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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: stirling dr. 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.
CellProfiler 4: improvements in speed, utility and usability.
Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A. Stirling DR, et al. BMC Bioinformatics. 2021 Sep 10;22(1):433. doi: 10.1186/s12859-021-04344-9. BMC Bioinformatics. 2021. PMID: 34507520 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: stirling dr. 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.
A postdoctoral training program in bioimage analysis.
Cimini BA, Tromans-Coia C, Stirling DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. Cimini BA, et al. Among authors: stirling dr. Mol Biol Cell. 2024 Sep 1;35(9):pe2. doi: 10.1091/mbc.E24-05-0214. Mol Biol Cell. 2024. PMID: 39105698 Free PMC article. Review.
A Postdoctoral Training Program in Bioimage Analysis.
Cimini BA, Tromans-Coia C, Stirling D, Sivagurunathan S, Senft R, Ryder P, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. Cimini BA, et al. bioRxiv [Preprint]. 2024 May 15:2024.05.13.593910. doi: 10.1101/2024.05.13.593910. bioRxiv. 2024. Update in: Mol Biol Cell. 2024 Sep 1;35(9):pe2. doi: 10.1091/mbc.E24-05-0214 PMID: 38798545 Free PMC article. Updated. Preprint.
Piximi - An Images to Discovery web tool for bioimages and beyond.
Moser LM, Gogoberidze N, Papaleo A, Lucas A, Dao D, Friedrich CA, Paavolainen L, Molnar C, Stirling DR, Hung J, Wang R, Tromans-Coia C, Li B, Evans EL 3rd, Eliceiri KW, Horvath P, Carpenter AE, Cimini BA. Moser LM, et al. Among authors: stirling dr. bioRxiv [Preprint]. 2024 Oct 10:2024.06.03.597232. doi: 10.1101/2024.06.03.597232. bioRxiv. 2024. PMID: 38895349 Free PMC article. Preprint.
CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools.
Weisbart E, Tromans-Coia C, Diaz-Rohrer B, Stirling DR, Garcia-Fossa F, Senft RA, Hiner MC, de Jesus MB, Eliceiri KW, Cimini BA. Weisbart E, et al. Among authors: stirling dr. ArXiv [Preprint]. 2023 Aug 15:arXiv:2306.01915v2. ArXiv. 2023. Update in: J Microsc. 2024 Dec;296(3):227-234. doi: 10.1111/jmi.13223 PMID: 37645041 Free PMC article. Updated. Preprint.
20 results