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.
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.
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.