TumbleScore: Run and tumble analysis for low frame-rate motility videos
TumbleScore: Run and tumble analysis for low frame-rate motility videos
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DOI：
10.2144/000114493
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发表时间：
2017-01-01
期刊：
影响因子：
2.7
通讯作者：
Bentley, William E.
中科院分区：
文献类型：
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作者：
Pottash, Alex Eli;McKay, Ryan;Bentley, William E.
科学家们经常利用富含鞭毛的细菌的能动性来进行各种应用。一种常见的变化是改变运动中期方向变化的频率，称为翻滚。事实证明，细菌游泳模式的这种差异很难量化，特别是对于那些无法获得高速光学设备的人。传统上，科学家要么求助于不太准确的技术，如软琼脂平板分析，要么被迫投资于昂贵的设备。在这里，我们介绍TumbleScore，这是一款设计用来跟踪和量化具有慢和快帧速率的细菌电影的软件。TumbleScore开发并完全包含在MATLAB中，它处理运动视频并返回相关的翻滚度量，包括：(I)线速度，(Ii)旋转速度，(Iii)低于给定阈值的角度变化百分比，以及(Iv)总路径长度与欧几里得距离的比率，即弧弦比(ACR)。此外，TumbleScore还生成了细菌路径的“玫瑰图”可视化。该软件使用编造的和实验的运动视频进行了验证。
Scientists often exploit the motility of peritrichously flagellated bacteria for various applications. A common alteration is modifying the frequency of mid-movement changes in direction, known as tumbles. Such differences in bacterial swimming patterns can prove difficult to quantify, especially for those without access to high-speed optical equipment. Traditionally, scientists have resorted to less accurate techniques, such as soft agar plate assays, or have been forced to invest in costly equipment. Here, we present TumbleScore, software designed to track and quantify bacterial movies with slow, as well as fast, frame-rates. Developed and fully contained within MATLAB, TumbleScore processes motility videos and returns pertinent tumbling metrics, including: (i) linear speed, (ii) rotational speed, (iii) percentage of angle changes below a given threshold, and (iv) ratio of total path length to Euclidian distance, or arc-chord ratio (ACR). In addition, TumbleScore produces a "rose graph" visualization of bacterial paths. The software was validated using both fabricated and experimental motility videos.