OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Bioimaging
Cloud
Community
Data
FAIR
Format
Journal
Histochemistry and cell biology
ISSN: 1432-119X
Titre abrégé: Histochem Cell Biol
Pays: Germany
ID NLM: 9506663
Informations de publication
Date de publication:
Sep 2023
Sep 2023
Historique:
accepted:
16
05
2023
medline:
11
9
2023
pubmed:
10
7
2023
entrez:
10
7
2023
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 37428210
doi: 10.1007/s00418-023-02209-1
pii: 10.1007/s00418-023-02209-1
pmc: PMC10492740
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
223-251Subventions
Organisme : NIH HHS
ID : P41 GM135019
Pays : United States
Organisme : NIH HHS
ID : R24MH114793
Pays : United States
Organisme : NIMH NIH HHS
ID : R24 MH114793
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG002295
Pays : United States
Organisme : Wellcome Trust
ID : 212962/Z/18/Z
Pays : United Kingdom
Organisme : NIH HHS
ID : R24MH117295
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM135019
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : 5T32HG002295
Pays : United States
Organisme : NIH HHS
ID : 1RF1MH126732-01
Pays : United States
Organisme : NCI NIH HHS
ID : R33 CA263666
Pays : United States
Organisme : NIH HHS
ID : OT2OD033758
Pays : United States
Organisme : NIH HHS
ID : OT2 OD033758
Pays : United States
Organisme : NIDA NIH HHS
ID : R21 DA052419
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. The Author(s).
Références
Digit Pathol (2019). 2019 Apr;2019:3-10
pubmed: 31579322
Nat Cancer. 2020 Feb;1(2):163-175
pubmed: 35122013
Nat Methods. 2015 Jun;12(6):481-3
pubmed: 26020499
Sci Data. 2016 Mar 15;3:160018
pubmed: 26978244
Nat Methods. 2022 Mar;19(3):262-267
pubmed: 35277708
J Mol Biol. 2022 Jun 15;434(11):167505
pubmed: 35189131
Nat Methods. 2023 Aug;20(8):1120-1121
pubmed: 37277559
Nat Methods. 2017 Aug;14(8):775-781
pubmed: 28775673
Science. 2021 Feb 26;371(6532):
pubmed: 33384301
Nat Methods. 2017 Jul;14(7):691-694
pubmed: 28604722
Nat Methods. 2022 Dec;19(12):1563-1567
pubmed: 36396787
Bioinformatics. 2011 Apr 15;27(8):1179-80
pubmed: 21349861
Front Neurosci. 2022 Apr 19;16:871228
pubmed: 35516811
Nat Methods. 2019 Dec;16(12):1199-1200
pubmed: 31780825
Structure. 2012 Mar 7;20(3):391-6
pubmed: 22404998
Methods Cell Biol. 2023;177:359-387
pubmed: 37451774
Nat Protoc. 2016 Sep;11(9):1757-74
pubmed: 27560178
Bioinformatics. 2016 Nov 15;32(22):3471-3479
pubmed: 27412095
Elife. 2020 Feb 11;9:
pubmed: 32041682
Nucleic Acids Res. 2015 Jan;43(Database issue):D921-7
pubmed: 25313160
J Appl Crystallogr. 2015 Jan 30;48(Pt 1):301-305
pubmed: 26089752
PLoS Biol. 2019 Jun 19;17(6):e3000340
pubmed: 31216269
Front Neuroinform. 2014 Feb 20;8:13
pubmed: 24600387
Nat Methods. 2023 Apr;20(4):475-476
pubmed: 36765247
Nature. 2019 Oct;574(7777):187-192
pubmed: 31597973
Nature. 2021 Nov;599(7883):141-146
pubmed: 34616042
Nat Methods. 2022 May;19(5):515-516
pubmed: 35545714
Nat Methods. 2019 Sep;16(9):870-874
pubmed: 31384047
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Kidney Int. 2021 Mar;99(3):498-510
pubmed: 33637194
Cell Syst. 2022 Nov 16;13(11):911-923.e9
pubmed: 36395727
Angew Chem Int Ed Engl. 2023 Feb 1;62(6):e202215200
pubmed: 36470851
Nat Methods. 2012 Feb 28;9(3):245-53
pubmed: 22373911
Nat Methods. 2021 Dec;18(12):1418-1422
pubmed: 34021280
Nat Methods. 2021 Dec;18(12):1496-1498
pubmed: 34845388
J Cell Biol. 2010 May 31;189(5):777-82
pubmed: 20513764
Nat Commun. 2020 May 18;11(1):2475
pubmed: 32424134
J Microsc. 2021 Oct;284(1):56-73
pubmed: 34214188
Cell. 2018 Oct 18;175(3):859-876.e33
pubmed: 30318151
Nucleic Acids Res. 2022 Jul 5;50(W1):W345-W351
pubmed: 35446428
HardwareX. 2023 Feb 06;13:e00400
pubmed: 36824447