Particle detection is based on "Analyze Particles" in ImageJ. It probably could also be used in spot detection, not limited to centromere.
This macro is described in Bodor et al. (2012). The macro recognizes centromere or kinetochore foci in Delta Vision or TIFF images and determines their centroid position. Fluorescent intensities are then measured for each centromere by placing a small box around the centroid position of the centromere. The peak intensity value within the box is corrected for local background by subtraction of the minimum pixel value. This process results in an accurate measurement of large numbers of centromere or kinetochore-specific signals.
Following papers uses CRaQ (picked up, maybe more):