A method for operating a flow cytometer having a forward scatter detector, a side scatter detector, and a plurality of fluorescent emission detectors (160a-f), each fluorescent emission detector corresponding to a fluorescence channel, comprising: measuring one or more forward scatter values at the forward scatter detector, one or more side scatter values at the side scatter detector, and one or more fluorescence intensity values at one or more of the plurality of fluorescent emission detectors for one or more events of an unstained sample using the flow cytometer; associating one or more fluorescence intensity values-for one of more of the plurality of fluorescent emission detectors with one or more forward scatter-side scatter plot regions based at least in part on the measuring the one or more events of the unstained sample; measuring one or more forward scatter values, one or more side scatter values, and one or more fluorescence intensity values at one or more of the plurality of fluorescent emission detectors for one or more events of a stained sample_using the flow cytometer; determining forward scatter-side scatter plot locations for the one or more events of the stained sample; and for each of the one or more events of the stained sample, subtracting a fluorescence intensity value of the unstained sample associated with the forward scatter-side scatter plot region that contains the forward scatter-side scatter plot location of the stained sample event for at least one of the plurality of fluorescent emission detectors from a measured fluorescence intensity value of the stained sample event at that forward scatter-side scatter plot location measured at the at least one of the plurality of fluorescent emission detectors. measuring one or more forward scatter values at the forward scatter detector, one or more side scatter values at the side scatter detector, and one or more fluorescence intensity values at one or more of the plurality of fluorescent emission detectors for one or more events of an unstained sample using the flow cytometer; associating one or more fluorescence intensity values-for one of more of the plurality of fluorescent emission detectors with one or more forward scatter-side scatter plot regions based at least in part on the measuring the one or more events of the unstained sample; measuring one or more forward scatter values, one or more side scatter values, and one or more fluorescence intensity values at one or more of the plurality of fluorescent emission detectors for one or more events of a stained sample_using the flow cytometer; determining forward scatter-side scatter plot locations for the one or more events of the stained sample; and for each of the one or more events of the stained sample, subtracting a fluorescence intensity value of the unstained sample associated with the forward scatter-side scatter plot region that contains the forward scatter-side scatter plot location of the stained sample event for at least one of the plurality of fluorescent emission detectors from a measured fluorescence intensity value of the stained sample event at that forward scatter-side scatter plot location measured at the at least one of the plurality of fluorescent emission detectors.