CellCognition : time-resolved phenotype annotation in high-throughput live cell imaging
Schmitz, Michael H. A.
Olma, Michael H.
Gerlich, Daniel W.
MetadataShow full item record
KeywordLive cell imaging; RNAi screening; GFP; Machine Learning; Image analysis; Hidden Markov model; Cdc20; Mitotic exit
Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here, we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. The incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions, and confusion between different functional states with similar morphology. We demonstrate generic applicability in a set of different assays and perturbation conditions, including a candidate-based RNAi screen for mitotic exit regulators in human cells. CellCognition is published as open source software, enabling live imaging-based screening with assays that directly score cellular dynamics.
Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Methods 7 (2010): 747-754, doi:10.1038/nmeth.1486.
Showing items related by title, author, creator and subject.
Live-cell imaging RNAi screen identifies PP2A–B55α and importin-β1 as key mitotic exit regulators in human cells Schmitz, Michael H. A.; Held, Michael; Janssens, Veerle; Hutchins, James R. A.; Hudecz, Otto; Ivanova, Elitsa; Goris, Jozef; Trinkle-Mulcahy, Laura; Lamond, Angus I.; Poser, Ina; Hyman, Anthony A.; Mechtler, Karl; Peters, Jan-Michael; Gerlich, Daniel W. (2010-07)When vertebrate cells exit mitosis, they reorganize various cellular structures to build functional interphase cells1. This depends on Cdk1 inactivation and subsequent dephosphorylation of its substrates2-4. Members of ...
Quantity, composition, and source of sediment collected in sediment traps along the fringing coral reef off Molokai, Hawaii Bothner, Michael H.; Reynolds, Richard L.; Casso, Michael A.; Storlazzi, Curt D.; Field, Michael E. (Elsevier B.V., 2006-03-20)Sediment traps were used to evaluate the frequency, cause, and relative intensity of sediment mobility/resuspension along the fringing coral reef off southern Molokai (February 2000–May 2002). Two storms with high rainfall, ...
Murawski, Steven A.; Steele, John H.; Taylor, Phillip; Fogarty, Michael J.; Sissenwine, Michael P.; Ford, Michael; Suchman, Cynthia (Oxford University Press, 2009-08-30)Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, ...