Tracking centerline of multiple cylindrical structure - fibres

Hi everyone,

I’m a PhD student at The University of Manchester, working on the fatigue and imaging of fibre reinforced composites.
First of all, let me thank you for the Trackmate software, it’s massively helpful although I am struggling to get the most use out of it.

I have a stack of 300 images thresholded from x-ray computed tomography, which contains fibre cross-sections and I am trying to use Trackmate to track/compute the fibre centerlines and generate some morphological information like track length, orientations, azimuth etc. Please find the image below:


As these are not time-lapse but rather just extended in z-direction for 300 frames, I want to compute the centerlines and do some morphological analysis, I have computed maxima/skeletonised them to get the image below, which is essentially one pixel per fibre blob per frame. As the problem is these single fibres are not connected throughout but essentially are a collection of smaller segments. I want them to be labelled or assigned a single track ID and then somehow manage to compute morphological insights.


Also when I use Trackmate for some reason it doesn’t detect blobs correctly if I don’t swap Z/T, and all I can generate is just movements in the same slice, which isn’t true since the blobs are not moving but are extended in Z direction.


Is that possible in Trackmate or any other plugin/macro in ImageJ?

Thanks a lot in advance,
Anuj Prajapati.

Just out of curiosity, if you have a full Z stack, can you skip straight to Skeletonize 2D/3D? Emphasis on the 3D!

Hello @Anuj_Prajapati

I think that what you see here are indeed the centerlines. You somehow tricked TrackMate into thinking this was a time-lapse and it probably gave you the centerlines.

But I am not sure this is the best solution. As RA said, you probably want to directly perform skeletonization in 3D.

1 Like