A high-throughput and open-source platform for embryo phenomics
A high-throughput and open-source platform for embryo phenomics
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DOI：
10.1371/journal.pbio.3000074
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发表时间：
2018-12-01
期刊：
影响因子：
9.8
通讯作者：
Rundle, Simon D.
中科院分区：
文献类型：
--
作者：
Tills, Oliver;Spicer, John I.;Rundle, Simon D.
表型组学具有促进生物学重大进步的潜力，但需要开发能够产生和分析高维数据的高通量技术。构建这样的技术面临着巨大的挑战，尤其是研究动态过程(如胚胎发育)所需的挑战，在此期间，很难捕捉到高速度的时间、空间和功能变化。在这里，我们介绍了EmbryoPhenology，这是一个可访问的高通量水生胚胎表型组学平台，包括一个开源视频显微镜(OpenVIM)，它可以在严格控制的环境条件下产生多个胚胎的高分辨率视频。然后，这些视频由Python程序包胚胎计算机视觉(EmbryoCV)进行分析，该程序提取胚胎发育过程中的形态、生理、行为和代理特征的物候学数据。我们在一系列实验中展示了胚胎表型组学的广泛适用性，这些实验评估了环境变化(温度和盐度)对慢性、急性和多应激源的响应。>；600的3000万张胚胎图像具有明显不同的发育模式-池塘蜗牛Radix balthica和海洋端足类Orchstia Gammarellus。表型组学的挑战是巨大的，但回报也是如此，它与评估复杂的有机体对当前环境变化速度的反应这一紧迫任务尤其相关。胚胎表型组学可以在最早、最动态的生命阶段获取和处理捕捉功能、时间和空间反应的数据，对于那些对更广泛地研究发育和表型组学感兴趣的人来说，这可能是游戏规则的改变。
Phenomics has the potential to facilitate significant advances in biology but requires the development of high-throughput technologies capable of generating and analysing high-dimensional data. There are significant challenges associated with building such technologies, not least those required for investigating dynamic processes such as embryonic development, during which high rates of temporal, spatial, and functional change are inherently difficult to capture. Here, we present EmbryoPhenomics, an accessible high-throughput platform for phenomics in aquatic embryos comprising an Open-source Video Microscope (OpenVIM) that produces high-resolution videos of multiple embryos under tightly controlled environmental conditions. These videos are then analysed by the Python package Embryo Computer Vision (EmbryoCV), which extracts phenomic data for morphological, physiological, behavioural, and proxy traits during the process of embryonic development. We demonstrate the broad-scale applicability of EmbryoPhenomics in a series of experiments assessing chronic, acute, and multistressor responses to environmental change (temperature and salinity) in >30 million images of >600 embryos of two species with markedly different patterns of development-the pond snail Radix balthica and the marine amphipod Orchestia gammarellus. The challenge of phenomics is significant but so too are the rewards, and it is particularly relevant to the urgent task of assessing complex organismal responses to current rates of environmental change. EmbryoPhenomics can acquire and process data capturing functional, temporal, and spatial responses in the earliest, most dynamic life stages and is potentially game changing for those interested in studying development and phenomics more widely.