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Visbrain:一个用于多模态脑数据可视化的多功能GPU加速开源套件。

Visbrain: A Multi-Purpose GPU-Accelerated Open-Source Suite for Multimodal Brain Data Visualization.

作者信息

Combrisson Etienne, Vallat Raphael, O'Reilly Christian, Jas Mainak, Pascarella Annalisa, Saive Anne-Lise, Thiery Thomas, Meunier David, Altukhov Dmitrii, Lajnef Tarek, Ruby Perrine, Guillot Aymeric, Jerbi Karim

机构信息

Computational and Cognitive Neuroscience Lab (CoCo Lab), Psychology Department, University of Montreal, Montreal, QC, Canada.

Lyon Neuroscience Research Center, Brain Dynamics and Cognition team, INSERM UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.

出版信息

Front Neuroinform. 2019 Mar 22;13:14. doi: 10.3389/fninf.2019.00014. eCollection 2019.

Abstract

We present Visbrain, a Python open-source package that offers a comprehensive visualization suite for neuroimaging and electrophysiological brain data. Visbrain consists of two levels of abstraction: (1) objects which represent highly configurable neuro-oriented visual primitives (3D brain, sources connectivity, etc.) and (2) graphical user interfaces for higher level interactions. The object level offers flexible and modular tools to produce and automate the production of figures using an approach similar to that of Matplotlib with subplots. The second level visually connects these objects by controlling properties and interactions through graphical interfaces. The current release of Visbrain (version 0.4.2) contains 14 different objects and three responsive graphical user interfaces, built with PyQt: , for the inspection of time-series and spectral properties, for any type of visualization involving a 3D brain and for polysomnographic data visualization and sleep analysis. Each module has been developed in tight collaboration with end-users, i.e., primarily neuroscientists and domain experts, who bring their experience to make Visbrain as transparent as possible to the recording modalities (e.g., intracranial EEG, scalp-EEG, MEG, anatomical and functional MRI). Visbrain is developed on top of VisPy, a Python package providing high-performance 2D and 3D visualization by leveraging the computational power of the graphics card. Visbrain is available on Github and comes with a documentation, examples, and datasets (http://visbrain.org).

摘要

我们展示了Visbrain,一个Python开源软件包,它为神经成像和脑电生理数据提供了一套全面的可视化工具。Visbrain包含两个抽象层次:(1)对象,代表高度可配置的面向神经的视觉原语(3D大脑、源连接性等);(2)用于更高级交互的图形用户界面。对象层提供了灵活且模块化的工具,使用类似于Matplotlib的子图方法来生成和自动生成图形。第二层通过图形界面控制属性和交互,在视觉上连接这些对象。Visbrain的当前版本(0.4.2版)包含14个不同的对象和三个响应式图形用户界面,这些界面是用PyQt构建的:用于检查时间序列和频谱特性,用于涉及3D大脑的任何类型的可视化,以及用于多导睡眠图数据可视化和睡眠分析。每个模块都是在与终端用户(主要是神经科学家和领域专家)紧密合作下开发的,他们凭借自身经验使Visbrain对于记录方式(例如颅内脑电图、头皮脑电图、脑磁图、解剖学和功能性磁共振成像)尽可能透明。Visbrain是在VisPy之上开发的,VisPy是一个Python软件包,通过利用图形卡的计算能力提供高性能的2D和3D可视化。Visbrain可在Github上获取,并附带文档、示例和数据集(http://visbrain.org)。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b01d/6439346/41a18b104ebb/fninf-13-00014-g0001.jpg

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