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Optimizing the Cell Painting assay for image-based profiling.
Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan DJ, Concannon JB, Lardeau CH, Mouchet E, Singh S, Shafqat Abbasi H, Aspesi P Jr, Boyd JD, Gilbert T, Gnutt D, Hariharan S, Hernandez D, Hormel G, Juhani K, Melanson M, Mervin LH, Monteverde T, Pilling JE, Skepner A, Swalley SE, Vrcic A, Weisbart E, Williams G, Yu S, Zapiec B, Carpenter AE. Cimini BA, et al. Among authors: weisbart e. Nat Protoc. 2023 Jul;18(7):1981-2013. doi: 10.1038/s41596-023-00840-9. Epub 2023 Jun 21. Nat Protoc. 2023. PMID: 37344608 Review.
Morphology and gene expression profiling provide complementary information for mapping cell state.
Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, Haghighi M, Weisbart E, Singh S, Subramanian A, Carpenter AE. Way GP, et al. Among authors: weisbart e. Cell Syst. 2022 Nov 16;13(11):911-923.e9. doi: 10.1016/j.cels.2022.10.001. Epub 2022 Oct 28. Cell Syst. 2022. PMID: 36395727 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: weisbart e. 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.
The multimodality cell segmentation challenge: toward universal solutions.
Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B. Ma J, et al. Among authors: weisbart e. Nat Methods. 2024 Mar 26. doi: 10.1038/s41592-024-02233-6. Online ahead of print. Nat Methods. 2024. PMID: 38532015
High-dimensional phenotyping to define the genetic basis of cellular morphology.
Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, Carpenter AE, Singh S, Nehme R, Raychaudhuri S. Tegtmeyer M, et al. Among authors: weisbart e. Nat Commun. 2024 Jan 6;15(1):347. doi: 10.1038/s41467-023-44045-w. Nat Commun. 2024. PMID: 38184653 Free PMC article.
Reproducible image-based profiling with Pycytominer.
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, Kern R, Bornholdt M, Fleming S, Pei R, Arevalo J, Tsang H, Rubinetti V, Tromans-Coia C, Becker T, Weisbart E, Bunne C, Kalinin AA, Senft R, Taylor SJ, Jamali N, Adeboye A, Abbasi HS, Goodman A, Caicedo JC, Carpenter AE, Cimini BA, Singh S, Way GP. Serrano E, et al. Among authors: weisbart e. ArXiv [Preprint]. 2023 Nov 22:arXiv:2311.13417v1. ArXiv. 2023. PMID: 38045474 Free PMC article. Preprint.
18 results