I’ve played around with the @msdanalyzer MATLAB script for recorded 2D particle tracks analyzed with Trackmate.
As I don’t have any Z dimension, I’ve excluded them when importing the tracks to MATLAB, like so:
[tracks, clipZ] = importTrackMateTracks('/path/to/track.xml');
This doesn’t remove the Z coordinates entirely. It just sets them all to 0. However, @msdanalyzer refuses to take the .xml if I don’t run it with 3 dimensions. It also refuses to take a file where I’ve manually removed all the Z-coordinates (e.g. so the XML file only shows
<detection t="0" x="48.31941812287789" y="23.572161216923433" />.
Will this affect the way the final diffusion coefficient is calculated?