Fast, accurate reconstruction of cell Lineages from Large-scale fluorescence microscopy data
Fast, accurate reconstruction of cell Lineages from Large-scale fluorescence microscopy data
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DOI：
10.1038/nmeth.3036
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发表时间：
2014-09-01
期刊：
影响因子：
48
通讯作者：
Keller, Philipp J.
中科院分区：
文献类型：
--
作者：
Amat, Fernando;Lemon, William;Keller, Philipp J.
复杂多细胞生物体中细胞谱系的全面重建是发育生物学的中心目标。我们提出了一个开放源码的计算框架，用于高精度和高速度的细胞核分割和跟踪。我们通过在用三种类型的荧光显微镜获取的四维、TB大小的图像数据集中重建果蝇、斑马鱼和小鼠胚胎的细胞谱系来展示其普遍性，(Ii)通过分析发育的高级阶段可伸缩性，在单个计算机工作站上最少26,000个细胞(-1)，并且(Iii)通过仅调整所有数据集的两个参数并且为高效的数据管理提供可视化和编辑工具来易于使用。我们的方法在所有物种和成像模式上平均达到97.0%的链接准确率。使用我们的系统，我们进行了早期果蝇神经系统发育的第一次细胞谱系重建，揭示了整个胚胎中的神经母细胞动力学。
The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for the segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (i) generality by reconstructing cell lineages in four-dimensional, terabyte-sized image data sets of fruit fly, zebrafish and mouse embryos acquired with three types of fluorescence microscopes, (ii) scalability by analyzing advanced stages of development with up to 20,000 cells per time point at 26,000 cells min(-1) on a single computer workstation and (iii) ease of use by adjusting only two parameters across all data sets and providing visualization and editing tools for efficient data curation. Our approach achieves on average 97.0% linkage accuracy across all species and imaging modalities. Using our system, we performed the first cell lineage reconstruction of early Drosophila melanogaster nervous system development, revealing neuroblast dynamics throughout an entire embryo.