Data and code:
Experiment_List.xlsx -- List of all experiments
Temperature_files [folder] -- IR camera images or thermistor readouts for all trials for which we have the temperature data
Txt files with numbered names -- Centroid trajectory for each segmented trial from Experiment_List.xlsx with file name corresponding to trial number
Data_analysis.ipynb -- Main data analysis file, used to generate most figures. Here, one can also find plots and analysis approaches that didn't make it into the paper.
Naringenin Data Processing-2.ipynb -- data analysis file for naringenin data (Fig 5 in main text)
Switch experiment.ipynb -- data analysis file for the temperature gradient switch experiment
Levy_Exponential_Trajectory_Length.m -- MATLAB script for trying Lévy and exponential fits for the step length data
MSD_AND_PERSISTENCE.m -- MATLAB script for analyzing MSD and persistence lengths
Overlaid_Traj_colored_by_time.m -- MATLAB script for visualizing trajectories
RMSD_last_x_points.m -- MATLAB script for analyzing RMSD
Sample Raw data [folder] -- one sample raw image folder each for thermal gradient and control conditions, along with MATLAB script for segmenting the organisms, and sample outputs (text file with centroid trajectory and trajectory visualizations folder) -- see Readme inside this subfolder. Because it's slow and painful to commit large files to Github (we had to break 2 raw image folders into around 5 commits), we are trying to explore Google Cloud and other options and will update.
Results and places where file/figure outputs from code are found:
Reciprocal BLAST results [folder] -- Folder with our Reciprocol BLAST results , as well as reference papers
PaperFigs [folder] -- Figures in the paper, generated by the various files
RMSD Results - Where the outputs of the MATLAB script, RMSD_last_x_points.m, go
BeadExperiment_Angles.xlsx -- Excel sheet with angles calculated from bead experiment image frames
Neurokit_results_V_many_window_sizes.xlsx -- Excel sheet with neurokit results for various window lenghts, non-overlapping windows
Neurokit_results_V_Overlap_Many_Window_Sizes.xlsx -- Excel sheet with neurokit results for various window lenghts, overlapping windows
Misc Plots - Trajectories that were visualized but weren't included in the paper
Taylor RMSD combined.xlsx -- Combined results for different experiment conditions, generated by above script.