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An image analysis toolbox for high-throughput C. elegans assays

Abstract

We present a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems. This WormToolbox is available through the open-source CellProfiler project and enables objective scoring of whole-worm high-throughput image-based assays of C. elegans for the study of diverse biological pathways that are relevant to human disease.

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Figure 1: Workflow and performance of the WormToolbox.
Figure 2: Scoring fluorescence signal distribution with the WormToolbox.

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Acknowledgements

Funding for this work was provided by the US National Institutes of Health to C.W. (R01 GM095672), A.E.C. (R01 GM089652), F.M.A. (R01 AI072508, P01 AI083214 and R01 AI085581), E.J.O. (K99DK087928) and P.G. (U54 EB005149). The Broad Institute SPARC (Scientific Planning and Allocation of Resources Committee) program also funded this work. The authors thank S.C. Pak and G.A. Silverman (University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA) for the images of assay 1, J. Larkins-Ford and P. Lim for technical assistance and members of the Imaging Platform and the international C. elegans community for scientific guidance and helpful comments.

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Authors and Affiliations

Authors

Contributions

A.E.C. and E.J.O. conceived of the idea for the study. C.W., L.K., Z.H.L., P.G., V.L. and T.R.-R. designed and implemented the algorithms of the WormToolbox. A.L.C., E.J.O. and O.V. developed sample assays and collected image data. J.E.I., G.R. and F.M.A. designed and supervised screens. C.W. and K.L.S. developed analysis pipelines and evaluated results, with input from E.J.O. and A.L.C., C.W., L.K., K.L.S., E.J.O. and A.E.C. wrote the manuscript.

Corresponding author

Correspondence to Carolina Wählby.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–14, Supplementary Table 1, Supplementary Methods 1 and 2, Supplementary Note (PDF 4239 kb)

Supplementary Software 1

Cell Profiler source code with WormToolbox (ZIP 25740 kb)

Supplementary Software 2

WormToolbox example pipelines (ZIP 4933 kb)

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Wählby, C., Kamentsky, L., Liu, Z. et al. An image analysis toolbox for high-throughput C. elegans assays. Nat Methods 9, 714–716 (2012). https://doi.org/10.1038/nmeth.1984

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