Abstract: The present invention provides a method useful for analysis of punctate distribution of supramolecular complexes that are compartmentalized in nuclear microenvironments. In preferred embodiments the method provides quantitative analysis of the assembly of regulatory machinery within the context of nuclear architecture and to provide a mechanistic link with biological control. In other embodiments, the invention provides a method of identifying a molecule by parameters of its subnuclear distribution, comprising the steps of quantifying organizational parameters of domains within subnuclear distributions of a molecule; performing factor analysis on the quantified organizational parameters; performing discriminant analysis on the quantified organizational parameters; comparing the results of the factor analysis and the results of the discriminant analysis to one or more standards, thereby identifying a molecule by parameters of its subnuclear distribution.