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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...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Springer Berlin Heidelberg
2023
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492740/ https://www.ncbi.nlm.nih.gov/pubmed/37428210 http://dx.doi.org/10.1007/s00418-023-02209-1 |
| _version_ | 1785104320482508800 |
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| author | Moore, Josh Basurto-Lozada, Daniela Besson, Sébastien Bogovic, John Bragantini, Jordão Brown, Eva M. Burel, Jean-Marie Casas Moreno, Xavier 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 Küpcü Yoldaş, Aybüke Kyoda, Koji le Tournoulx de la Villegeorges, Albane 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. |
| author_facet | Moore, Josh Basurto-Lozada, Daniela Besson, Sébastien Bogovic, John Bragantini, Jordão Brown, Eva M. Burel, Jean-Marie Casas Moreno, Xavier 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 Küpcü Yoldaş, Aybüke Kyoda, Koji le Tournoulx de la Villegeorges, Albane 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. |
| author_sort | Moore, Josh |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-10492740 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | Springer Berlin Heidelberg |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-104927402023-09-11 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 Casas Moreno, Xavier 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 Küpcü Yoldaş, Aybüke Kyoda, Koji le Tournoulx de la Villegeorges, Albane 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. Histochem Cell Biol Original Paper 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. Springer Berlin Heidelberg 2023-07-10 2023 /pmc/articles/PMC10492740/ /pubmed/37428210 http://dx.doi.org/10.1007/s00418-023-02209-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Original Paper Moore, Josh Basurto-Lozada, Daniela Besson, Sébastien Bogovic, John Bragantini, Jordão Brown, Eva M. Burel, Jean-Marie Casas Moreno, Xavier 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 Küpcü Yoldaş, Aybüke Kyoda, Koji le Tournoulx de la Villegeorges, Albane 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. OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title | OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title_full | OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title_fullStr | OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title_full_unstemmed | OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title_short | OME-Zarr: a cloud-optimized bioimaging file format with international community support |
| title_sort | ome-zarr: a cloud-optimized bioimaging file format with international community support |
| topic | Original Paper |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492740/ https://www.ncbi.nlm.nih.gov/pubmed/37428210 http://dx.doi.org/10.1007/s00418-023-02209-1 |
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