Recent advances in fluorescence microscopy technology have enabled the development of a wide variety of image-based assays that are applicable to such areas as drug discovery, RNAi screens in neuroscience, yeast genetics, and cancer research. These assays are rich in phenotypic information such as cell morphology and protein localization and activity. However, despite the technological progress and promise of rich new sources of cellular data, significant difficulties remain in the interpretation of image data by researchers. Most notably, easy to use tools for producing rapid and comprehensive summaries of image data are lacking. A turnkey software package for the analysis of image data will be developed, tested, and deployed to the research community. The software will automatically classify experimental conditions by image phenotypes, and display specific examples of image phenotypes that distinguish experimental conditions. This classification will be able to group images either with or without prior knowledge of specific cell phenotypes. The software will be capable of running on a single desktop computer, requiring no specialized expertise for most biological applications. Thus, the goal of this proposal is to make the extraction of summarized information from large image data sets as routine as analyzing microarray data. The results of this work will provide a significant expansion of the capacity of fluorescence microscopy as a basic research tool, providing researchers with a new ability to inquire into such fundamental processes as the mechanisms of cellular signaling, and cellular responses to therapeutics such as sensitivity, resistance, and toxicity. Project narrative: In this proposal, a turnkey software tool for the automatic identification of important cellular phenotypes in images obtained by fluorescence microscopy will be developed, tested and delivered to the research community. This is important because general tools for producing rapid and compressive summaries of image data are lacking. The results of this work will provide a significant expansion of the capacity of fluorescence microscopy as a basic research tool, providing researchers with a new ability to inquire into such fundamental processes as the mechanisms of cellular signaling, and cellular responses to therapeutics such as sensitivity, resistance, and toxicity.
In this proposal, a turnkey software tool for the automatic identification of important cellular phenotypes in images obtained by fluorescence microscopy will be developed, tested and delivered to the research community. This is important because general tools for producing rapid and compressive summaries of image data are lacking. The results of this work will provide a significant expansion of the capacity of fluorescence microscopy as a basic research tool, providing researchers with a new ability to inquire into such fundamental processes as the mechanisms of cellular signaling, and cellular responses to therapeutics such as sensitivity, resistance, and toxicity.
| Steininger 3rd, Robert J; Rajaram, Satwik; Girard, Luc et al. (2015) On comparing heterogeneity across biomarkers. Cytometry A 87:558-67 |
| Pavie, Benjamin; Rajaram, Satwik; Ouyang, Austin et al. (2014) Rapid analysis and exploration of fluorescence microscopy images. J Vis Exp : |
| Rajaram, Satwik; Pavie, Benjamin; Wu, Lani F et al. (2012) PhenoRipper: software for rapidly profiling microscopy images. Nat Methods 9:635-7 |
| Rajaram, Satwik; Pavie, Benjamin; Hac, Nicholas E F et al. (2012) SimuCell: a flexible framework for creating synthetic microscopy images. Nat Methods 9:634-5 |
| Thorne, Curtis A; Lafleur, Bonnie; Lewis, Michelle et al. (2011) A biochemical screen for identification of small-molecule regulators of the Wnt pathway using Xenopus egg extracts. J Biomol Screen 16:995-1006 |
| Singh, Dinesh Kumar; Ku, Chin-Jen; Wichaidit, Chonlarat et al. (2010) Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Mol Syst Biol 6:369 |
| Altschuler, Steven J; Wu, Lani F (2010) Cellular heterogeneity: do differences make a difference? Cell 141:559-63 |
| Loo, Lit-Hsin; Lin, Hai-Jui; Steininger 3rd, Robert J et al. (2009) An approach for extensibly profiling the molecular states of cellular subpopulations. Nat Methods 6:759-65 |
