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Resources » Paper

Christensen, R.P. et al. (2019) International Worm Meeting "Creating a pan-nuclear atlas in the post-twitching Caenorhabditis elegans embryo."

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  • Comments on Christensen, R.P. et al. (2019) International Worm Meeting "Creating a pan-nuclear atlas in the post-twitching Caenorhabditis elegans embryo." (0)

  • Overview

    Status:
    Publication type:
    Meeting_abstract
    WormBase ID:
    WBPaper00057922

    Christensen, R.P., Bokinsky, A., Santella, A., Moyle, M., Wu, Y., Guo, M., Harvey, B., Duncan, L., Ardiel, E., Lauziere, A., Levin, M., Karaj, N., McCreedy, E., Mohler, W., Colon-Ramos, D., Bao, Z., & Shroff, H. (2019). Creating a pan-nuclear atlas in the post-twitching Caenorhabditis elegans embryo presented in International Worm Meeting. Unpublished information; cite only with author permission.

    The Caenorhabditis elegans embryo represents an excellent model system in which to study tissue formation. However, the onset of twitching and elongation makes data analysis during the second half of embryogenesis difficult. Previously, we developed software to enable computational untwisting of the C. elegans embryo, removing the effects of embryo movement and placing embryo images in a common reference frame for analysis. We have now improved our software suite to incorporate more user-friendly positional tracking and better segmentation, reducing clipping of images around the edges of the embryo. We also apply deep learning to segment nuclei in a semi-automated fashion. We apply our software to generate a map showing the position of 158 nuclei in the post-twitching worm embryo, as a partial step in the generation of a complete embryonic nuclear atlas. Tracked nuclei include 16 neurons and 81 body wall muscles. Our improved tools, combined with pre-twitching work from our collaborators on the WormGUIDES project, allow us to pursue the goal of developing a complete nuclear and neurite outgrowth atlas for the nematode embryo from the two cell stage until hatching.

    Authors: Christensen, R.P., Bokinsky, A., Santella, A., Moyle, M., Wu, Y., Guo, M., Harvey, B., Duncan, L., Ardiel, E., Lauziere, A., Levin, M., Karaj, N., McCreedy, E., Mohler, W., Colon-Ramos, D., Bao, Z., Shroff, H.

    Affiliations:
    - Center for Information Technology, NIH, Bethesda, MD
    - Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT
    - Developmental Biology Program, Sloan-Kettering Institute, New York, NY
    - National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD
    - Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT


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