TrackMate: An open and extensible platform for single-particle tracking
TrackMate: An open and extensible platform for single-particle tracking
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DOI：
10.1016/j.ymeth.2016.09.016
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发表时间：
2017-02-15
期刊：
影响因子：
4.8
通讯作者：
Eliceiri, Kevin W.
中科院分区：
文献类型：
--
作者：
Tinevez, Jean-Yves;Perry, Nick;Eliceiri, Kevin W.
我们介绍TrackMate，一个开源的斐济插件，用于自动化，半自动化和手动跟踪单个粒子。它提供了一个通用的模块化解决方案，通过简单直观的用户界面为最终用户提供开箱即用的功能。它也很容易编写脚本和自适应，在1D随时间推移，2D随时间推移，3D随时间推移，或其他单通道和多通道图像变体上运行同样良好。TrackMate提供了几个可视化和分析工具，有助于评估结果的相关性。TrackMate的实用性通过其易于定制以满足特定跟踪问题的能力得到进一步增强。TrackMate是一个可扩展的平台，开发人员可以在TrackMate环境中轻松编写自己的检测，粒子链接，可视化或分析算法。这个不断发展的框架为研究人员提供了一个机会，快速开发和优化新的算法的基础上现有的TrackMate模块，而不需要编写从头用户界面，包括可视化，分析和导出工具。TrackMate的当前功能的背景下，三个不同的生物问题。首先，我们进行秀丽隐杆线虫谱系分析，以评估成像过程中光诱导的损伤如何损害其早期发育。我们基于TrackMate的谱系分析表明缺乏细胞特异性光敏机制。其次，我们研究了细胞因子IL-1刺激后成纤维细胞中NEMO（NE-KB必需调节剂）簇的募集，并表明光损伤可以产生TrackMate特征运动形状的伪影，从而混淆运动分析。最后，我们验证使用TrackMate的网格蛋白介导的植物细胞内吞作用的定量寿命分析。(C)2016作者（S）爱思唯尔公司出版
We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools.The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NE-KB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells. (C) 2016 The Author(s). Published by Elsevier Inc.