Wu, Yicong, Shroff, Hari, Catena, Raul, Kovacevic, Ismar, Christensen, Ryan, Marquina-Solis, Javier, Santella, Anthony, Mohler, William A., Kumar, Abhishek, Bao, Zhirong, Moyle, Mark, Colon-Ramos, Daniel
[
International Worm Meeting,
2015]
WormGUIDES is a 4D interactive atlas of C. elegans embryogenesis. Its purpose is to support the exploration and analysis of embryogenesis at the molecular, cellular, tissue and organism levels. The current WormGUIDES release contains a minute-by-minute record of nuclear positions for all cells until twitching. Current efforts focus on adding records of 3D cell morphology to reconstruct neural morphogenesis and the dynamics of neurite outgrowth. Our strategy consists of acquiring 3D time-lapse images of embryogenesis using promoter-driven fluorescent markers to sparsely label subsets of neurons. Ubiquitous histone markers enable automated lineaging to identify cells and align datasets acquired from different embryos into a digital composite record.Data from our initial set of markers reveals dynamic processes that contribute to the architecture of the major neural organs such as the nerve ring, ventral nerve cord and the head nerve bundles. Much of this morphogenesis occurs before twitching. Surprisingly, some morphogenetic modules are formed in neural progenitors and maintained through two cell cycles. Perturbations suggest novel collective cell behaviors and unexpected roles for surrounding tissue in shaping the nervous system.Lineage-based cell identification has yielded a list of approximately 50 neurons that are currently being tracked and segmented. These cells account for about a quarter of embryonic neurons and include critical components of the major neural structures. To support the throughput needed for systematic reconstruction, we have developed computational pipelines for semi-automated segmentation and alignment of cell shapes from multiple embryos and markers. In addition, we have developed computational tools to untwist the elongating embryo and trace post-twitching events. We are making additional markers, and developing a desktop application extending the current mobile app. Ultimately, the goal is to produce a complete, dynamic record of the assembly of the C. elegans connectome.