Problem with the particle detection using MosaicIA

Hi all,
I was trying to do interaction analyses by the MosaicIA suite but I encountered problems in the very first step which is to identify particles in my images.
I used the Particle Tracking 2D/3D function in the Mosaic suite to find good parameters (radius, cutoff, and percentile r) and I could detect particles perfectly. But when I used the same parameters under the Interaction Analysis mode, I got either no particles at all or weird detected areas. It seemed that the software considered dark as signal and bright as background…
I am wondering if anyone had the same problem. How should I do to detect the correct particles?
Thanks a ton in advance!
Qinyu