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Providing open imaging data at scale: An EMBL-EBI perspective.
Hartley M, Iudin A, Padwardhan A, Sarkans U, Yoldaş AK, Kleywegt GJ. Hartley M, et al. Histochem Cell Biol. 2023 Sep;160(3):211-221. doi: 10.1007/s00418-023-02216-2. Epub 2023 Aug 3. Histochem Cell Biol. 2023. PMID: 37537341 Free PMC article.
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.
Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J. Thakur M, et al. Among authors: hartley m. Nucleic Acids Res. 2023 Jan 6;51(D1):D9-D17. doi: 10.1093/nar/gkac1098. Nucleic Acids Res. 2023. PMID: 36477213 Free PMC article.
Public archiving of volume EM data.
Iudin A, Hartley M, Kleywegt GJ, Patwardhan A. Iudin A, et al. Among authors: hartley m. Methods Cell Biol. 2023;177:389-399. doi: 10.1016/bs.mcb.2023.02.002. Epub 2023 Mar 27. Methods Cell Biol. 2023. PMID: 37451775
Ten recommendations for organising bioimaging data for archival.
Korir PK, Iudin A, Somasundharam S, Weyand S, Salih O, Hartley M, Sarkans U, Patwardhan A, Kleywegt GJ. Korir PK, et al. Among authors: hartley m. F1000Res. 2024 Feb 27;12:ELIXIR-1391. doi: 10.12688/f1000research.129720.2. eCollection 2023. F1000Res. 2024. PMID: 38486614 Free PMC article.
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.
Thakur M, Buniello A, Brooksbank C, Gurwitz KT, Hall M, Hartley M, Hulcoop DG, Leach AR, Marques D, Martin M, Mithani A, McDonagh EM, Mutasa-Gottgens E, Ochoa D, Perez-Riverol Y, Stephenson J, Varadi M, Velankar S, Vizcaino JA, Witham R, McEntyre J. Thakur M, et al. Among authors: hartley m. Nucleic Acids Res. 2024 Jan 5;52(D1):D10-D17. doi: 10.1093/nar/gkad1088. Nucleic Acids Res. 2024. PMID: 38015445 Free PMC article. Review.
Community-developed checklists for publishing images and image analyses.
Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Schmied C, et al. Among authors: hartley m. ArXiv [Preprint]. 2023 Sep 14:arXiv:2302.07005v2. ArXiv. 2023. PMID: 36824427 Free PMC article. Updated. Preprint.
DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible.
Hidalgo-Cenalmor I, Pylvänäinen JW, G Ferreira M, Russell CT, Saguy A, Arganda-Carreras I, Shechtman Y; AI4Life Horizon Europe Program Consortium; Jacquemet G, Henriques R, Gómez-de-Mariscal E. Hidalgo-Cenalmor I, et al. Nat Methods. 2024 May 17. doi: 10.1038/s41592-024-02295-6. Online ahead of print. Nat Methods. 2024. PMID: 38760611 No abstract available.
441 results