Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.
Neuroscience Interdepartmental Program, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States.
Front Neural Circuits. 2020 May 15;14:25. doi: 10.3389/fncir.2020.00025. eCollection 2020.
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 like , , 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 named .
使用多种显微镜方法(如双光子激发或头戴式“微型显微镜”)进行荧光钙成像,是记录各种实验条件下神经元活动和神经胶质信号的首选方法之一,这些实验条件包括急性脑切片、脑类器官和行为动物。由于遗传编码或化学钙指示剂的荧光强度变化与神经元的动作电位发射相关,因此数据分析基于通过在不同感兴趣区域内随时间变化的像素强度值推断这种尖峰。然而,从这些荧光信号中提取生物学相关信息所需的算法很复杂,需要在编程方面有丰富的专业知识才能开发出强大的分析管道。几十年来,执行这些分析的唯一方法是让各个实验室编写自己的定制代码。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难以采用它们。尽管最近的一些工具(如、和其他工具)正在改变这种情况,但对于许多实验室来说,采用这些软件包仍然存在障碍,特别是对于没有复杂编程技能的潜在用户来说。由于双光子显微镜的价格越来越实惠,瓶颈不再是硬件,而是用于在不同组之间最佳和一致地分析钙数据的软件。我们通过将最新的软件解决方案(即 NoRMCorre 和 CaImAn)纳入开源、易于使用、基于 GUI、直观和自动化数据分析软件包中,解决了这一未满足的需求,该软件包名为。