References

References#

[ASE+24]

John Arevalo, Ellen Su, Jessica D. Ewald, Robert van Dijk, Anne E. Carpenter, and Shantanu Singh. Evaluating batch correction methods for image-based cell profiling. Nature Communications, Aug 2024. URL: http://dx.doi.org/10.1038/s41467-024-50613-5, doi:10.1038/s41467-024-50613-5.

[BSH+16]

Mark-Anthony Bray, Shantanu Singh, Han Han, Chadwick T Davis, Blake Borgeson, Cathy Hartland, Maria Kost-Alimova, Sigrun M Gustafsdottir, Christopher C Gibson, and Anne E Carpenter. Cell painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nature Protocols, 11(9):1757–1774, Aug 2016. URL: http://dx.doi.org/10.1038/nprot.2016.105, doi:10.1038/nprot.2016.105.

[CWIO+10]

Peter D. Caie, Rebecca E. Walls, Alexandra Ingleston-Orme, Sandeep Daya, Tom Houslay, Rob Eagle, Mark E. Roberts, and Neil O. Carragher. High-content phenotypic profiling of drug response signatures across distinct cancer cells. Molecular Cancer Therapeutics, 9(6):1913–1926, June 2010. URL: http://dx.doi.org/10.1158/1535-7163.MCT-09-1148, doi:10.1158/1535-7163.mct-09-1148.

[CAA+23]

Srinivas Niranj Chandrasekaran, Jeanelle Ackerman, Eric Alix, D. Michael Ando, John Arevalo, Melissa Bennion, Nicolas Boisseau, Adriana Borowa, Justin D. Boyd, Laurent Brino, Patrick J. Byrne, Hugo Ceulemans, Carolyn Ch’ng, Beth A. Cimini, Djork-Arne Clevert, Nicole Deflaux, John G Doench, Thierry Dorval, Regis Doyonnas, Vincenza Dragone, Ola Engkvist, Patrick W. Faloon, Briana Fritchman, Florian Fuchs, Sakshi Garg, Tamara J. Gilbert, David Glazer, David Gnutt, Amy Goodale, Jeremy Grignard, Judith Guenther, Yu Han, Zahra Hanifehlou, Santosh Hariharan, Desiree Hernandez, Shane R Horman, Gisela Hormel, Michael Huntley, Ilknur Icke, Makiyo Iida, Christina B. Jacob, Steffen Jaensch, Jawahar Khetan, Maria Kost-Alimova, Tomasz Krawiec, Daniel Kuhn, Charles-Hugues Lardeau, Amanda Lembke, Francis Lin, Kevin D. Little, Kenneth R. Lofstrom, Sofia Lotfi, David J. Logan, Yi Luo, Franck Madoux, Paula A. Marin Zapata, Brittany A. Marion, Glynn Martin, Nicola Jane McCarthy, Lewis Mervin, Lisa Miller, Haseeb Mohamed, Tiziana Monteverde, Elizabeth Mouchet, Barbara Nicke, Arnaud Ogier, Anne-Laure Ong, Marc Osterland, Magdalena Otrocka, Pieter J. Peeters, James Pilling, Stefan Prechtl, Chen Qian, Krzysztof Rataj, David E Root, Sylvie K. Sakata, Simon Scrace, Hajime Shimizu, David Simon, Peter Sommer, Craig Spruiell, Iffat Sumia, Susanne E Swalley, Hiroki Terauchi, Amandine Thibaudeau, Amy Unruh, Jelle Van de Waeter, Michiel Van Dyck, Carlo van Staden, Michał Warchoł, Erin Weisbart, Amélie Weiss, Nicolas Wiest-Daessle, Guy Williams, Shan Yu, Bolek Zapiec, Marek Żyła, Shantanu Singh, and Anne E. Carpenter. Jump cell painting dataset: morphological impact of 136,000 chemical and genetic perturbations. bioRxiv, Mar 2023. URL: http://dx.doi.org/10.1101/2023.03.23.534023, doi:10.1101/2023.03.23.534023.

[Cha20]

Sourav Chatterjee. A new coefficient of correlation. Journal of the American Statistical Association, 116(536):2009–2022, May 2020. URL: http://dx.doi.org/10.1080/01621459.2020.1758115, doi:10.1080/01621459.2020.1758115.

[ETB+26]

Jessica D. Ewald, Katherine L. Titterton, Alex Bäuerle, Alex Beatson, Daniil A. Boiko, Ángel A. Cabrera, Jaime Cheah, Beth A. Cimini, Bram L. Gorissen, Joshua Harrill, Thouis R. Jones, Konrad J. Karczewski, Christine E. Crute, David Rouquie, Srijit Seal, Erin Weisbart, Brandon White, Anne E. Carpenter, and Shantanu Singh. Cell painting for cytotoxicity and mode-of-action analysis in primary human hepatocytes. Cell Systems, 17(5):101566, May 2026. URL: http://dx.doi.org/10.1016/j.cels.2026.101566, doi:10.1016/j.cels.2026.101566.

[KAS+25]

Alexandr A. Kalinin, John Arevalo, Erik Serrano, Loan Vulliard, Hillary Tsang, Michael Bornholdt, Alán F. Muñoz, Suganya Sivagurunathan, Bartek Rajwa, Anne E. Carpenter, Gregory P. Way, and Shantanu Singh. A versatile information retrieval framework for evaluating profile strength and similarity. Nature Communications, June 2025. URL: http://dx.doi.org/10.1038/s41467-025-60306-2, doi:10.1038/s41467-025-60306-2.

[KMF+19]

Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-ru Loh, and Soumya Raychaudhuri. Fast, sensitive and accurate integration of single-cell data with harmony. Nature Methods, 16(12):1289–1296, Nov 2019. URL: http://dx.doi.org/10.1038/s41592-019-0619-0, doi:10.1038/s41592-019-0619-0.

[LZH+23]

Zheng Li, Yue Zhao, Xiyang Hu, Nicola Botta, Cezar Ionescu, and George H. Chen. Ecod: unsupervised outlier detection using empirical cumulative distribution functions. IEEE Transactions on Knowledge and Data Engineering, 35(12):12181–12193, Dec 2023. URL: http://dx.doi.org/10.1109/TKDE.2022.3159580, doi:10.1109/tkde.2022.3159580.

[LH22]

Z Lin and F Han. On boosting the power of chatterjee’s rank correlation. Biometrika, 110(2):283–299, Aug 2022. URL: http://dx.doi.org/10.1093/biomet/asac048, doi:10.1093/biomet/asac048.

[LCtH+13]

Vebjorn Ljosa, Peter D. Caie, Rob ter Horst, Katherine L. Sokolnicki, Emma L. Jenkins, Sandeep Daya, Mark E. Roberts, Thouis R. Jones, Shantanu Singh, Auguste Genovesio, Paul A. Clemons, Neil O. Carragher, and Anne E. Carpenter. Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. SLAS Discovery, 18(10):1321–1329, Dec 2013. URL: http://dx.doi.org/10.1177/1087057113503553, doi:10.1177/1087057113503553.

[LSC12]

Vebjorn Ljosa, Katherine L Sokolnicki, and Anne E Carpenter. Annotated high-throughput microscopy image sets for validation. Nature Methods, 9(7):637–637, June 2012. URL: http://dx.doi.org/10.1038/nmeth.2083, doi:10.1038/nmeth.2083.

[RSW+17]

Mohammad Hossein Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S Boehm, and Anne E Carpenter. Systematic morphological profiling of human gene and allele function via cell painting. eLife, Mar 2017. URL: http://dx.doi.org/10.7554/eLife.24060, doi:10.7554/elife.24060.

[SDS+25]

Srijit Seal, William Dee, Adit Shah, Andrew Zhang, Katherine Titterton, Ángel Alexander Cabrera, Daniil Boiko, Alex Beatson, Jordi Carreras Puigvert, Shantanu Singh, Ola Spjuth, Andreas Bender, and Anne E. Carpenter. Small molecule bioactivity benchmarks are often well-predicted by counting cells. bioRxiv, Apr 2025. URL: http://dx.doi.org/10.1101/2025.04.27.650853, doi:10.1101/2025.04.27.650853.

[SCB+25]

Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen J. Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, and Gregory P. Way. Reproducible image-based profiling with pycytominer. Nature Methods, 22(4):677–680, Mar 2025. URL: http://dx.doi.org/10.1038/s41592-025-02611-8, doi:10.1038/s41592-025-02611-8.

[VBH+23]

Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, 41(5):604–606, Apr 2023. URL: http://dx.doi.org/10.1038/s41587-023-01733-8, doi:10.1038/s41587-023-01733-8.

[WKA+24]

Erin Weisbart, Ankur Kumar, John Arevalo, Anne E. Carpenter, Beth A. Cimini, and Shantanu Singh. Cell painting gallery: an open resource for image-based profiling. Nature Methods, 21(10):1775–1777, Sept 2024. URL: http://dx.doi.org/10.1038/s41592-024-02399-z, doi:10.1038/s41592-024-02399-z.