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YSMR: a video tracking and analysis program for bacterial motility
Julian Schwanbeck1, Ines Oehmig2, Jerôme Dretzke3
1Institute for Medical Microbiology, University Medical Center Göttingen, Göttingen, Germany. julian.schwanbeck@med.uni-goettingen.de.
BMC Bioinformatics
|May 1, 2020
Summary
YSMR is a new open-source software for bacterial motility recognition. This tool enables tracking of hundreds of bacterial cells for extended periods on standard hardware, aiding virulence and taxis research.
Area of Science:
- Microbiology
- Biophysics
Background:
- Bacterial motility is crucial for taxis and virulence in pathogenic species.
- Individual cell tracking is essential for understanding molecular mechanisms of motility.
Purpose of the Study:
- To develop an accessible, open-source software for bacterial motility analysis.
- To enable high-throughput tracking of bacterial swimming behavior.
Main Methods:
- Developed YSMR (Your Software for Motility Recognition), an open-source Python program.
- Implemented a simple grey-value and position-based detection and tracking algorithm.
- Included stringent data selection to filter out artifacts.
Main Results:
- YSMR can simultaneously track hundreds of bacterial cells from video files.
- Tracking is performed on standard computer hardware.
- Data is compatible with YSMR or external statistical analysis programs.
Conclusions:
- YSMR offers a cost-effective alternative to existing tracking software.
- It allows for extended (5+ minutes) 2-D tracking of numerous bacterial cells.
- The software is freely available for research purposes.
