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UID:pretalx-juliacon-2026-BK783X@pretalx.com
DTSTART;TZID=CET:20260813T111500
DTEND;TZID=CET:20260813T113000
DESCRIPTION:Caenorhabditis elegans\, a small roundworm\, is widely used as 
 a model for studying how cells and tissues develop and function. Using a f
 orm of light‑sheet imaging that records the embryo from two views (dual
 ‑view selective plane illumination microscopy\, diSPIM)\, we capture thr
 ee‑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 alon
 g the body wall and fit a flexible mesh to the organism’s surface. To en
 sure continuity and accuracy\, we represent shapes and motions with smooth
  curves and periodic functions (natural cubic B‑splines and Fourier seri
 es)\, which provide robust interpolation across space and time. We also de
 veloped Julia‑based software that “untwists” each worm by transformi
 ng the 3D mesh into a cylindrical coordinate system centered on the embryo
 ’s anterior–posterior axis. Individual models are then averaged over t
 ime and registered to a shared coordinate frame to create a common referen
 ce. 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 transcriptom
 ics\, the atlas can support spatially and temporally resolved maps of gene
  expression during development. Overall\, these tools provide a flexible a
 nd accurate modeling framework with fast runtimes that enable rapid analys
 is and feedback. \n\nhttps://github.com/JaneliaSciComp/ShroffCelegansModel
 s.jl (currently public) \nhttps://github.com/JaneliaSciComp/Transcriptome4
 D (currently private)
DTSTAMP:20260502T102649Z
LOCATION:Room 4
SUMMARY:Modeling and Visualizing Late Embryogenesis in the Caenorhabditis e
 legans - Mark Kittisopikul\, Ph.D.
URL:https://pretalx.com/juliacon-2026/talk/BK783X/
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