Plotting Velocity vs. Time with TrackMate


#1

@tinevez

I am interested in Plotting Velocity vs Time for tracks in Trackmate, but cannot come up with any way to do this.

Any help would be appreciated!


#2

Dear @Jacob_Goldberg,

what exactly do you want to plot: the velocity between two frames over time? If so, do your tracking and click Next after the display options dialog. Select the Links tab and make Time (mean) the x feature and Velocity the y feature. Click Plot features:

Best,
Stefan


#3

Thanks @stelfrich

I will try to describe in a bit more detail: I imagine a scatter plot of velocity vs time (just like you displayed). I imagine there is a separate line in the scatter plot for each track in the image being analyzed. The goal of the plot would be to compare how the velocities of different particles are changing over time.

It looks like the plot you posted may be what I am interested in, but I am not sure, because when I try what you mentioned, I end up with a completely blank plot. Hmmm.


#4

Could you maybe try to have spots in subsequent frames and try again?


#5

@stelfrich : [quote=“stelfrich, post:4, topic:4855”]
Could you maybe try to have spots in subsequent frames and try again?
[/quote]

You are right! With the spots in subsequent frames, the plot is exactly what I am looking for.

Unfortunately it is not feasible to do my analysis for every frame.

My data is not amenable to automatic tracking with TrackMate, so all tracking is manual. I am not really tracking spots, but rather the growing tip of a polarly expanding cell (pollen tube). Each time series has a very large number of cells to be tracked, and the temporal resolution is relatively high. (For reference, each time series has 121 time points, and I can effectively track the cell tip movement/growth with 5-10 spots)

Is there any way to have TrackMate to use the average velocity between two spots for all time points between those spots in order to produce this type of plot without spots in all frames?

Alternatively, is there a way to interpolate spots linearly between those that I have already placed so that there can, in fact be spots on all frames.

Thank you


#6

I am not aware of such an option.

I assumed that this what TrackMate does. But I think I have found a problem with the computation of Mean(time). Could you open your image sequence and open Image > Properties. I have a feeling that the Frame interval might be set to 0. If so, could you change that to whatever the time between two acquisitions was for your experiment and follow up?


#7

Worked perfectly. I realized I was misleading you a bit when I posted about the blank plot. The test file I was using did not have proper temporal and spacial parameters assigned to it, like you thought, when all my other files do. I tried with another file with the proper frame interval set and it worked fine.
The improper file is actually another problem I am having. @stelfrich I would appreciate it if you could take a look at it.

Thanks again for your help!