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

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.

附带的文件夹包含用于从注释后的胚胎肾外植体生成表面高度图的Rhino Grasshopper模型文件（.gh）、Matlab分析代码（.m）以及关联数据文件（.csv）。
论文标题：《发育中的肾脏主动协调几何排布冲突以避免发育缺陷》
摘要：多项器官的生理功能依赖于带有特定结构以实现分泌、气体交换或过滤功能的分支上皮小管网络。目前学界对发育过程中，为实现足够功能所需构建的小管数量与器官尺寸带来的几何约束之间的冲突知之甚少。本研究表明，小鼠胚胎肾脏上皮细胞需协调两类物理排布冲突：通过分支增殖增加小管尖端数量，与器官表面积有限的限制。通过对完整肾脏外植体进行成像，并结合小管簇的计算建模与软物质建模，我们确定了六种可能的几何排布阶段，其中包含两种缺陷型排布。外植体实验证实，对小管簇施加径向张力，是使其切换至垂直排布模式的充分必要条件，该模式既可提升表面尖端密度，又能避免发育缺陷。本研究结果揭示了机体响应物理限制的发育应变机制，并为先天性肾脏缺陷的分类构建了理论框架。