Castro-Gonzalez Carlos, Luengo-Oroz Miguel Angel, Douloquin Louise, Savy Thierry, Melani Camilo, Desnoulez Sophie, Ledesma-Carbayo Maria Jesus, Bourginey Paul, Peyrieras Nadine, Santos Andres
Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, 28040, Spain.
Annu Int Conf IEEE Eng Med Biol Soc. 2010;2010:5520-3. doi: 10.1109/IEMBS.2010.5626769.
We elaborate on a general framework composed of a set of computational tools to accurately quantificate cellular position and gene expression levels throughout early zebrafish embryogenesis captured over a time-lapse series of in vivo 3D images. Our modeling strategy involves nuclei detection, cell geometries extraction, automatic gene levels quantification and cell tracking to reconstruct cell trajectories and lineage tree which describe the animal development. Each cell in the embryo is then precisely described at each given time t by a vector composed of the cell 3D spatial coordinates (x; y; z) along with its gene expression level g. This comprehensive description of the embryo development is used to assess the general connection between genetic expression and cell movement. We also investigate genetic expression propagation between a cell and its progeny in the lineage tree. More to the point, this paper focuses on the evolution of the expression pattern of transcriptional factor goosecoid (gsc) through the gastrulation process between 6 and 9 hours post fertilization (hpf).
我们详细阐述了一个由一组计算工具组成的通用框架，用于在一系列体内3D延时图像中精确量化斑马鱼早期胚胎发育过程中的细胞位置和基因表达水平。我们的建模策略包括细胞核检测、细胞几何形状提取、自动基因水平量化和细胞追踪，以重建描述动物发育的细胞轨迹和谱系树。然后，胚胎中的每个细胞在每个给定时间t都由一个向量精确描述，该向量由细胞的3D空间坐标（x；y；z）及其基因表达水平g组成。这种对胚胎发育的全面描述用于评估基因表达与细胞运动之间的总体联系。我们还研究了谱系树中一个细胞与其后代之间的基因表达传播。更确切地说，本文重点关注受精后6至9小时（hpf）原肠胚形成过程中转录因子gsc（goosecoid）表达模式的演变。
