TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.
TubULAR: tracking in toto deformations of dynamic tissues via constrained maps.
复制标题
TubULAR：通过约束图跟踪动态组织的全部变形。
DOI：
10.1038/s41592-023-02081-w
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发表时间：
2023
期刊：
影响因子：
48
通讯作者：
Cislo,DillonJ
中科院分区：
文献类型：
--
作者：
Mitchell,NoahP;Cislo,DillonJ
生物学中一个常见的主题是将细胞排列成管状，然后进一步转化为复杂的形状。传统上，动态组织的分析依赖于检查静态快照，横截面的实时成像或三维跟踪孤立细胞。然而，捕捉平面内和平面外行为之间的相互作用需要在整个表面变形时跟随它，并将细胞尺度的运动整合到集体的组织尺度变形中。在这里，我们提出了一个分析框架，建立在toto地图的组织变形以下组织包裹在一个静态的材料参考系。然后，我们的方法涉及面内和面外的行为，并将复杂的变形映射分解成基本的贡献。管状表面拉格朗日分析资源（TubULAR）提供了一个开源的实现，可以作为一个独立的工具包，也可以作为发育生物学社区中使用的ImSAnE包的扩展。我们通过分析胚胎果蝇肠和跳动的斑马鱼心脏的形状变化来证明我们的方法。该方法自然地推广到体外和合成系统，并提供了方便的机械机制，遗传图案的器官形状变化。
A common motif in biology is the arrangement of cells into tubes, which further transform into complex shapes. Traditionally, analysis of dynamic tissues has relied on inspecting static snapshots, live imaging of cross-sections or tracking isolated cells in three dimensions. However, capturing the interplay between in-plane and out-of-plane behaviors requires following the full surface as it deforms and integrating cell-scale motions into collective, tissue-scale deformations. Here, we present an analysis framework that builds in toto maps of tissue deformations by following tissue parcels in a static material frame of reference. Our approach then relates in-plane and out-of-plane behaviors and decomposes complex deformation maps into elementary contributions. The tube-like surface Lagrangian analysis resource (TubULAR) provides an open-source implementation accessible either as a standalone toolkit or as an extension of the ImSAnE package used in the developmental biology community. We demonstrate our approach by analyzing shape change in the embryonicDrosophilamidgut and beating zebrafish heart. The method naturally generalizes to in vitro and synthetic systems and provides ready access to the mechanical mechanisms relating genetic patterning to organ shape change.