Hi,
I have done some time lapses last year of my cells moving on different substrates. I already analysed these videos with Fiji and the TrackMate PlugIn for velocity, track displacement etc.
Now, I would like to plot the trajectories/directions of their movement.
After some research, I have found the rose plot as a good way to both show velocity and also the direction, but wasn't able to plot it.
I have already tried some R and MATLAB tips online (but as I am not very proficient in both, it didn't work too well) and also found a Chemotaxis and Migration Tool (which didn't work because of format issues...).
If anyone, knows a good way to plot these info, I would be so grateful.
I'd suggest you contact some specialist person - Ibidi technical support might be able to help you somehow.
All the best
Teresa
Hi.
How do you collect trajectories? As somekind of txt file with 4 colums for example:
x-coord y-coord z-coord time
Can you attach some sample? And did you try Python (Numpy, Matplotlib)?
Kind Regards
Hi Lisa, first you have to find a way to export the tracking data from FIJI into an excel file or .csv. These formats can be read by any programming environment. For example in Matlab try this:
num=xlsread(insert filename here);
% Find the measurement that interests you, for example velocity
vdata=num(:, correct column);
Then you can generate a number of complex plots including rose().
- Badges
- Science topic
- Similar topics
- Mathematics
- Statistics
- Statistical Software
- R Statistical Package