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OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.
Moore J, Allan C, Besson S, Burel JM, Diel E, Gault D, Kozlowski K, Lindner D, Linkert M, Manz T, Moore W, Pape C, Tischer C, Swedlow JR. Moore J, et al. Among authors: burel jm. Nat Methods. 2021 Dec;18(12):1496-1498. doi: 10.1038/s41592-021-01326-w. Epub 2021 Nov 29. Nat Methods. 2021. PMID: 34845388 Free PMC article.
Metadata matters: access to image data in the real world.
Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, Macdonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri KW, Swedlow JR. Linkert M, et al. Among authors: burel jm. J Cell Biol. 2010 May 31;189(5):777-82. doi: 10.1083/jcb.201004104. J Cell Biol. 2010. PMID: 20513764 Free PMC article.
OMERO: flexible, model-driven data management for experimental biology.
Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, Macdonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. Allan C, et al. Among authors: burel jm. Nat Methods. 2012 Feb 28;9(3):245-53. doi: 10.1038/nmeth.1896. Nat Methods. 2012. PMID: 22373911 Free PMC article.
Publishing and sharing multi-dimensional image data with OMERO.
Burel JM, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Li S, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Tarkowska A, Walczysko P, Allan C, Moore J, Swedlow JR. Burel JM, et al. Mamm Genome. 2015 Oct;26(9-10):441-7. doi: 10.1007/s00335-015-9587-6. Epub 2015 Jul 30. Mamm Genome. 2015. PMID: 26223880 Free PMC article.
Metadata management for high content screening in OMERO.
Li S, Besson S, Blackburn C, Carroll M, Ferguson RK, Flynn H, Gillen K, Leigh R, Lindner D, Linkert M, Moore WJ, Ramalingam B, Rozbicki E, Rustici G, Tarkowska A, Walczysko P, Williams E, Allan C, Burel JM, Moore J, Swedlow JR. Li S, et al. Among authors: burel jm. Methods. 2016 Mar 1;96:27-32. doi: 10.1016/j.ymeth.2015.10.006. Epub 2015 Oct 22. Methods. 2016. PMID: 26476368 Free PMC article.
Bringing Open Data to Whole Slide Imaging.
Besson S, Leigh R, Linkert M, Allan C, Burel JM, Carroll M, Gault D, Gozim R, Li S, Lindner D, Moore J, Moore W, Walczysko P, Wong F, Swedlow JR. Besson S, et al. Among authors: burel jm. Digit Pathol (2019). 2019 Apr;2019:3-10. doi: 10.1007/978-3-030-23937-4_1. Epub 2019 Jul 3. Digit Pathol (2019). 2019. PMID: 31579322 Free PMC article.
OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, 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, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. Moore J, et al. Among authors: burel jm. Histochem Cell Biol. 2023 Sep;160(3):223-251. doi: 10.1007/s00418-023-02209-1. Epub 2023 Jul 10. Histochem Cell Biol. 2023. PMID: 37428210 Free PMC article.
"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.
David R, Rybina A, Burel JM, Heriche JK, Audergon P, Boiten JW, Coppens F, Crockett S, Exter K, Fahrner S, Fratelli M, Goble C, Gormanns P, Grantner T, Grüning B, Gurwitz KT, Hancock JM, Harmse H, Holub P, Juty N, Karnbach G, Karoune E, Keppler A, Klemeier J, Lancelotti C, Legras JL, Lister AL, Longo DL, Ludwig R, Madon B, Massimi M, Matser V, Matteoni R, Mayrhofer MT, Ohmann C, Panagiotopoulou M, Parkinson H, Perseil I, Pfander C, Pieruschka R, Raess M, Rauber A, Richard AS, Romano P, Rosato A, Sánchez-Pla A, Sansone SA, Sarkans U, Serrano-Solano B, Tang J, Tanoli Z, Tedds J, Wagener H, Weise M, Westerhoff HV, Wittner R, Ewbank J, Blomberg N, Gribbon P. David R, et al. Among authors: burel jm. EMBO J. 2023 Dec 1;42(23):e115008. doi: 10.15252/embj.2023115008. Epub 2023 Nov 15. EMBO J. 2023. PMID: 37964598 Free PMC article.
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