An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.
An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.
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DOI：
10.1371/journal.pcbi.1005526
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发表时间：
2017-06
影响因子：
4.3
通讯作者：
Sumbre G
中科院分区：
文献类型：
--
作者：
Romano SA;Pérez-Schuster V;Jouary A;Boulanger-Weill J;Candeo A;Pietri T;Sumbre G
研究大型神经元回路动力学的新成像和光遗传学技术的发展正在产生前所未有的体积和复杂性的数据集，要求开发适当的分析工具。我们提出了一个全面的计算工作流，用于分析神经元种群钙动力学。工具箱包括新开发的算法和交互式工具，用于图像预处理和分割，估计重要的单个神经元单次试验信号，映射事件相关的神经元响应，检测活动相关的神经元簇，探索种群动态，以及针对替代控制数据集分析簇的特征。这些模块集成在一个模块化和通用的处理管道中，可适应不同的需求。聚类模块能够检测灵活的、动态激活的神经元集合，与大脑的分布式种群编码一致。我们展示了工具箱对各种钙成像数据集的适用性。工具箱的开源代码、分步教程和案例研究数据集可在https://github.com/zebrain-lab/Toolbox-Romano-et-al上获得。
The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.