Moving particle identification and measuring in video

I am involved in the R package bemovi which is doing movable particle identification and measuring based on a video file, recorded e.g. from a microscope (for examples see Videos used for the worked example).

It uses ImageJ to do the processing and therefore Java. The package works, but we regularly have problems caused by Java versions and the whole processing is a bit cumbersome (creating ImageJ macros to do the processing based on a template).

So we would like to switch to another image processor engine and OpenCV seems to be the best option. Could somebody here give their opinion if you think that would be possible using rOpenCV?

It would be great, if we could get some ideas and suggestions in this regard, as one of us have used OpenCV before.

definitely sounds doable.

OpenCV has plenty of low level algorithms for background subtraction, binarization, morphology, connected components/contours, …

I can’t comment on the domain-specific algorithms though.

Thanks a lot - this sounds very promising!

I already found a few approaches to subtract the background, do the binarisation or determine the boundaries of the moving particles.

What I am looking for, is now a way of tracing the particles, i.e. to get trajectories for each particle, and than get morphological measurements from the particle (size, longest diameter, shortest diameter, etc) or export the boundaries of the particles.

Any suggestions how these could be done?