Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany.
Institute of Applied Mathematics, Leibniz University Hannover, Hannover, Germany.
BMC Bioinformatics. 2020 Apr 29;21(1):166. doi: 10.1186/s12859-020-3495-9.
Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on the level of individual cells, which is a prerequisite to study the underlying molecular mechanisms.
The open-source python program YSMR (Your Software for Motility Recognition) was designed to simultaneously track a large number of bacterial cells on standard computers from video files in various formats. In order to cope with the high number of tracked objects, we use a simple detection and tracking approach based on grey-value and position, followed by stringent selection against suspicious data points. The generated data can be used for statistical analyses either directly with YSMR or with external programs.
In contrast to existing video tracking software, which either requires expensive computer hardware or only tracks a limited number of bacteria for a few seconds, YSMR is an open-source program which allows the 2-D tracking of several hundred objects over at least 5 minutes on standard computer hardware. The code is freely available at https://github.com/schwanbeck/YSMR.
细菌的运动能力是趋性行为的基础，在某些致病性细菌中，它对毒力很重要。运动细菌的视频跟踪允许监测单个细胞水平上的细菌游动行为和趋化性，这是研究潜在分子机制的前提。
我们设计了一个名为 YSMR 的开源 Python 程序，用于从各种格式的视频文件中同时跟踪大量标准计算机上的细菌细胞。为了应对大量跟踪对象，我们使用了一种基于灰度值和位置的简单检测和跟踪方法，然后对可疑数据点进行严格筛选。生成的数据可以直接在 YSMR 中或外部程序中进行统计分析。
与现有的视频跟踪软件相比，YSMR 是一个开源程序，它不需要昂贵的计算机硬件，也可以在标准计算机硬件上至少 5 分钟内跟踪几百个物体的 2D 运动，而其他软件要么需要昂贵的计算机硬件，要么只能跟踪少数几个细菌几秒钟。代码可在 https://github.com/schwanbeck/YSMR 上免费获取。
