Tracking and counting ''shooting stars'' like particles

Hello all,

I wanted to ask you about advice how to process my data which are basically recordings of tube with running liquid with occasional bubbles flowing from left to right (I can provide more details if needed). Main information what I need is a number of bubbles, additionally, I need velocity and size.

Below you can find .gif of raw data footage.

Result of 1500V_20pulsu_5mls_before

I was able to clean the footage from static background (dirt on tube, etc.) via fiji. Basically, I created Z project (projection type=AVG) and then subtract that image from all images in stack. That gave me better footage.

Result of 1500V_20pulsu_5mls_after

After that, I was feeling confident to try some tracking plugins. I tried Trackmate and Particle Tracker (Mosaics), however mostly unsuccessfully.

I think my problem is that the bubbles have different velocity so sometimes they are in view 2-3 slides and sometimes only 1 slide and also they move only in one direction. That, I thought was actually advantage but I think tracking plugins (or at least those i used) are made for different type of movement and velocity.

Can you please give me advice, how to make this? Below you can find cleaned and shortened testfile in .tiff.

In the end i would like to automate this process via macro as I have quite a lot of recordings, but that won’t be any problem.

Thank you,


Hi Šimon,

Can you maybe infer the velocity of your bubbles by measuring the length of their tracks in single frames and dividing this by the acquisition/exposure time per frame?


Hi Anne,

thank you for the suggestion. Yea, I bealive I can, however velocity is somewhat secondary info I need. Mainly I need information about particle count, which is rather tricky so far…

Dear Hadson,
I think the problem of using algorithm like Trackmate and Mosaic is that they strongly infer a circle-like shape, and your images have objects to track which are more like straight lines.

I think you should approach them with more generic tracking algos maybe starting to explore from here:

The other thing you shold maybe is to increase the frame rate if possible to facilitate the tracking.

Emanuele Martini