OME-NGFF: a next-generation file format for expanding bioimaging data access strategies

Josh Moore; Christopher Allan; Sebastien Besson; Jean-Marie Burel; Erin Diel; David Gault; Kevin Kozlowski; Dominik Lindner; Melissa Linkert; Trevor Manz; William Moore; Constantin Pape; Christian Tischer; Jason R. Swedlow

doi:10.1038/s41592-021-01326-w

OME-NGFF: a next-generation file format for expanding bioimaging data access strategies

Josh Moore, Christopher Allan, Sebastien Besson, Jean-Marie Burel, Erin Diel, David Gault, Kevin Kozlowski, Dominik Lindner, Melissa Linkert, Trevor Manz, William Moore, Constantin Pape, Christian Tischer, Jason R. Swedlow (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

64 Citations (Scopus)

91 Downloads (Pure)

Abstract

The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

Original language	English
Pages (from-to)	1496-1498
Number of pages	3
Journal	Nature Methods
Volume	18
Early online date	29 Nov 2021
DOIs	https://doi.org/10.1038/s41592-021-01326-w
Publication status	Published - Dec 2021

Keywords

Computational platforms and environments
Data publication and archiving

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

Access to Document

10.1038/s41592-021-01326-wLicence: CC BY

Final Published VersionFinal published version, 2.05 MBLicence: CC BY

Cite this

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title = "OME-NGFF: a next-generation file format for expanding bioimaging data access strategies ",

abstract = "The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.",

keywords = "Computational platforms and environments, Data publication and archiving",

author = "Josh Moore and Christopher Allan and Sebastien Besson and Jean-Marie Burel and Erin Diel and David Gault and Kevin Kozlowski and Dominik Lindner and Melissa Linkert and Trevor Manz and William Moore and Constantin Pape and Christian Tischer and Swedlow, {Jason R.}",

note = "Work on the bioformats2raw and raw2ometiff converters was funded by awards from InnovateUK to Glencoe Software Ltd (PathLAKE, Ref: 104689 and iCAIRD Ref: 104690). Work on OME-NGFF by J.M., J-M.B., S.B., D.G., D.L. and W.M. was funded by grant number 2019-207272 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation, the Wellcome Trust (Ref: 212962/Z/18/Z) and BBSRC (Ref: BB/R015384/1). Work by C.T. has been made possible in part by grant number 2020- 225265 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. C.P. has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme under grant agreement No 824087. T.M. has received funding from the National Science Foundation Graduate Research Fellowship under Grant No. DGE1745303. ",

year = "2021",

month = dec,

doi = "10.1038/s41592-021-01326-w",

language = "English",

volume = "18",

pages = "1496--1498",

journal = "Nature Methods",

issn = "1548-7091",

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T2 - a next-generation file format for expanding bioimaging data access strategies

AU - Moore, Josh

AU - Allan, Christopher

AU - Besson, Sebastien

AU - Burel, Jean-Marie

AU - Diel, Erin

AU - Gault, David

AU - Kozlowski, Kevin

AU - Lindner, Dominik

AU - Linkert, Melissa

AU - Manz, Trevor

AU - Moore, William

AU - Pape, Constantin

AU - Tischer, Christian

AU - Swedlow, Jason R.

N1 - Work on the bioformats2raw and raw2ometiff converters was funded by awards from InnovateUK to Glencoe Software Ltd (PathLAKE, Ref: 104689 and iCAIRD Ref: 104690). Work on OME-NGFF by J.M., J-M.B., S.B., D.G., D.L. and W.M. was funded by grant number 2019-207272 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation, the Wellcome Trust (Ref: 212962/Z/18/Z) and BBSRC (Ref: BB/R015384/1). Work by C.T. has been made possible in part by grant number 2020- 225265 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. C.P. has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824087. T.M. has received funding from the National Science Foundation Graduate Research Fellowship under Grant No. DGE1745303.

PY - 2021/12

Y1 - 2021/12

N2 - The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.

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OME-NGFF: a next-generation file format for expanding bioimaging data access strategies

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

New Open File Formats for the Biological Imaging Community

Cite this

OME-NGFF: a next-generation file format for expanding bioimaging data access strategies

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Projects

The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

New Open File Formats for the Biological Imaging Community

Cite this