A method of operating a data analysis system for analyzing microscopic data acquired by a charged particle microscope from an object comprising a plurality of sample particles; wherein the microscopic data comprises X-ray intensity measurement data and charged particle intensity measurement data, which have been acquired by scanning a primary beam of the charged particle microscope in a first and a second scanning region; wherein the first and the second scanning regions are adjacent to each other or partially overlapping with each other; wherein the method comprises: identifying at least one sample particle of the plurality of sample particles, which is at least partially located in the first and in the second scanning region; and generating X-ray intensity data assigned to surface locations of the identified sample particle depending on at least a portion of the X-ray intensity measurement data of the first scanning region, at least a portion of the X-ray intensity measurement data of the second scanning region, and further depending on at least a portion of the particle intensity measurement data of the first and the second scanning regions; wherein the generating of the assigned X-ray intensity data comprises: generating, for each of the first and second scanning regions, an image depending on the particle intensity measurement data of the respective scanning region; and determining positions of impingement locations of the primary beam in the first and in the second scanning region relative to each other; wherein at the impingement locations, the portions of the X-ray intensity measurement data of the first and second scanning regions have been acquired; characterized in that the determining of the positions of the impingement locations relative to each other is performed depending on the image of the first scanning region and the image of the second scanning region; wherein the determining of the positions of the impingement locations relative to each other comprises: (a) determining a position and an orientation of the image of the first scanning region relative to the image of the second scanning region; and/or (b) comparing the image of the first scanning region with the image of the second scanning region. identifying at least one sample particle of the plurality of sample particles, which is at least partially located in the first and in the second scanning region; and generating X-ray intensity data assigned to surface locations of the identified sample particle depending on at least a portion of the X-ray intensity measurement data of the first scanning region, at least a portion of the X-ray intensity measurement data of the second scanning region, and further depending on at least a portion of the particle intensity measurement data of the first and the second scanning regions; generating, for each of the first and second scanning regions, an image depending on the particle intensity measurement data of the respective scanning region; and determining positions of impingement locations of the primary beam in the first and in the second scanning region relative to each other; wherein at the impingement locations, the portions of the X-ray intensity measurement data of the first and second scanning regions have been acquired; (a) determining a position and an orientation of the image of the first scanning region relative to the image of the second scanning region; and/or (b) comparing the image of the first scanning region with the image of the second scanning region.