The aim of this repo is to quickly find and analyze the position of spherical particles (beads, cells, droplets...) in microfluidic channels. Because of the nature of the experiments (high Re, high FPS, high resolution), the traditional cineRead.m and analysis scripts would take too long. The data for this project is located in Drobo.
To speed up the process, the raw .cine data is read directly from Drobo, using cineRead2.m, which reads only a specified region of each movie frame. The analysis is based on the assumption that the particles are focused! If the particles are not focused, or the channel is not straigh with respect to the field of view, it won't work.
To find the particles we use the MATLAB function findpeaks.m. One should be familiar with its inner workings before trying to analyzed any data, as the results are completly determined by the input parameters. The detection and analysis is carried out in Droplet_Detection_fixed_Xeq.m. There's also the opposite analysis (find the "Xeq" at specific channel position) in Droplet_Detection_find_Xeq.m. All the analysis parameters and results are saved to analyzed.xlsx.
Present in utils there's also scripts that will compare the results to random distributions of particles, and in extras old functions, and essential files like LinLUT.mat and importfile.m
When running the code on MATLAB, make sure to import all the subfolders, and run one block of code at a time. Check the output (often some plot) and evelaute the results. If necessary change parameters and re-run block.