Repeated localizations of single molecules in one frame may occur due to overlapping fitting sub-regions when using the multiple-emitter analysis approach. To deal with the problem, ThunderSTORM uses a post-processing method suggested by Huang et al. [1]. Here molecules with a mutual distance smaller than their localization uncertainty are grouped together, and in each group, only the molecule with the smallest localization uncertainty is kept. The other molecules are rejected. ThunderSTORM generalizes this algorithm by allowing users to specify the distance threshold for grouping the molecules as a mathematical expression. A different distance threshold can be applied to individual molecules if the mathematical expression results in a vector. The same distance threshold is applied to all molecules if the result is a scalar.