This algorithm utilises openPIV Python package for analysing the collective movements of particles in biological systems.
PIV_main.ipynb contains code for generating:
- (a) velocity field video;
- (b) velocity distribution histogram.
The folder imageJ_macro_code contains macro code that performs the following functions:
- (a) auto brightness & contrast;
- (b) brightness adjustment;
- (c) adjust contrast and despeckle;
- (d) cropping images;
- (e) FFT bandpass filter;
- (f) combine image sequence into stack.
S2N_checking.py contains code for checking the signal to noise ratio of the images after post-processing.
To run the code, download the repository and run it on any IDE that supports .ipynb files.