I have been using TrackMate and selecting my tracks from my single-particle tracking videos. So far, I am able to plot and analyze the MSD for all my tracks in their full length by using MSDanalyzer by @tinevez. However, I’m curious if there is a way to just get the MSD curves for the first x number of steps (let’s say for example, the first 6 steps in each track)?
At present I’ve managed to import just the first 6 time points, but when performing the analysis I’ve run into several issues, but the one I’m struggling with the most is that there are matrix mismatch issues. For instance if I use the first 6 steps, and most of my particles show up for 6 consecutive frames (e.g. 1,2,3,4,5,6) but sometimes I encounter particles where one or more frames are missing (e.g. 1,3,4,5,7,8). In these instances, the matrix created for particles with missing frames are bigger than the matrix created for particles that show up in consecutive frames.
Any help would be great appreciated, thanks!