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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: ghosh ss. 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.
A very simple, re-executable neuroimaging publication.
Ghosh SS, Poline JB, Keator DB, Halchenko YO, Thomas AG, Kessler DA, Kennedy DN. Ghosh SS, et al. F1000Res. 2017 Feb 10;6:124. doi: 10.12688/f1000research.10783.2. eCollection 2017. F1000Res. 2017. PMID: 28781753 Free PMC article.
TemplateFlow: FAIR-sharing of multi-scale, multi-species brain models.
Ciric R, Thompson WH, Lorenz R, Goncalves M, MacNicol EE, Markiewicz CJ, Halchenko YO, Ghosh SS, Gorgolewski KJ, Poldrack RA, Esteban O. Ciric R, et al. Among authors: ghosh ss. Nat Methods. 2022 Dec;19(12):1568-1571. doi: 10.1038/s41592-022-01681-2. Epub 2022 Dec 1. Nat Methods. 2022. PMID: 36456786 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, 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: ghosh ss. bioRxiv [Preprint]. 2023 May 7:2023.02.17.528834. doi: 10.1101/2023.02.17.528834. bioRxiv. 2023. Update in: Histochem Cell Biol. 2023 Sep;160(3):223-251. doi: 10.1007/s00418-023-02209-1 PMID: 36865282 Free PMC article. Updated. Preprint.
Data sharing in neuroimaging research.
Poline JB, Breeze JL, Ghosh S, Gorgolewski K, Halchenko YO, Hanke M, Haselgrove C, Helmer KG, Keator DB, Marcus DS, Poldrack RA, Schwartz Y, Ashburner J, Kennedy DN. Poline JB, et al. Front Neuroinform. 2012 Apr 5;6:9. doi: 10.3389/fninf.2012.00009. eCollection 2012. Front Neuroinform. 2012. PMID: 22493576 Free PMC article.
Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.
Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M. Kennedy DN, et al. Front Neuroinform. 2019 Feb 7;13:1. doi: 10.3389/fninf.2019.00001. eCollection 2019. Front Neuroinform. 2019. PMID: 30792636 Free PMC article.
The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments.
Gorgolewski KJ, Auer T, Calhoun VD, Craddock RC, Das S, Duff EP, Flandin G, Ghosh SS, Glatard T, Halchenko YO, Handwerker DA, Hanke M, Keator D, Li X, Michael Z, Maumet C, Nichols BN, Nichols TE, Pellman J, Poline JB, Rokem A, Schaefer G, Sochat V, Triplett W, Turner JA, Varoquaux G, Poldrack RA. Gorgolewski KJ, et al. Among authors: ghosh ss. Sci Data. 2016 Jun 21;3:160044. doi: 10.1038/sdata.2016.44. Sci Data. 2016. PMID: 27326542 Free PMC article.
Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.
Gau R, Noble S, Heuer K, Bottenhorn KL, Bilgin IP, Yang YF, Huntenburg JM, Bayer JMM, Bethlehem RAI, Rhoads SA, Vogelbacher C, Borghesani V, Levitis E, Wang HT, Van Den Bossche S, Kobeleva X, Legarreta JH, Guay S, Atay SM, Varoquaux GP, Huijser DC, Sandström MS, Herholz P, Nastase SA, Badhwar A, Dumas G, Schwab S, Moia S, Dayan M, Bassil Y, Brooks PP, Mancini M, Shine JM, O'Connor D, Xie X, Poggiali D, Friedrich P, Heinsfeld AS, Riedl L, Toro R, Caballero-Gaudes C, Eklund A, Garner KG, Nolan CR, Demeter DV, Barrios FA, Merchant JS, McDevitt EA, Oostenveld R, Craddock RC, Rokem A, Doyle A, Ghosh SS, Nikolaidis A, Stanley OW, Uruñuela E; Brainhack Community. Gau R, et al. Among authors: ghosh ss. Neuron. 2021 Jun 2;109(11):1769-1775. doi: 10.1016/j.neuron.2021.04.001. Epub 2021 Apr 30. Neuron. 2021. PMID: 33932337 Free PMC article.
Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data.
Bourget MH, Kamentsky L, Ghosh SS, Mazzamuto G, Lazari A, Markiewicz CJ, Oostenveld R, Niso G, Halchenko YO, Lipp I, Takerkart S, Toussaint PJ, Khan AR, Nilsonne G, Castelli FM; BIDS Maintainers; Cohen-Adad J. Bourget MH, et al. Among authors: ghosh ss. Front Neurosci. 2022 Apr 19;16:871228. doi: 10.3389/fnins.2022.871228. eCollection 2022. Front Neurosci. 2022. PMID: 35516811 Free PMC article.
358 results