Based on Extraction of spots in biological images using multiscale products , Jean-Christophe Olivo-Marin Pattern Recognition 35 . This plugin uses currently some GPL code form Icy. To change the threshold factors using flow variables, you have to change the (2 * (n + 1) - 1)th value of the scaleConfig array. For example if you want to change threshold factor 0, you have to change value (2 * (0 + 1) - 1) = 1 of the scaleConfig, or if you want to change threshold factor 2 you have to change the (2 * (2 + 1) - 1) = 5th value in the scaleConfig array.