OME-Zarr: a cloud-optimized bioimaging file format with international community support
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 des...
| Main Authors: | , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Berlin Heidelberg
2023
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| Online Access: | https://hdl.handle.net/1721.1/151126 |
| _version_ | 1826214711420518400 |
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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. |
| author2 | McGovern Institute for Brain Research at MIT |
| author_facet | McGovern Institute for Brain Research at MIT 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. |
| author_sort | Moore, Josh |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T16:10:16Z |
| format | Article |
| id | mit-1721.1/151126 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T16:10:16Z |
| publishDate | 2023 |
| publisher | Springer Berlin Heidelberg |
| record_format | dspace |
| spelling | mit-1721.1/1511262024-01-31T20:25:38Z 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. McGovern Institute for Brain Research at MIT 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. 2023-07-17T13:46:26Z 2023-07-17T13:46:26Z 2023-07-10 2023-07-16T03:10:34Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/151126 Moore, Josh, Basurto-Lozada, Daniela, Besson, Sébastien, Bogovic, John, Bragantini, Jordão et al. 2023. "OME-Zarr: a cloud-optimized bioimaging file format with international community support." PUBLISHER_CC en https://doi.org/10.1007/s00418-023-02209-1 Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ The Author(s) application/pdf Springer Berlin Heidelberg Springer Berlin Heidelberg |
| spellingShingle | 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. 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 |
| url | https://hdl.handle.net/1721.1/151126 |
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