Particle tracking in video(s)



Hi all,

I was hoping that someone would be able to give me a few pointers with regards to object tracking as I am a novice with regards to this area (I usually work on ‘still’ objects in micro-CT volumes, which are much easier!).

What I have are videos of particles settling in water; I’ve attached a few still frames that show what I’m dealing with. What I’d like to do is to track the particles as they settle, and measure the velocity at which each of these particles is moving. I’d also like to extract some basic quantitative information regarding the particle (e.g., size, shape, grey-scale range, angle of at which particles are settling etc.). I have a problem that some particles are outside the focal area of the camera, and so are out of focus and appear ‘fuzzy’. These out of focus particles I would like to exclude from quantification/measurement of settling.

Would anyone be able to suggest a plugin I could use? I know there are a couple out there and have begun to have a bit of a play but am not sure which one would be best for what I want to do…



Instead of attaching individual files I’ve uploaded a link to a Dropbox folder containing a section of the movie




Trackmate looks like the perfect plugin for this kind of video. Before running it, you should invert the pixels intensities and maybe do a Gaussian filter in order to smooth the noise.

Here you’ll find all you need for installation and usage of Trackmate:


Hi @hadim,

Thanks, I’ve had a play with TrackMate like you suggested and it and its working well. I was wondering if you had any advice regarding selecting spot sizes? The particles in my videos vary in size considerably, and to capture the smaller size range requires a small spot size. However, this results in large particles being represented by more than one tracking dot. Setting a large spot size gets around this problem but obviously excludes all small particles. What would your suggestion be to tackle this problem?



Is there also a way to assign a new track name/id to a track that has been split in the TrackScheme editor?



It might be best to ‘split’ your analysis in two parts?? First segment/track the small particles and get that track data… and then segment/track the larger particles - being sure to take care of overlapping data, etc.

Would you be able to upload a dataset - so we can see/test your images/objects?



I would also suggest you to split your analysis in two parts.

That being said that would be nice to add a detector to Trackmate that run two detections with two différent diameters. It should not be that hard since it would basically be a wrapper over the already existing detectors.


Super idea @hadim ! I posted an issue on Trackmate’s github page…



After splitting… just press the Redo-Layout button and then you can rename the new track by double-clicking on the title cell above it.

eta :slight_smile:


Thank’s everyone, I’ve had a go at splitting my analysis into two parts and it seems to be working!