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连接组学视图工具包：一个用于管理、分析和可视化连接组学的开源框架。

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

机构信息

Signal Processing Laboratory 5, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland.

出版信息

Front Neuroinform. 2011 Jun 6;5:3. doi: 10.3389/fninf.2011.00003. eCollection 2011.

DOI:10.3389/fninf.2011.00003
PMID:21713110
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3112315/
Abstract

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

摘要

需要高级神经信息学工具来进行连接组图谱绘制、分析和可视化方法的研究。连接组数据集固有的多模态性质为数据组织、整合和共享带来了新的挑战。我们设计并实现了 Connectome Viewer Toolkit——一套用 Python 编写的免费且可扩展的开源神经影像学工具。该工具包的主要组件如下：（1）Connectome File Format 是一种基于 XML 的容器格式，用于规范多模态数据集成和结构化元数据标注。（2）Connectome File Format Library 支持连接组文件的管理和共享。（3）Connectome Viewer 是一个用于多模态连接组数据可视化和分析的综合研究和开发环境。Connectome Viewer 的插件架构支持使用网络分析包和交互式脚本外壳进行扩展，从而便于开发和社区贡献。与科学 Python 社区的工具集成可利用众多现有的库来进行强大的连接组数据挖掘、探索和比较。我们使用 Connectome Mapper 处理的扩散 MRI 数据集演示了 Connectome Viewer Toolkit 的适用性。Connectome Viewer Toolkit 可从 http://www.cmtk.org/ 获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45df/3112315/9893388d9c51/fninf-05-00003-g012.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/45df/3112315/b65e5b044525/fninf-05-00003-g008.jpg
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