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Elife. 2015 Dec 3;4. pii: e10070. doi: 10.7554/eLife.10070.

Untwisting the Caenorhabditis elegans embryo.

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Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States.
Biomedical Imaging Research Services Section, Center for Information Technology, National Institutes of Health, Bethesda, United States.
Developmental Biology Program, Sloan-Kettering Institute, New York, United States.
Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Cell Biology, Yale University School of Medicine, New Haven, United States.
State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States.


The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software ( that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (Supplementary file 1) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.


C. elegans; C.elegans embryo untwisting; computational biology; developmental biology; embryonic morphogenesis; embryonic neurodevelopment; light sheet microscopy; stem cells; systems biology

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