EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data
EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data
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EZcalcium：用于钙成像数据分析的开源工具
DOI：
10.3389/fncir.2020.00025
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发表时间：
2020-05-15
影响因子：
3.5
通讯作者：
Portera-Cailliau, Carlos
中科院分区：
文献类型：
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作者：
Cantu, Daniel A.;Wang, Bo;Portera-Cailliau, Carlos
使用诸如双光子激发或头戴式“微型显微镜”等一系列显微镜方法的荧光钙成像是在各种实验环境中记录神经元活动和神经胶质信号的首选方法之一，包括急性脑片、脑器官和行为动物。由于遗传编码或化学钙指示剂的荧光强度的变化与神经元中的动作电位放电相关，因此数据分析是基于从不同感兴趣区域内像素强度值随时间的变化来推断这种尖峰。然而，从这些荧光信号中提取生物相关信息所需的算法是复杂的，需要编程方面的大量专业知识来开发强大的分析管道。几十年来，执行这些分析的唯一方法是由各个实验室编写他们的定制代码。这些例程通常没有很好的注释，并且缺乏直观的图形用户界面(GUI)，这使得其他实验室的科学家很难采用它们。尽管最近的工具如CaImAn、Suite2P和其他工具正在改变全景图，但对于许多实验室来说，采用这些包仍然存在障碍，特别是对于没有复杂编程技能的潜在用户。随着双光子显微镜变得越来越便宜，瓶颈不再是硬件，而是用于对不同群体的钙数据进行最佳和一致分析的软件。我们通过将最新的钙成像数据运动校正、分割、信号提取和去卷积软件解决方案(即NoRMCorre和CAIMAN)整合到一个开源、易于使用、基于图形用户界面、直观和自动化的数据分析软件包中，从而满足了这一未得到满足的需求，我们将其命名为EZcala。
Fluorescence calcium imaging using a range of microscopy approaches, such as two-photon excitation or head-mounted "miniscopes," is one of the preferred methods to record neuronal activity and glial signals in various experimental settings, including acute brain slices, brain organoids, and behaving animals. Because changes in the fluorescence intensity of genetically encoded or chemical calcium indicators correlate with action potential firing in neurons, data analysis is based on inferring such spiking from changes in pixel intensity values across time within different regions of interest. However, the algorithms necessary to extract biologically relevant information from these fluorescent signals are complex and require significant expertise in programming to develop robust analysis pipelines. For decades, the only way to perform these analyses was for individual laboratories to write their custom code. These routines were typically not well annotated and lacked intuitive graphical user interfaces (GUIs), which made it difficult for scientists in other laboratories to adopt them. Although the panorama is changing with recent tools likeCaImAn,Suite2P, and others, there is still a barrier for many laboratories to adopt these packages, especially for potential users without sophisticated programming skills. As two-photon microscopes are becoming increasingly affordable, the bottleneck is no longer the hardware, but the software used to analyze the calcium data optimally and consistently across different groups. We addressed this unmet need by incorporating recent software solutions, namely NoRMCorre and CaImAn, for motion correction, segmentation, signal extraction, and deconvolution of calcium imaging data into an open-source, easy to use, GUI-based, intuitive and automated data analysis software package, which we namedEZcalcium.