PhAT: A flexible open-source GUI-driven toolkit for photometry analysis.
PhAT: A flexible open-source GUI-driven toolkit for photometry analysis.
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PhAT：一个灵活的开源 GUI 驱动工具包，用于光度分析。
DOI：
10.1101/2023.03.14.532489
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Donaldson,ZoeR
中科院分区：
文献类型：
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作者：
Murphy,KathleenZ;Haile,Eyobel;McTigue,Anna;Pierce,AnneF;Donaldson,ZoeR
光度学方法检测传感器介导的荧光变化，作为大脑内快速分子变化的代理。作为一种实施成本相对较低的灵活技术，光度学正迅速被纳入神经科学实验室。然而，尽管现在存在多个光度学数据采集系统，但用于产生数据的强大分析管道仍然有限。在这里，我们介绍了光度测量分析工具包(PHAT)--这是一个免费的开源分析管道，提供了信号标准化、合并多个数据流以使光度数据与行为和其他事件相一致、计算与事件相关的荧光变化以及比较荧光痕迹的相似性的选项。图形用户界面(GUI)使用户无需事先具备编码知识即可使用该软件。除了提供基本的分析工具外，PHAT还旨在方便地整合社区驱动的新模块开发，以进行更多定制分析，并使数据能够轻松导出，以实现后续的统计测试和/或基于代码的分析。此外，我们还提供了关于光度学实验的技术方面的建议，包括传感器的选择和验证、参考信号的考虑以及实验设计和数据收集的最佳实践。我们希望该软件和协议的分发将降低新的测光用户的进入门槛，并提高收集的数据的质量，增加测光分析的透明度和重复性。©2023 Wiley期刊LLC基本协议1：软件和环境安装替代协议1：软件和环境更新基本协议2：图形用户界面驱动的光纤光度分析支持协议1：检查信号质量支持协议2：与图形交互基本协议3：将模块添加到Phat替代协议2：创建用于Jupyter笔记本的功能
Photometry approaches detect sensor‐mediated changes in fluorescence as a proxy for rapid molecular changes within the brain. As a flexible technique with a relatively low cost to implement, photometry is rapidly being incorporated into neuroscience laboratories. Yet, although multiple data acquisition systems for photometry now exist, robust analytical pipelines for the resulting data remain limited. Here we present thePhotometryAnalysisToolkit (PhAT)—a free open‐source analysis pipeline that provides options for signal normalization, incorporation of multiple data streams to align photometry data with behavior and other events, calculation of event‐related changes in fluorescence, and comparison of similarity across fluorescent traces. A graphical user interface (GUI) enables use of this software without prior coding knowledge. In addition to providing foundational analytical tools, PhAT is designed to readily incorporate community‐driven development of new modules for more bespoke analyses, and enables data to be easily exported to enable subsequent statistical testing and/or code‐based analyses. In addition, we provide recommendations regarding technical aspects of photometry experiments, including sensor selection and validation, reference signal considerations, and best practices for experimental design and data collection. We hope that the distribution of this software and protocols will lower the barrier to entry for new photometry users and improve the quality of collected data, increasing transparency and reproducibility in photometry analyses. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Software and environment installationAlternate Protocol 1: Software and environment updateBasic Protocol 2: GUI‐driven fiber photometry analysisSupport Protocol 1: Examining signal qualitySupport Protocol 2: Interacting with graphsBasic Protocol 3: Adding modules to PhATAlternate Protocol 2: Creating functions for use in Jupyter Notebook