Architectural changes at the cellular and organism level are integral and necessary to successful development and growth. During mammalian preimplantation development, cells reduce in size and the architecture of the embryo changes significantly. Such changes must be coordinated correctly to ensure continued development of the embryo and, ultimately, a successful pregnancy. However, the nature of such transformations is poorly defined during mammalian preimplantation development. In order to quantitatively describe changes in cell environment and organism architecture, we designed Internal Versus External Neighbourhood (IVEN). IVEN is a user-interactive, open-source pipeline that classifies cells into different populations based on their position and quantifies the number of neighbours of every cell within a dataset in a 3D environment. Through IVEN-driven analyses, we show how transformations in cell environment, defined here as changes in cell neighbourhood, are related to changes in embryo geometry and major developmental events during preimplantation mammalian development. Moreover, we demonstrate that modulation of the FGF pathway alters spatial relations of inner cells and neighbourhood distributions, leading to overall changes in embryo architecture. In conjunction with IVEN-driven analyses, we uncover differences in the dynamic of cell size changes over the preimplantation period and determine that cells within the mammalian embryo initiate growth phase only at the time of implantation.

中文翻译：

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IVEN：描述 3D 细胞位置和邻域的定量工具揭示了 FGF4 处理的植入前胚胎的结构变化。

细胞和有机体水平的结构变化对于成功的发育和生长是不可或缺的和必要的。在哺乳动物植入前发育过程中，细胞尺寸减小，胚胎结构发生显着变化。这些变化必须正确协调，以确保胚胎的持续发育并最终成功怀孕。然而，在哺乳动物植入前发育过程中，这种转化的性质尚不清楚。为了定量描述细胞环境和生物体结构的变化，我们设计了内部与外部邻域（IVEN）。IVEN 是一个用户交互的开源管道，它根据细胞的位置将细胞分类为不同的群体，并量化 3D 环境中数据集中每个细胞的邻居数量。通过 IVEN 驱动的分析，我们展示了细胞环境的转变（此处定义为细胞邻域的变化）如何与胚胎几何形状的变化和植入前哺乳动物发育过程中的主要发育事件相关。此外，我们证明 FGF 通路的调节改变了内部细胞的空间关系和邻域分布，导致胚胎结构的整体变化。结合 IVEN 驱动的分析，我们发现了植入前期间细胞大小动态变化的差异，并确定哺乳动物胚胎内的细胞仅在植入时开始生长期。