A Python-OpenCV based software for processing single-bacterium tracking microscopy videos.

Abstract

Real-time single-bacterium tracking (SBT) is a powerful microscopy technique that allows for direct observation of the motility of individual bacteria. This technique requires microscopy video processing methods to localize individual bacteria from microscopy videos, followed by obtaining bacterial trajectories by linking the localizations in successive video frames. These analysis steps are usually labor-intensive. In addition, many existing analysis softwares are developed using commercial programming languages, which makes it difficult to be further developed and used for larger contexts of usage. In this regard, a Python-OpenCV based software is presented which is capable of obtaining bacterial trajectories from SBT microscopy videos. The developed software does not require additional commercial software licenses. Also, the software can perform video processing and bacterial trajectory extraction steps in an automated way. The developed open-source software could thus be listed as one of the useful tools for related quantitative investigations. This work is supported by the National Natural Science Foundation of China (NSFC) under grant number 12104405.