In order to analyse the tracks generated from the @trackmate program, I was using @msdanalyzer ([@msdanalyzer ]. Again thank you for a wonderful program and the detailed explanation in the book chapter The NEMO Dots Assembly.
I understand the tutorial content on how to generate tracks for Brownian, Directed and Confined motion and the tutorial has been really helpful.
For synthetic tracks for the confined or directed motion, we define the parameters beforehand such as N_Particles, N_TIME_Steps, SIZE, Ltrap, Ktrap, Initial position of the particle, etc, however, I am having a little problem with the actual experimental data. I want to separate the trajectories depicting the confined motion and then plotting an MSD for only confined trajectories.
On adding all the tracks (using ma.addall()) from different cells, how shall I now define these parameters to determine the confined motion for the experimental data? Suppose, for each image stack, the number of frames is 5000 each for 10 cells in the same condition then should I put N_Time_Steps as 5000 or 50000? The same goes for the input value for the number of particles detected over all the frames and how shall I then define the particle initial position in this case?
Is there a preprocess I need to do for the experimental data in order to reach to point to separate trajectories showing confined, directed and Brownian?
When these trajectories are plotted, are the colour of tracks based on the track displacement and if not, how can we display tracks based on their displacement value?