The invention relates to a method of examining a sample using a charged particle microscope, comprising the steps of providing a charged particle beam, as well as a sample; scanning said charged particle beam over said sample at a plurality of sample locations; and detecting, using a first detector, emissions of a first type from the sample in response to the beam scanned over the plurality of sample locations. Spectral information of detected emissions of the first type is used to assign a plurality of mutually different phases to said sample at said plurality of sample locations. Information relating to at least one previously assigned phase and its respective sample location is used for establishing an estimated phase for at least one other of the plurality of sample locations. Said estimated phase is assigned to said other sample location. A control unit is used to provide a data representation of said sample containing at least information on said plurality of sample locations and said phases.