flagella3D

Code for analyzing helical flagellum diffusing in 3D acquired using the OPM described here

See also https://github.com/fdjutant/6-DOF-Flagella

scripts

contains a record of data analysis and other calculations.

2022_04_19_diffusion_analysis.py

Old data analysis script

2022_06_15_diffusion_analysis.py

The primary data analysis script

2023_02_13_plots_for_figures_3_and_4.py

Extract data for figures 3, 4, and S6, as well as our experimental non-dimensionalized propulsion matrices for the table in Fig. 4d

2022_04_27_syn-diffusion.py

Simulation used in figure S5

Comparing non-dimensionalized propulsion matrix values to previous work

See 2022_07_04_compute_chattopadhyay_abd.py, 2022_07_04_rodenborn_abd_results.py, and 2022_07_04_compute_purcell_abd_table1.py

modules

contains code for computing mean-squared displacement (MSD) values

moviecommands

scripts for working with naparimovie

running

To run this code, first create a conda environment with python 3.9, activate your environment, then navigate to this directory and run

pip install -e .

which will run the setup file and install all required packages to your current environment