lumen-shape

Supplementary Software for the manuscript:

Physical basis for the determination of lumen shape in a simple epithelium

Claudia G. Vasquez, Vipul T. Vachharajani, Carlos O. Garzon Coral, and Alexander R. Dunn, Nature Communications (to appear, 2021)

Index of files

• lumen_vm.py - Defines simulation objects and methods for vertex-based model of lumen shape.

  • Example usage:

    from lumen_vm import *
    
    
    params = {
          'P_lumen':0.1,
          'k':2,
          'l_a':0.6,
          'l_b':1.5,
          'l_l':0,
          }
    grow_cyst(params,stretched=True)
    

• 2D_shape_analysis - functions and notebook for 2D lumen and cyst shape segmentation using gp135/PDX signal
• 3D_shape_analysis - functions and notebook for 3D lumen and cyst shape segmentation using Lifeact-RFP (F-actin) signal