WormSizer: high-throughput analysis of nematode size and shape.
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The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer.
Published Version (Please cite this version)
Moore, Brad T, James M Jordan and L Ryan Baugh (2013). WormSizer: high-throughput analysis of nematode size and shape. PLoS One, 8(2). p. e57142. 10.1371/journal.pone.0057142 Retrieved from https://hdl.handle.net/10161/10401.
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The Baugh Lab is interested in phenotypic plasticity and physiological adaptation to variable environmental conditions. We are using the roundworm C. elegans to understand how animals adapt to starvation using primarily genetic and genomic approaches. We are studying how development is governed by nutrient availability, how animals survive starvation, and the long-term consequences of starvation including adult disease and transgenerational epigenetic inheritance.
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