Dataset Information

YSMR: a video tracking and analysis program for bacterial motility.

ABSTRACT: BACKGROUND: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. RESULTS: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. CONCLUSION: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.

SUBMITTER: Schwanbeck J

PROVIDER: S-EPMC7191716 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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YSMR: a video tracking and analysis program for bacterial motility.

Schwanbeck Julian J Oehmig Ines I Dretzke Jerôme J Zautner Andreas E AE Groß Uwe U Bohne Wolfgang W

BMC bioinformatics 20200429 1

<h4>Background</h4>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.<h4>Results</h4>The open-source python program YSMR (Your Software for Motility Recognition) was designed to simultaneously track a large number of bacterial cells on standa ...[more]

PMID: 32349658

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Project description:The present study aimed to validate and compare the football-specific measurement accuracy of two optical tracking systems engineered by TRACAB. The "Gen4" system consists of two multi-camera units (a stereo pair) in two locations either side of the halfway line, whereas the distributed "Gen5" system combines two stereo pairs on each side of the field as well as two monocular systems behind the goal areas. Data were collected from 20 male football players in two different exercises (a football sport-specific running course and small-sided games) in a professional football stadium. For evaluating the accuracy of the systems, measures were compared against simultaneously recorded measures of a reference system (VICON motion capture system). Statistical analysis uses RMSE for kinematic variables (position, speed and acceleration) and the difference in percentages for performance indicators (e.g. distance covered, peak speed) per run compared to the reference system. Frames in which players were obviously not tracked were excluded. Gen5 had marginally better accuracy (0.08 m RMSE) for position measurements than Gen4 (0.09 m RMSE) compared to the reference. Accuracy difference in instantaneous speed (Gen4: 0.09 m⋅s-1 RMSE; Gen5: 0.08 m⋅s-1 RMSE) and acceleration (Gen4: 0.26 m⋅s-2 RMSE; Gen5: 0.21 m⋅s-2 RMSE) measurements were significant, but also trivial in terms of the effect size. For total distance travelled, both Gen4 (0.42 ± 0.60%) and Gen5 (0.27 ± 0.35%) showed only trivial deviations compared to the reference. Gen4 showed moderate differences in the low-speed distance travelled category (-19.41 ± 13.24%) and small differences in the high-speed distance travelled category (8.94 ± 9.49%). Differences in peak speed, acceleration and deceleration were trivial (<0.5%) for both Gen4 and Gen5. These findings suggest that Gen5's distributed camera architecture has minor benefits over Gen4's single-view camera architecture in terms of accuracy. We assume that the main benefit of the Gen5 towards Gen4 lies in increased robustness of the tracking when it comes to optical overlapping of players. Since differences towards the reference system were very low, both TRACAB's tracking systems can be considered as valid technologies for football-specific performance analyses in the settings tested as long as players are tracked correctly.

Project description:The alphaproteobacterium Magnetospirillum gryphiswaldense has the intriguing ability to navigate within magnetic fields, a behavior named magnetotaxis, governed by the formation of magnetosomes, intracellular membrane-enveloped crystals of magnetite. Magnetosomes are aligned in chains along the cell's motility axis by a dedicated multipart cytoskeleton ("magnetoskeleton"); however, precise estimates of its significance for magnetotaxis have not been reported. Here, we estimated the alignment of strains deficient in various magnetoskeletal constituents by live-cell motility tracking within defined magnetic fields ranging from 50 μT (reflecting the geomagnetic field) up to 400 μT. Motility tracking revealed that ΔmamY and ΔmamK strains (which assemble mispositioned and fragmented chains, respectively) are partially impaired in magnetotaxis, with approximately equal contributions of both proteins. This impairment was reflected by a required magnetic field strength of 200 μT to achieve a similar degree of alignment as for the wild-type strain in a 50-μT magnetic field. In contrast, the ΔmamJ strain, which predominantly forms clusters of magnetosomes, was only weakly aligned under any of the tested field conditions and could barely be distinguished from a nonmagnetic mutant. Most findings were corroborated by a soft agar swimming assay to analyze magnetotaxis based on the degree of distortion of swim halos formed in magnetic fields. Motility tracking further revealed that swimming speeds of M. gryphiswaldense are highest within the field strength equaling the geomagnetic field. In conclusion, magnetic properties and intracellular positioning of magnetosomes by a dedicated magnetoskeleton are required and optimized for bacterial magnetotaxis and most efficient locomotion within the geomagnetic field.IMPORTANCE In Magnetospirillum gryphiswaldense, magnetosomes are aligned in quasi-linear chains in a helical cell by a complex cytoskeletal network, including the actin-like MamK and adapter MamJ for magnetosome chain concatenation and segregation and MamY to position magnetosome chains along the shortest cellular axis of motility. Magnetosome chain positioning is assumed to be required for efficient magnetic navigation; however, the significance and contribution of all key constituents have not been quantified within defined and weak magnetic fields reflecting the geomagnetic field. Employing two different motility-based methods to consider the flagellum-mediated propulsion of cells, we depict individual benefits of all magnetoskeletal constituents for magnetotaxis. Whereas lack of mamJ resulted almost in an inability to align cells in weak magnetic fields, an approximately 4-fold-increased magnetic field strength was required to compensate for the loss of mamK or mamY In summary, the magnetoskeleton and optimal positioning of magnetosome chains are required for efficient magnetotaxis.

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YSMR: a video tracking and analysis program for bacterial motility.

Publications

YSMR: a video tracking and analysis program for bacterial motility.

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