A scanning microscope system configured for material analysis and mineralogy comprising a first detector and a second detector, and a data-processing system comprising a data-storage component and a segmentation component. The data-storage component is configured for providing image(s) of a sample based on first emissions from a plurality of first scan locations. The segmentation component is configured for determining at least one or a plurality of second scan locations for at least one or a plurality of region(s) of the at least one image. The second detector is configured for detecting second emissions from at least one of the second scan locations of at least one of the regions. The system is further configured for determining the second scan location(s) for the region(s) and detecting the second emissions from the at least one of the second scan locations of the at least one of the regions in parallel.