A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage.
A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage.
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DOI：
10.1038/ncomms9674
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发表时间：
2016-02-25
影响因子：
16.6
通讯作者：
Bourgine P
中科院分区：
文献类型：
--
作者：
Faure E;Savy T;Rizzi B;Melani C;Stašová O;Fabrèges D;Špir R;Hammons M;Čúnderlík R;Recher G;Lombardot B;Duloquin L;Colin I;Kollár J;Desnoulez S;Affaticati P;Maury B;Boyreau A;Nief JY;Calvat P;Vernier P;Frain M;Lutfalla G;Kergosien Y;Suret P;Remešíková M;Doursat R;Sarti A;Mikula K;Peyriéras N;Bourgine P
从体内3D+时间图像数据集定量和系统地分析胚胎细胞动力学是发育生物学前沿的主要挑战。尽管最近在生命系统的显微成像方面取得了突破，但为任何发育中的生物体生成准确的细胞谱系树仍然是一项艰巨的任务。我们在这里介绍BioEmergences工作流程，集成了从图像采集和处理到重建数据交互式可视化的所有重建步骤。原始的数学方法和算法是图像滤波、细胞核中心检测、细胞核和细胞膜分割以及细胞跟踪的基础。它们在斑马鱼、海鞘和海胆胚胎上被证明具有染色的细胞核和细胞膜。随后的验证和注释使用Mov-IT进行，这是一个定制的图形界面。与其他八个软件工具相比，我们的工作流程取得了最好的血统分数。BioEmergences和Mov-IT以独立或网络服务模式提供，为计算机实验胚胎学提供了一套独特的工具。 从大量数据中定量分析胚胎细胞动力学仍然是发育生物学领域的一个主要挑战。在这里，作者开发了软件和工作流程，从斑马鱼、被囊动物和海胆等几种发育中的生物的3D延时成像数据集重建细胞谱系树。
The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology. Quantitative analysis of embryonic cell dynamics from large data sets remains a major challenge in the field of developmental biology. Here the authors develop software and a workflow to reconstruct cell lineage trees from 3D time lapse imaging data sets from several developing organisms including zebrafish, tunicates and sea urchins.
影响因子：
7.6
作者：
Rizzi B;Sarti A
通讯作者：
Sarti A