ArticleHistochemistry and cell biology2023
OME-Zarr: a cloud-optimized bioimaging file format with international community support.
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Article in Histochemistry and cell biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 2 of them syntheses that pooled it.
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76citing papers in PubMed, 2 pooled it
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76 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- The HuBMAP Framework for Advancing Data FAIRness.bioRxiv : the preprint server for biology · 2026Article
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- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
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- High-throughput, organ-scale 3D tubule tracking using TubuleMAP.bioRxiv : the preprint server for biology · 2026Article
- A Community Standard Multispecies Cell Atlas of the Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- A scoping study of the whole-cell imaging literature as a foundation for the emerging field of cell anatomy.BMC biology · 2026Article
- The Extremely Brilliant Brain: An Isotropic Microscale Human Brain Dataset.bioRxiv : the preprint server for biology · 2026Article
- Microscopy Nodes: versatile 3D microscopy visualization with Blender.EMBO reports · 2026Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
69 authors.
Josh MooreGerman BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany. josh@openmicroscopy.org.ORCID http://orcid.org/0000-0003-4028-811X
Daniela Basurto-LozadaBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0003-3943-8424
Sébastien BessonDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0001-8783-1429
John BogovicJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-4829-9457
Jordão BragantiniChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7652-2735
Eva M BrownAllen Institute for Cell Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-2564-0373
Jean-Marie BurelDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0002-1789-1861
Xavier Casas MorenoScience for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-9583-9022
Gustavo de MedeirosFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID http://orcid.org/0000-0001-5877-3012
Erin E DielGlencoe Software Inc., Seattle, WA, USA.ORCID http://orcid.org/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 http://orcid.org/0000-0002-5312-6729
Ilan GoldHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-5823-1026
Yaroslav O HalchenkoDartmouth College, Hanover, NH, USA.ORCID http://orcid.org/0000-0003-3456-2493
Matthew HartleyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.ORCID http://orcid.org/0000-0001-6178-2884
Dave HorsfallBiosciences Institute, Newcastle University, Newcastle upon Tyne, UK.ORCID http://orcid.org/0000-0002-8086-812X
Mark S KellerHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3003-874X
Mark KittisopikulJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-9558-6248
Gabor KovacsAllen Institute for Neural Dynamics, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-1779-775X
Aybüke Küpcü YoldaşEuropean Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK.ORCID http://orcid.org/0000-0001-6191-5069
Koji KyodaRIKEN Center for Biosystems Dynamics Research, Kobe, Japan.ORCID http://orcid.org/0000-0001-9455-2153
Albane le Tournoulx de la Villegeorgesscalable minds GmbH, Potsdam, Germany.ORCID http://orcid.org/0000-0001-7394-8941
Tong LiWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-8240-4476
Prisca LiberaliFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID http://orcid.org/0000-0003-0695-6081
Dominik LindnerDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0001-8038-1250
Melissa LinkertGlencoe Software Inc., Seattle, WA, USA.
Joel LüthiFriedrich Miescher Institute for Biomedical Imaging, Basel, Switzerland.ORCID http://orcid.org/0000-0003-3023-170X
Jeremy Maitin-ShepardGoogle Research, Mountain View, CA, USA.ORCID http://orcid.org/0000-0001-8453-7961
Trevor ManzHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-7694-5164
Luca MarconatoGenome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.ORCID http://orcid.org/0000-0003-3198-1326
Matthew McCormickKitware, Inc, Carrboro, NC, USA.ORCID http://orcid.org/0000-0001-9475-3756
Merlin LangeChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-0534-4374
Khaled MohamedDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0003-1480-8695
William MooreDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0002-7264-8338
Nils NorlinDepartment of Experimental Medical Science & Lund Bioimaging Centre, Lund University, Lund, Sweden.ORCID http://orcid.org/0000-0003-1970-3198
Wei OuyangScience for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-0291-926X
Bugra ÖzdemirEuro-BioImaging Bio-Hub, EMBL, Heidelberg, Germany.ORCID http://orcid.org/0000-0001-9823-0581
Giovanni PallaInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID http://orcid.org/0000-0002-8004-4462
Constantin PapeGeorg-August-Universität Göttingen, Göttingen, Germany.ORCID http://orcid.org/0000-0001-6562-7187
Lucas PelkmansUniversity of Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0002-6754-9730
Tobias PietzschJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-9477-3957
Stephan PreibischJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-0276-494X
Martin PreteWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-5946-821X
Norman Rzepkascalable minds GmbH, Potsdam, Germany.ORCID http://orcid.org/0000-0002-8168-7929
Sameeul SameeAxle Research and Technology, Rockville, USA.ORCID http://orcid.org/0009-0006-9305-7146
Nicholas SchaubInformation Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA.ORCID http://orcid.org/0000-0001-6581-7191
Hythem SidkyAxle Research and Technology, Rockville, USA.ORCID http://orcid.org/0000-0003-3532-4809
Ahmet Can SolakChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-1381-8309
David R StirlingGlencoe Software Inc., Seattle, WA, USA.ORCID http://orcid.org/0000-0001-6802-4103
Jonathan Striebelscalable minds GmbH, Potsdam, Germany.ORCID http://orcid.org/0000-0002-5547-5973
Christian TischerEMBL, Heidelberg, Germany.ORCID http://orcid.org/0000-0003-4105-1990
Daniel ToloudisAllen Institute for Cell Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-2620-1233
Isaac VirshupInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID http://orcid.org/0000-0002-1710-8945
Petr WalczyskoDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0003-0302-8247
Alan M WatsonUniversity of Pittsburgh, Pittsburgh, PA, USA.ORCID http://orcid.org/0000-0003-0632-8296
Erin WeisbartImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6437-2458
Frances WongDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0001-7397-8251
Kevin A YamauchiDepartment of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland.ORCID http://orcid.org/0000-0002-7818-1388
Omer BayraktarWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0001-6055-277X
Beth A CiminiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9640-9318
Nils GehlenborgHarvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-0327-8297
Muzlifah HaniffaWellcome Sanger Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-3927-2084
Nathan HotalingInformation Technology Branch, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, USA.ORCID http://orcid.org/0000-0001-8423-6464
Shuichi OnamiRIKEN Center for Biosystems Dynamics Research, Kobe, Japan.ORCID http://orcid.org/0000-0002-8255-1724
Loic A RoyerChan Zuckerberg Biohub, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9991-9724
Stephan SaalfeldJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-4106-1761
Oliver StegleGenome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.ORCID http://orcid.org/0000-0002-8818-7193
Fabian J TheisInstitute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.ORCID http://orcid.org/0000-0002-2419-1943
Jason R SwedlowDivisions of Molecular Cell and Developmental Biology, and Computational Biology, University of Dundee, Dundee, Scotland, UK.ORCID http://orcid.org/0000-0002-2198-1958
Funding
Research Services Section (RSS)ZICTR000242 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI WILSON, KELLI · 2015 to 2025
$64.9MTraining 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
$11.6MA 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
$5.0MCell-type specific role of circadian-dependent transcription in fentanyl-induced synaptic and behavioral plasticity - SupplementR01HL150432 · NHLBI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI LOGAN, RYAN W · 2019 to 2020
$2.0MIntegrative 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
$1.4MUltra-fast high-resolution imaging of whole mouse brain for the study of drug addictionR21DA052419 · NIDA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI FREYBERG, ZACHARY, LOGAN, RYAN W · 2021 to 2022
$448kNCI NIH HHS R33 CA263666NHGRI NIH HHS 5T32HG002295NHGRI NIH HHS T32 HG002295NHLBI NIH HHS R01 HL150432NIGMS NIH HHS P41 GM135019NIH HHS 1RF1MH126732-01NIH HHS OT2 OD033758NIH HHS OT2OD033758NIH HHS P41 GM135019NIH HHS R24MH114793NIH HHS R24MH117295NIMH NIH HHS R24 MH114793NIMH NIH HHS R24 MH117295NIMH NIH HHS RF1 MH126732Wellcome TrustWellcome Trust 212962/Z/18/Z
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.
Indexed as
MicroscopySoftwareCommunity SupportHumansBioimagingCloudCommunityDataFAIRFormat
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