2026-08-13 –, Room 4
Caenorhabditis elegans, a small roundworm, is widely used as a model for studying how cells and tissues develop and function. Using a form of light‑sheet imaging that records the embryo from two views (dual‑view selective plane illumination microscopy, diSPIM), we capture three‑dimensional movies of late embryogenesis. From these data, we build a smooth, time‑resolved anatomical model of the embryo’s surface and interior. We first mark a set of easily identifiable “seam” cells along the body wall and fit a flexible mesh to the organism’s surface. To ensure continuity and accuracy, we represent shapes and motions with smooth curves and periodic functions (natural cubic B‑splines and Fourier series), which provide robust interpolation across space and time. We also developed Julia‑based software that “untwists” each worm by transforming the 3D mesh into a cylindrical coordinate system centered on the embryo’s anterior–posterior axis. Individual models are then averaged over time and registered to a shared coordinate frame to create a common reference. Positions of tracked, fluorescently labeled cells can be mapped into this reference, yielding a four‑dimensional (3D + time) cellular atlas of C. elegans embryogenesis. When combined with single‑cell transcriptomics, the atlas can support spatially and temporally resolved maps of gene expression during development. Overall, these tools provide a flexible and accurate modeling framework with fast runtimes that enable rapid analysis and feedback.
https://github.com/JaneliaSciComp/ShroffCelegansModels.jl (currently public)
https://github.com/JaneliaSciComp/Transcriptome4D (currently private)
Authors: Mark Kittisopikul*, Ben Arthur, Ryan Christensen, Diyi Chen, Matthew Chaw, Stephen Xu, Alyssa Stark, John Walsh, Brie Yarbrough, Hari Shroff
- Presenting
Caenorhabditis elegans, a small roundworm, is widely used as a model for studying how cells and tissues develop and function. Using a form of light‑sheet imaging that records the embryo from two views (dual‑view selective plane illumination microscopy, diSPIM), we capture three‑dimensional movies of late embryogenesis. From these data, we build a smooth, time‑resolved anatomical model of the embryo’s surface and interior. We first mark a set of easily identifiable “seam” cells along the body wall and fit a flexible mesh to the organism’s surface. To ensure continuity and accuracy, we represent shapes and motions with smooth curves and periodic functions (natural cubic B‑splines and Fourier series), which provide robust interpolation across space and time. We also developed Julia‑based software that “untwists” each worm by transforming the 3D mesh into a cylindrical coordinate system centered on the embryo’s anterior–posterior axis. Individual models are then averaged over time and registered to a shared coordinate frame to create a common reference. Positions of tracked, fluorescently labeled cells can be mapped into this reference, yielding a four‑dimensional (3D + time) cellular atlas of C. elegans embryogenesis. When combined with single‑cell transcriptomics, the atlas can support spatially and temporally resolved maps of gene expression during development. Overall, these tools provide a flexible and accurate modeling framework with fast runtimes that enable rapid analysis and feedback.
https://github.com/JaneliaSciComp/ShroffCelegansModels.jl (currently public)
https://github.com/JaneliaSciComp/Transcriptome4D (currently private)
Software Engineer, Scientific Computing Software at the Howard Hughes Medical Institute Janelia Research Campus