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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 LU ; Casas Moreno, Xavier ; de Medeiros, Gustavo and Diel, Erin E , et al. (2023) In Histochemistry and Cell Biology 160(3). p.223-251
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,... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Histochemistry and Cell Biology
volume
160
issue
3
pages
223 - 251
publisher
Springer
external identifiers
  • scopus:85164336665
  • pmid:37428210
ISSN
1432-119X
DOI
10.1007/s00418-023-02209-1
language
English
LU publication?
yes
additional info
© 2023. The Author(s).
id
eb2b9cba-7e7e-45c3-b032-1d9a779e5a8c
date added to LUP
2023-07-16 10:28:39
date last changed
2024-04-19 23:33:44
@article{eb2b9cba-7e7e-45c3-b032-1d9a779e5a8c,
  abstract     = {{<p>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.</p>}},
  author       = {{Moore, Josh and Basurto-Lozada, Daniela and Besson, Sébastien and Bogovic, John and Bragantini, Jordão and Brown, Eva M and Burel, Jean-Marie and Casas Moreno, Xavier and de Medeiros, Gustavo and Diel, Erin E and Gault, David and Ghosh, Satrajit S and Gold, Ilan and Halchenko, Yaroslav O and Hartley, Matthew and Horsfall, Dave and Keller, Mark S and Kittisopikul, Mark and Kovacs, Gabor and Küpcü Yoldaş, Aybüke and Kyoda, Koji and le Tournoulx de la Villegeorges, Albane and Li, Tong and Liberali, Prisca and Lindner, Dominik and Linkert, Melissa and Lüthi, Joel and Maitin-Shepard, Jeremy and Manz, Trevor and Marconato, Luca and McCormick, Matthew and Lange, Merlin and Mohamed, Khaled and Moore, William and Norlin, Nils and Ouyang, Wei and Özdemir, Bugra and Palla, Giovanni and Pape, Constantin and Pelkmans, Lucas and Pietzsch, Tobias and Preibisch, Stephan and Prete, Martin and Rzepka, Norman and Samee, Sameeul and Schaub, Nicholas and Sidky, Hythem and Solak, Ahmet Can and Stirling, David R and Striebel, Jonathan}},
  issn         = {{1432-119X}},
  language     = {{eng}},
  month        = {{07}},
  number       = {{3}},
  pages        = {{223--251}},
  publisher    = {{Springer}},
  series       = {{Histochemistry and Cell Biology}},
  title        = {{OME-Zarr : A cloud-optimized bioimaging file format with international community support}},
  url          = {{http://dx.doi.org/10.1007/s00418-023-02209-1}},
  doi          = {{10.1007/s00418-023-02209-1}},
  volume       = {{160}},
  year         = {{2023}},
}