3D trajectory data and code for "Vibrio cholerae motility in aquatic and mucus-mimicking environments"

2021-07-30 Trajectory Data and turn detection code for "Vibrio cholerae motility in aquatic and mucus-mimicking environments" by Marianne Grognot, Anisha Mittal, Mattia A. Mah’moud, Katja M. Taute* Rowland Institute at Harvard 100 Edwin H Land Blvd Cambridge, MA 02142 USA *taute@rowland.harvard.edu Applied & Environmental Microbiology 87:e01293-21, 2021. An earlier version of the manuscript is available on bioRxiv at https://doi.org/10.1101/2021.07.06.451398 The .mat files gather trajectories under dataset numbered as in SI Table 1 nomenclature (column 1). Trajectory position data are ADMM filtered as described in the Methods section of the manuscript. Each file contains one or multiple Matlab structures starting with "V_", each corresponding to one medium (column 2 of SI Table 1) or strain (wt, for dataset 2). Each structure V contains the following fields: * V.Speeds is a cell array where each cell corresponds to one trajectory. The trajectory is described by an array with the following columns: - column 1: frame number - column 2-4 : x, y and z positions (in micrometers) - column 6-8 : instantaneous speed in x, y and z (micrometer per second) - column 9 : absolute value of instantaneous speed (micrometer per second) - column 10 : angular change in direction between frames (degrees) * V.Parameters is a simplified structure with descriptive parameters, containing only the field V. parameters.fps which gives the frame rate of the acquisitions (frames per second) *** DATASET1_M9MM.mat *** All motile trajectories sorted by biological replicate, named after the replicate number (_biotriplicateX), in M9MM. As well as all the motile trajectories from the triplicates gathered for analysis (_all). *** DATASET2_WT.mat *** All motile trajectories of wt strain in M9MM. *** DATASET3_Sodium.mat *** All trajectories sorted by the Na+ molar concentration of the medium The structure's name indicates the [Na+] in mM and the ADMM filtering factor used e. g. V_1p8_admm08 are trajectories in modified M9MM with 1.8 mM Na+, where the ADMM filtering was applied with a factor 0.8 (instead of the default 0.3) *** DATASET4_PVP.mat *** All trajectories sorted by the PVP K90 concentration. The structure's name indicates the (rounded) polymer % in the media (e. g. V_0p9K90 is all trajectories in 0.9% PVP K90) *** DATASET5_Mucin.mat *** All motile trajectories in 1.2% mucin. *** The file BugTurns.m is a Matlab function that can be run on the V_ structures to detect turn events.