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

Josh Moore; Daniela Basurto-Lozada; Sébastien Besson; John Bogovic; Jordão Bragantini; Eva M Brown; Jean-Marie Burel; Xavier Casas Moreno; Gustavo de Medeiros; Erin E Diel; David Gault; Satrajit S Ghosh; Ilan Gold; Yaroslav O Halchenko; Matthew Hartley; Dave Horsfall; Mark S Keller; Mark Kittisopikul; Gabor Kovacs; Aybüke Küpcü Yoldaş; Koji Kyoda; Albane le Tournoulx de la Villegeorges; Tong Li; Prisca Liberali; Dominik Lindner; Melissa Linkert; Joel Lüthi; Jeremy Maitin-Shepard; Trevor Manz; Luca Marconato; Matthew McCormick; Merlin Lange; Khaled Mohamed; William Moore; Nils Norlin; Wei Ouyang; Bugra Özdemir; Giovanni Palla; Constantin Pape; Lucas Pelkmans; Tobias Pietzsch; Stephan Preibisch; Martin Prete; Norman Rzepka; Sameeul Samee; Nicholas Schaub; Hythem Sidky; Ahmet Can Solak; David R Stirling; Jonathan Striebel

doi:10.1007/s00418-023-02209-1

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

Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John Bogovic, Jordão Bragantini, Eva M Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, Dave Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü YoldaşKoji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Bugra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas Schaub, Hythem Sidky, Ahmet Can Solak, David R Stirling, Jonathan Striebel

Forskningsoutput: Tidskriftsbidrag › Artikel i vetenskaplig tidskrift › Peer review

Sammanfattning

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.

Originalspråk	engelska
Sidor (från-till)	223-251
Tidskrift	Histochemistry and Cell Biology
Volym	160
Nummer	3
Tidigt onlinedatum	2023 juli 10
DOI	https://doi.org/10.1007/s00418-023-02209-1
Status	Published - 2023

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Moore, J., Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, J.-M., Casas Moreno, X., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G., ... Striebel, J. (2023). OME-Zarr: A cloud-optimized bioimaging file format with international community support. Histochemistry and Cell Biology, 160(3), 223-251. https://doi.org/10.1007/s00418-023-02209-1

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title = "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 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.",

author = "Josh Moore and Daniela Basurto-Lozada and S{\'e}bastien Besson and John Bogovic and Jord{\~a}o Bragantini and Brown, {Eva M} and Jean-Marie Burel and {Casas Moreno}, Xavier and {de Medeiros}, Gustavo and Diel, {Erin E} and David Gault and Ghosh, {Satrajit S} and Ilan Gold and Halchenko, {Yaroslav O} and Matthew Hartley and Dave Horsfall and Keller, {Mark S} and Mark Kittisopikul and Gabor Kovacs and {K{\"u}pc{\"u} Yolda{\c s}}, Ayb{\"u}ke and Koji Kyoda and {le Tournoulx de la Villegeorges}, Albane and Tong Li and Prisca Liberali and Dominik Lindner and Melissa Linkert and Joel L{\"u}thi and Jeremy Maitin-Shepard and Trevor Manz and Luca Marconato and Matthew McCormick and Merlin Lange and Khaled Mohamed and William Moore and Nils Norlin and Wei Ouyang and Bugra {\"O}zdemir and Giovanni Palla and Constantin Pape and Lucas Pelkmans and Tobias Pietzsch and Stephan Preibisch and Martin Prete and Norman Rzepka and Sameeul Samee and Nicholas Schaub and Hythem Sidky and Solak, {Ahmet Can} and Stirling, {David R} and Jonathan Striebel",

note = "{\textcopyright} 2023. The Author(s).",

year = "2023",

doi = "10.1007/s00418-023-02209-1",

language = "English",

volume = "160",

pages = "223--251",

journal = "Histochemistry and Cell Biology",

issn = "1432-119X",

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}

Moore, J, Basurto-Lozada, D, Besson, S, Bogovic, J, Bragantini, J, Brown, EM, Burel, J-M, Casas Moreno, X, de Medeiros, G, Diel, EE, Gault, D, Ghosh, SS, Gold, I, Halchenko, YO, Hartley, M, Horsfall, D, Keller, MS, Kittisopikul, M, Kovacs, G, Küpcü Yoldaş, A, Kyoda, K, le Tournoulx de la Villegeorges, A, Li, T, Liberali, P, Lindner, D, Linkert, M, Lüthi, J, Maitin-Shepard, J, Manz, T, Marconato, L, McCormick, M, Lange, M, Mohamed, K, Moore, W, Norlin, N, Ouyang, W, Özdemir, B, Palla, G, Pape, C, Pelkmans, L, Pietzsch, T, Preibisch, S, Prete, M, Rzepka, N, Samee, S, Schaub, N, Sidky, H, Solak, AC, Stirling, DR & Striebel, J 2023, 'OME-Zarr: A cloud-optimized bioimaging file format with international community support', Histochemistry and Cell Biology, vol. 160, nr. 3, s. 223-251. https://doi.org/10.1007/s00418-023-02209-1

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T2 - A cloud-optimized bioimaging file format with international community support

AU - Moore, Josh

AU - Basurto-Lozada, Daniela

AU - Besson, Sébastien

AU - Bogovic, John

AU - Bragantini, Jordão

AU - Brown, Eva M

AU - Burel, Jean-Marie

AU - Casas Moreno, Xavier

AU - de Medeiros, Gustavo

AU - Diel, Erin E

AU - Gault, David

AU - Ghosh, Satrajit S

AU - Gold, Ilan

AU - Halchenko, Yaroslav O

AU - Hartley, Matthew

AU - Horsfall, Dave

AU - Keller, Mark S

AU - Kittisopikul, Mark

AU - Kovacs, Gabor

AU - Küpcü Yoldaş, Aybüke

AU - Kyoda, Koji

AU - le Tournoulx de la Villegeorges, Albane

AU - Li, Tong

AU - Liberali, Prisca

AU - Lindner, Dominik

AU - Linkert, Melissa

AU - Lüthi, Joel

AU - Maitin-Shepard, Jeremy

AU - Manz, Trevor

AU - Marconato, Luca

AU - McCormick, Matthew

AU - Lange, Merlin

AU - Mohamed, Khaled

AU - Moore, William

AU - Norlin, Nils

AU - Ouyang, Wei

AU - Özdemir, Bugra

AU - Palla, Giovanni

AU - Pape, Constantin

AU - Pelkmans, Lucas

AU - Pietzsch, Tobias

AU - Preibisch, Stephan

AU - Prete, Martin

AU - Rzepka, Norman

AU - Samee, Sameeul

AU - Schaub, Nicholas

AU - Sidky, Hythem

AU - Solak, Ahmet Can

AU - Stirling, David R

AU - Striebel, Jonathan

PY - 2023

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AB - 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.

U2 - 10.1007/s00418-023-02209-1

DO - 10.1007/s00418-023-02209-1

M3 - Article

C2 - 37428210

SN - 1432-119X

VL - 160

SP - 223

EP - 251

JO - Histochemistry and Cell Biology

JF - Histochemistry and Cell Biology

IS - 3

ER -

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

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