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Methods Cell Biol. 2012;110:179-93. doi: 10.1016/B978-0-12-388403-9.00007-2.

CellOrganizer: Image-derived models of subcellular organization and protein distribution.

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  • 1Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.


This chapter describes approaches for learning models of subcellular organization from images. The primary utility of these models is expected to be from incorporation into complex simulations of cell behaviors. Most current cell simulations do not consider spatial organization of proteins at all, or treat each organelle type as a single, idealized compartment. The ability to build generative models for all proteins in a proteome and use them for spatially accurate simulations is expected to improve the accuracy of models of cell behaviors. A second use, of potentially equal importance, is expected to be in testing and comparing software for analyzing cell images. The complexity and sophistication of algorithms used in cell-image-based screens and assays (variously referred to as high-content screening, high-content analysis, or high-throughput microscopy) is continuously increasing, and generative models can be used to produce images for testing these algorithms in which the expected answer is known.

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