Supplementary Material - The developing kidney actively negotiates geometric packing conflicts to avoid defects

Published: 1 December 2022| Version 1 | DOI: 10.17632/w6zfwfn8hj.1
, John Viola,


The enclosed folder contains a Rhino Grasshopper model file (.gh) and Matlab analysis code (.m) and associated data file (.csv) for creating surface height maps from annotated embryonic kidney explants. Paper title: The developing kidney actively negotiates geometric packing conflicts to avoid defects Abstract: The physiological functions of several organs rely on branched epithelial tubule networks bearing specialized structures for secretion, gas exchange, or filtration. Little is known about conflicts in development between building enough tubules for adequate function and geometric constraints imposed by organ size. We show that the mouse embryonic kidney epithelium negotiates a physical packing conflict between increasing tubule tip numbers through branching and limited organ surface area. By imaging whole kidney explants, combined with computational and soft material modeling of tubule families, we identify six possible geometric packing phases, including two defective ones. Experiments in explants show that a radially-oriented tension on tubule families is necessary and sufficient for them to switch to a vertical packing arrangement that increases surface tip density while avoiding defects. These results reveal developmental contingencies in response to physical limitations and create a framework for classifying congenital kidney defects.



University of Pennsylvania


Biomedical Engineering, Developmental Biology, Biological Modeling


National Institute of General Medical Sciences


National Science Foundation

CAREER 2047271