Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Histochemistry and C...arrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Europe PubMed Central
Other literature type . 2023
Data sources: PubMed Central
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
Research Collection
Article . 2023
License: CC BY
versions View all 8 versions
addClaim

This Research product is the result of merged Research products in OpenAIRE.

You have already added 0 works in your ORCID record related to the merged Research product.

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Authors: Josh Moore; Daniela Basurto-Lozada; Sébastien Besson; John Bogovic; Jordão Bragantini; Eva M. Brown; Jean-Marie Burel; +62 Authors

OME-Zarr: a cloud-optimized bioimaging file format with international community support

Abstract

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.

National Human Genome Research Institute http://dx.doi.org/10.13039/100000051

Japan Science and Technology Agency http://dx.doi.org/10.13039/501100002241

National Bioscience Database Center http://dx.doi.org/10.13039/501100004696

European Molecular Biology Laboratory http://dx.doi.org/10.13039/100013060

Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659

Science for Life Laboratory http://dx.doi.org/10.13039/501100009252

National Institutes of Health http://dx.doi.org/10.13039/100000002

Chan Zuckerberg Initiative http://dx.doi.org/10.13039/100014989

UK Research and Innovation http://dx.doi.org/10.13039/100014013

Wellcome Trust http://dx.doi.org/10.13039/100010269

VINNOVA http://dx.doi.org/10.13039/501100001858

EOSC-Life http://dx.doi.org/10.13039/100020348

Wellcome http://dx.doi.org/10.13039/100004440

National Institutes of Health,United States

NSF Graduate Research Fellowship

Countries
Germany, Switzerland
Related Organizations
Keywords

Data, Microscopy, Histology, Community, Cell Biology, Bioimaging, Article, Medical Laboratory Technology, FAIR; Community; Bioimaging; Data; Cloud; Format, Humans, Format, Community Support, Cloud, Molecular Biology, Software, FAIR

19 references, page 1 of 2

Allan C, Burel J-M, Moore J, et al (2012) OMERO: flexible, model-driven data management for experimental biology. Nat Methods 9:245-253. https://doi.org/10.1038/nmeth.1896 [OpenAIRE]

Alted F (2010) Why Modern CPUs Are Starving and What Can Be Done about It. Comput Sci Eng 12:68-71. https://doi.org/10.1109/MCSE.2010.51 [OpenAIRE]

Bahry E, Breimann L, Zouinkhi M, et al (2022) RS-FISH: precise, interactive, fast, and scalable FISH spot detection. Nat Methods 19:1563-1567. https://doi.org/10.1038/s41592-022-01669-y [OpenAIRE]

Besson S, Leigh R, Linkert M, et al (2019) Bringing Open Data to Whole Slide Imaging. In: Digital Pathology. Springer International Publishing, pp 3-10

Boergens KM, Berning M, Bocklisch T, et al (2017) webKnossos: efficient online 3D data annotation for connectomics. Nat Methods 14:691-694. https://doi.org/10.1038/nmeth.4331 [OpenAIRE]

Bourget M-H, Kamentsky L, Ghosh SS, et al (2022) Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data. Front Neurosci 16:871228. https://doi.org/10.3389/fnins.2022.871228

Bray M-A, Singh S, Han H, et al (2016) Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc 11:1757-1774. https://doi.org/10.1038/nprot.2016.105 [OpenAIRE]

Casas Moreno X, Silva MM, Roos J, et al (2023) An open-source microscopy framework for simultaneous control of image acquisition, reconstruction, and analysis. HardwareX 13:e00400. https://doi.org/10.1016/j.ohx.2023.e00400

Halchenko Y, Meyer K, Poldrack B, et al (2021) DataLad: distributed system for joint management of code, data, and their relationship. J Open Source Softw 6:3262. https://doi.org/10.21105/joss.03262

Heinrich L, Bennett D, Ackerman D, et al (2021) Whole-cell organelle segmentation in volume electron microscopy. Nature 599:141-146. https://doi.org/10.1038/s41586-021-03977-3

  • BIP!
    Impact byBIP!
    citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    18
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
  • citations
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    18
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
    Powered byBIP!BIP!
Powered by OpenAIRE graph
Found an issue? Give us feedback
citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
18
Top 10%
Average
Top 10%
Green
hybrid