Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, United States.
Translational Imaging Center, University of Southern California, Los Angeles, CA 90089, United States.
Bioinformatics. 2023 Sep 2;39(9). doi: 10.1093/bioinformatics/btad568.
In functional imaging studies, accurately synchronizing the time course of experimental manipulations and stimulus presentations with resulting imaging data is crucial for analysis. Current software tools lack such functionality, requiring manual processing of the experimental and imaging data, which is error-prone and potentially non-reproducible. We present VoDEx, an open-source Python library that streamlines the data management and analysis of functional imaging data. VoDEx synchronizes the experimental timeline and events (e.g. presented stimuli, recorded behavior) with imaging data. VoDEx provides tools for logging and storing the timeline annotation, and enables retrieval of imaging data based on specific time-based and manipulation-based experimental conditions.
VoDEx is an open-source Python library and can be installed via the "pip install" command. It is released under a BSD license, and its source code is publicly accessible on GitHub (https://github.com/LemonJust/vodex). A graphical interface is available as a napari-vodex plugin, which can be installed through the napari plugins menu or using "pip install." The source code for the napari plugin is available on GitHub (https://github.com/LemonJust/napari-vodex). The software version at the time of submission is archived at Zenodo (version v1.0.18, https://zenodo.org/record/8061531).
在功能成像研究中，准确地将实验操作和刺激呈现的时间进程与成像数据同步对于分析至关重要。当前的软件工具缺乏这种功能，需要手动处理实验和成像数据，这容易出错，并且可能无法重现。我们提出了 VoDEx，这是一个用于功能成像数据管理和分析的开源 Python 库。VoDEx 可以将实验时间轴和事件（例如呈现的刺激、记录的行为）与成像数据同步。VoDEx 提供了用于记录和存储时间轴注释的工具，并允许根据特定的基于时间和基于操作的实验条件检索成像数据。
VoDEx 是一个开源 Python 库，可以通过 "pip install" 命令进行安装。它遵循 BSD 许可证发布，其源代码可在 GitHub（https://github.com/LemonJust/vodex）上公开获取。一个图形界面作为 napari-vodex 插件提供，可以通过 napari 插件菜单或使用 "pip install" 进行安装。napari 插件的源代码可在 GitHub（https://github.com/LemonJust/napari-vodex）上获取。提交时的软件版本已在 Zenodo 存档（版本 v1.0.18，https://zenodo.org/record/8061531）。
