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This paper describes a qualitative research methodology developed for experimental studies of collaborative visual analysis. In much of this work we build upon Herbert H. Clark's Joint Activity Theory to infer cognitive processes from field experiments testing collaborative decision making over data. As is true of any methodology, it provides the underlying conceptual structure and analytic processes that can be adapted by other researchers to devise their own studies and analyze their results. Our focus is on collaborative use of visual information systems for aircraft safety analysis, however the methods can be/have been extended to other tasks and analysts.