Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans
Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans
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DOI：
10.1186/s12915-020-0745-2
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发表时间：
2020-03-19
期刊：
影响因子：
5.4
通讯作者：
Iino, Yuichi
中科院分区：
文献类型：
--
作者：
Toyoshima, Yu;Wu, Stephen;Iino, Yuichi
细胞身份标注是神经科学中一个重要的过程，它允许对细胞进行比较，包括不同动物的神经活动。在秀丽隐杆线虫（Caenorhabditis elegans）中，尽管所有神经元都被赋予了独特的身份，但由于缺乏神经元位置和身份的定量信息，完整动物中可注释神经元的数量有限。在这里，我们提出了一个数据集，促进了神经元身份的注释，并展示了其在全脑成像综合分析中的应用。我们使用35个细胞特异性启动子系统地鉴定了311只成虫头部区域的神经元，并创建了神经元表达模式和位置的数据集。我们发现了很大的位置变化，说明了注释任务的难度。我们研究了驱动不同荧光的细胞特异性启动子的多种组合，并为动物中大多数头部神经元的注释生成了最佳菌株。我们还开发了一种具有人机交互功能的自动注释方法，便于全脑成像所需的注释。结论我们的神经元ID数据集和最优荧光菌株能够对成年秀丽隐杆线虫头部区域的大多数神经元进行全自动化和半自动化的注释，其中包括人类交互功能。我们的方法可以潜在地应用于除秀丽隐杆线虫以外的研究中使用的模型物种，其中可用的细胞类型特异性启动子的数量及其多样性将是一个重要的考虑因素。
Background Annotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has been limited due to the lack of quantitative information on the location and identity of neurons. Results Here, we present a dataset that facilitates the annotation of neuronal identities, and demonstrate its application in a comprehensive analysis of whole-brain imaging. We systematically identified neurons in the head region of 311 adult worms using 35 cell-specific promoters and created a dataset of the expression patterns and the positions of the neurons. We found large positional variations that illustrated the difficulty of the annotation task. We investigated multiple combinations of cell-specific promoters driving distinct fluorescence and generated optimal strains for the annotation of most head neurons in an animal. We also developed an automatic annotation method with human interaction functionality that facilitates annotations needed for whole-brain imaging. Conclusion Our neuron ID dataset and optimal fluorescent strains enable the annotation of most neurons in the head region of adult C. elegans, both in full-automated fashion and a semi-automated version that includes human interaction functionalities. Our method can potentially be applied to model species used in research other than C. elegans, where the number of available cell-type-specific promoters and their variety will be an important consideration.