Release of TraJClassifier - Classification of diffusion trajectories

fiji
imagej
plugin

#1

Dear community,

I would like to put your attention on my TraJClassifier plugin for diffusion trajectory classification. It builds upon trackmate and classifies diffusion trajectories into 4 classes: normal (or free) diffusion, confined diffusion, anomalous diffusion and directed motion.

Here is a little example:
The following figure shows several cells that are gathered within the field of view (left image). While cell borders are not visible in this focal plane, nuclear envelopes stand out clearly under darkfield illumination (white arrows). A total of 246 particle trajectories were identified as either normal diffusion (red), confined diffusion (yellow), anomalous diffusion (green) or directed motion (magenta). Boxed areas (A-D) show selected cases of directed motion:


It available since a few month but I didn’t announce it because the corresponding PLOS ONE publication was not online! Now it is:

Here the corresponding wiki website:

Best,
Thorsten


#2

Hey Thorsten,
i have tested TraJectory Classifier with some single particle tracking data. I really like it, as it gives me more information about the tracks as my previous workflow (TrackMate / MSDAnalyzer / Excel). I also really like the “Plot trajectories” function.

However, i am missing a simple “Save Results” function. Is there a way to for example save the results of the confined trajectories? I know that I can save the results as csv and that i can export the tracks, but the MSD data will not be saved. Is there a way to save the data and not loosing the plotting function? Or simple to export the MSDs of the tracks?

Best,
Thomas


#3

Dear @T-Zobel,

sorry for the late reply. I was on vacation.

If you plot a single trajectory a results table with the MSD data should pop up. You can then export the MSD values.

At the moment, it is not possible to export the msd data of all tracks with a single click. This was what you are looking for, right?

Best,
Thorsten


#4

Dear @twagner,
thanks for your reply.

Right, this would be a great option.
Unfortunately, if I plot a single track no result table will pop up. I will check this tomorrow on another workstation on a clean Fiji installation and report how it worked out.

Best
Thomas


#5

@T-Zobel
As you can see, if you click in a results table on Trajectory classifier > Plot trajectory another dialog will pop up which contains the MSD Data:


#6

@twagner
I tried it on three different windows (win10 and win7) computer and with new Fiji installations. In all cases I do not get the MSD Data result table. I can test it also on a Mac, don´t know if it makes a difference.

Best
Thomas


#7

@T-Zobel

I guess I didnt release some changes. I will do that today.

Best,
Thorsten


#8