From ZEN help: "evaluates two characteristics, the intensity (first moment) and the size (second moment). These two moments are calculated for every localized bead. Then the beads are sorted according to these characteristics, resulting in two sorted lists of beads. The beads that are closer to the medians in both orderings are assumed to have higher quality. The Beads quality defines how far the beads characteristics (intensity and size) may be away from the median value. The smaller the threshold, the closer beads should be to the median."