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 *[e-mail] 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.

2021年7月30日发布的《水生环境及模拟黏液环境中霍乱弧菌运动性》轨迹数据与转向检测代码，作者为Marianne Grognot、Anisha Mittal、Mattia A. Mah’moud、Katja M. Taute*，所属单位：哈佛大学罗兰研究所，地址：美国马萨诸塞州剑桥市埃德温·H·兰德大道100号，邮编02142；*通讯邮箱：[e-mail]。本研究成果发表于《应用与环境微生物学》（*Applied & Environmental Microbiology*）87卷:e01293-21, 2021，论文预印本早期版本可于bioRxiv平台获取，链接：https://doi.org/10.1101/2021.07.06.451398。

本数据集的.mat文件遵循补充附表1（SI Table 1）的命名规则（参见第一列），其中收录的轨迹数据已按论文方法部分所述完成ADMM滤波（ADMM filtering）处理。每个文件包含一个或多个以“V_”开头的Matlab结构体，分别对应补充附表1第二列中的一种培养基或菌株（如数据集2的野生型wt菌株）。每个V结构体包含以下字段：
* `V.Speeds`：细胞数组，每个细胞对应一条运动轨迹。轨迹由包含如下列的数组描述：
- 第1列：帧编号
- 第2-4列：x、y、z轴位置（单位：微米）
- 第6-8列：x、y、z轴瞬时速度（单位：微米/秒）
- 第9列：瞬时速度绝对值（单位：微米/秒）
- 第10列：相邻帧间的方向角变化量（单位：度）
* `V.Parameters`：简化的描述性参数字结构体，仅包含`V.Parameters.fps`字段，用于给出采集帧率（单位：帧/秒）

***** DATASET1_M9MM.mat *****
包含M9MM培养基中按生物学重复分类的所有运动轨迹，文件名以重复编号命名（如`_biotriplicateX`），同时收录用于合并分析的全部重复轨迹文件（`_all`）。

***** DATASET2_WT.mat *****
包含M9MM培养基中野生型（wt）菌株的所有运动轨迹。

***** DATASET3_Sodium.mat *****
按培养基钠离子摩尔浓度分类的所有轨迹。结构体名称对应钠离子浓度（单位：mM）与ADMM滤波因子，例如`V_1p8_admm08`代表在改性M9MM培养基中添加1.8 mM Na+，且采用因子0.8（而非默认0.3）完成ADMM滤波的轨迹数据。

***** DATASET4_PVP.mat *****
按PVP K90浓度分类的所有轨迹。结构体名称对应培养基中聚合物的百分比（已取整），例如`V_0p9K90`代表所有处于0.9% PVP K90培养基中的轨迹。

***** DATASET5_Mucin.mat *****
包含1.2%黏蛋白培养基中的所有运动轨迹。

**********************************
文件`BugTurns.m`为Matlab函数，可针对上述V_结构体运行，用于检测轨迹中的转向事件。