Trajectory data for bacterial motility in semi-solid agar

Description of data

This directory contains the trajectory data of bacterial swimming experiments, using the soil bacterium Pseudomonas putida, in porous agar gels. The subdirectories named WT_025 and WT_03 refer to the trajectory data corresponding to wild type Pseudomonas putida cells in 0.25% and 0.3% agar, respectively. The subdirectories motAB_025 and motCD_025 correspond to the trajectory data associated with the swimming experiments of two knockout mutants (MotAB and MotCD) of the same bacterium, details of which can be found in the references below [1,3].

Each subdirectory contains further subdirectories, including raw data (raw) and processed data for Refs. [1,2]. For experimental Materials and Methods, we refer to the respective publications.

In the raw subdirectory, each .csv file corresponds to a single trajectory (not processed), where the headers X and Y correspond to the coordinates of a single bacterium, in units of micrometers, with a temporal resolution of 20 frames per second, i.e. two successive coordinates are 0.05 seconds apart.
In the processed_motility_paper subdirectory, each .csv file corresponds to a single processed and labeled trajectory (meaning of labels: run corresponds to motile swimming phases of bacteria whereas turn correspond to the intermittent non-motile phases). This dataset was used in Ref. [1].

Additionally, inside WT_025 and WT_03 datasets, a third subdirectory exists, namely, processed_chemotaxis_paper that contains labeled trajectories that were used in Ref. [2]. The spatial and temporal resolutions as well as the run-turn distinction criterion are identical to Ref. [1].

References

1. Agniva Datta, Sönke Beier, Veronika Pfeifer, Robert Großmann, and Carsten Beta. "Bacterial swimming in porous gels exhibits intermittent run motility with active turns and mechanical trapping." Scientific Reports 15 20320 (2025). URL
2. Sönke Beier, Veronika Pfeifer, Agniva Datta, Robert Großmann, and Carsten Beta. "Deciphering the dual chemotaxis strategy of bacteria in porous media." arXiv:2503.05286 (2025). URL
3. Veronika Pfeifer, Sönke Beier, Zahra Alirezaeizanjani, and Carsten Beta. "Role of the two flagellar stators in swimming motility of Pseudomonas putida." mBio 13(6) e02182-22 (2022) URL

Ref. [1] is based on the data in:

• `/WT_025/processed_motility_paper'
• `/WT_03/processed_motility_paper'
• `/motAB_025/processed_motility_paper'
• `/motCD_025/processed_motility_paper'

Ref. [2] is based on the data in:

• `/WT_025/processed_chemotaxis_paper'
• `/WT_03/processed_chemotaxis_paper'