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Toward scalable reuse of vEM data: OME-Zarr to the rescue.
Methods Cell Biol. 2023;177:359-387. doi: 10.1016/bs.mcb.2023.01.016. Epub 2023 Mar 9.
Methods Cell Biol. 2023.
PMID: 37451774
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, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldaş AK, Kyoda K, de la Villegeorges ALT, 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: rzepka n.
bioRxiv [Preprint]. 2023 May 7:2023.02.17.528834. doi: 10.1101/2023.02.17.528834.
bioRxiv. 2023.
PMID: 36865282
Free PMC article.
Updated.
Preprint.
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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: rzepka n.
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.
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Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images.
An J, Wendt L, Wiese G, Herold T, Rzepka N, Mueller S, Koch SP, Hoffmann CJ, Harms C, Boehm-Sturm P.
An J, et al. Among authors: rzepka n.
Sci Rep. 2023 Aug 16;13(1):13341. doi: 10.1038/s41598-023-39826-8.
Sci Rep. 2023.
PMID: 37587160
Free PMC article.
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webKnossos: efficient online 3D data annotation for connectomics.
Boergens KM, Berning M, Bocklisch T, Bräunlein D, Drawitsch F, Frohnhofen J, Herold T, Otto P, Rzepka N, Werkmeister T, Werner D, Wiese G, Wissler H, Helmstaedter M.
Boergens KM, et al. Among authors: rzepka n.
Nat Methods. 2017 Jul;14(7):691-694. doi: 10.1038/nmeth.4331. Epub 2017 Jun 12.
Nat Methods. 2017.
PMID: 28604722
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Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.
Bosch C, Ackels T, Pacureanu A, Zhang Y, Peddie CJ, Berning M, Rzepka N, Zdora MC, Whiteley I, Storm M, Bonnin A, Rau C, Margrie T, Collinson L, Schaefer AT.
Bosch C, et al. Among authors: rzepka n.
Nat Commun. 2022 May 25;13(1):2923. doi: 10.1038/s41467-022-30199-6.
Nat Commun. 2022.
PMID: 35614048
Free PMC article.
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