Using Manual Tracking and TrackMate to Measure Distances in 3D

Trying to measure the length of flexible cell appendages in a confocal z-stack (in one time point). They wind through all three planes (X, Y, Z), and we’d like to track them through the three planes and measure their length from tip to tail. Manual Tracking seemed to just measure separate slices in 2D, allowing us to add those segment lengths up, but still not giving us a more accurate 3D measurement. TrackMate has far more features than I need and I’m not sure what settings I need to select as I progress through the windows. Any help would be appreciated! Thanks!

I am struggling with this as well! Any help would be much appreciated.


I would say TrackMate is not the best tool to do so.
It seems like you have a single time-point. TrackMate does track particles has they move through time.
There is little data in your question, but it seems what you need is something like the Simple Neurite Tracer.

Thanks for the response. I hear what you are saying–yes, we have a single time point and TrackMate tracks particle movement through time. However, when opening “Manual Tracking with TrackMate” with one of our 3D z-stacks open, a window appears saying, for example, “It appears this image has 1 timepoint but 46 slices. Do you want to swap Z and T?” This led me to believe we could get the plugin to recognize our z-slices as images taken in different time points, meaning the plugin could work with our image stack. As a result, I thought we would be able to track (and then measure the distance of) a cilium (the flexible cell appendage referred to in my first post) through three dimensions. The distances Manual Tracking gives us are measured only in 2D, though, which is not what we want. I do appreciate the suggestion, but NeuronJ (Neurite Tracer) also only measures in 2D. My additional questions are: 1) Do you know of any plugin that will allow us to measure lengths/distances for a structure that exists in three dimensions (cilia bend/snake around); 2) What is the difference between the capabilities of “Manual Tracking” and Manual “Tracking with TrackMate”? Thanks for your time and any assistance you may be able to provide. It is much appreciated!

Hi @Lasagna

Ok for what you wanted to do, TrackMate is just NOT the right tool. Do not use the artificial swap Z and T it cannot lead to a proper approach.
As for the differences with Manual Tracking, I do not know.

Finally, Simple Neurite Tracer can do what you want, as I said above.