Method and system for generating a diffraction image comprises acquiring multiple frames from a direct-detection detector responsive to irradiating a sample with an electron beam. Multiple diffraction peaks in the multiple frames are identified. A first dose rate of at least one diffraction peak in the identified diffraction peaks is estimated in the counting mode. If the first dose rate is not greater than a threshold dose rate, a diffraction image including the diffraction peak is generated by counting electron detection events. Values of pixels belonging to the diffraction peak are determined with a first set of counting parameter values corresponding to a first coincidence area. Values of pixels not belonging to any of the multiple diffraction peaks are determined using a second, set of counting parameter values corresponding to a second, different, coincidence area.