0003-0327-8297
Muzlifah HaniffaWellcome Sanger Institute, Hinxton, UK.ORCID 0000-0002-3927-2084
Nathan HotalingInformation Technology Branch, National Center for Advancing Translational Science, National Institutes of Health.ORCID 0000-0001-8423-6464
Shuichi OnamiRIKEN Center for Biosystems Dynamics Research, Kobe, Japan.ORCID 0000-0002-8255-1724
Loic A RoyerChan Zuckerberg Biohub, San Francisco, CA, United States.ORCID 0000-0002-9991-9724
Stephan SaalfeldJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID 0000-0002-4106-1761
Oliver StegleEuropean Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.ORCID 0000-0002-8818-7193
Fabian J TheisInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID 0000-0002-2419-1943
Jason R SwedlowDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID 0000-0002-2198-1958
Funding
Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8MDANDI: Distributed Archives for Neurophysiology Data IntegrationR24MH117295 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Satrajit Sujit Ghosh, Yaroslav O Halchenko · 2019 to 2026
$11.6MMultiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data IntegrationUM1HG011593 · NHGRI · CARNEGIE-MELLON UNIVERSITY · PI ALBER, FRANK, BELMONT, ANDREW STEVEN · 2020 to 2024
$10.4MA Confocal Fluorescence Microscopy Brain Data ArchiveR24MH114793 · NIMH · CARNEGIE-MELLON UNIVERSITY · PI ALEXANDER J ROPELEWSKI, Alan Michael Watson · 2017 to 2026
$10.1MCenter for Open Bioimage AnalysisP41GM135019 · NIGMS · BROAD INSTITUTE, INC. · PI CARPENTER, ANNE E. · 2020 to 2024
$6.9MData Exploration and Visualization Tools for HuBMAP and a Human Reference AtlasOT2OD033758 · OD · HARVARD MEDICAL SCHOOL · PI GEHLENBORG, NILS · 2022 to 2024
$5.0MIntegrative Visualization of Spatiotemporal Tumor AtlasesR33CA263666 · NCI · HARVARD MEDICAL SCHOOL · PI GEHLENBORG, NILS · 2021 to 2021
$1.5MA Computational Framework for Distributed Registration of Massive Neuroscience ImagesRF1MH126732 · NIMH · KITWARE, INC. · PI ENQUOBAHRIE, ANDINET ASMAMAW · 2021 to 2021
$1.4MNCI NIH HHS R33 CA263666NHGRI NIH HHS T32 HG002295NHGRI NIH HHS UM1 HG011593NIGMS NIH HHS P41 GM135019NIH HHS OT2 OD033758NIMH NIH HHS R24 MH114793NIMH NIH HHS R24 MH117295NIMH NIH HHS RF1 MH126732Wellcome Trust
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.
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