A microscope-based system for image-guided microscopic illumination of varying patterns on a sample through a plurality of fields of view of the sample, comprising: a microscope comprising an objective and a stage ; an imaging assembly comprising a controllable camera and an imaging light source ; an illuminating assembly comprising a pattern illumination device and an illuminating light source which provides an illuminating light through an illuminating light path to illuminate the sample (S); and a processing module which is coupled to the microscope , the imaging assembly , and the illuminating assembly , wherein the processing module is configured to perform the following cyclical procedure: - control the imaging assembly to illuminate the sample (S) with the imaging light source such that the camera acquires at least one image of a field of view of the sample (S), - process the at least one image automatically in real-time based on a predefined criterion so as to determine targeted points in the at least one image and so as to obtain a coordinate information of the targeted points, - control the pattern illumination device and the illuminating light source of the illuminating assembly to illuminate the field of view with a pattern corresponding only to the targeted points of the sample (S) according to the coordinate information of the targeted points, and - after all the targeted points having been illuminated by the illuminating assembly , move the stage to a subsequent field of view. a microscope comprising an objective and a stage ; an imaging assembly comprising a controllable camera and an imaging light source ; an illuminating assembly comprising a pattern illumination device and an illuminating light source which provides an illuminating light through an illuminating light path to illuminate the sample (S); and a processing module which is coupled to the microscope , the imaging assembly , and the illuminating assembly , wherein the processing module is configured to perform the following cyclical procedure: - control the imaging assembly to illuminate the sample (S) with the imaging light source such that the camera acquires at least one image of a field of view of the sample (S), - process the at least one image automatically in real-time based on a predefined criterion so as to determine targeted points in the at least one image and so as to obtain a coordinate information of the targeted points, - control the pattern illumination device and the illuminating light source of the illuminating assembly to illuminate the field of view with a pattern corresponding only to the targeted points of the sample (S) according to the coordinate information of the targeted points, and - after all the targeted points having been illuminated by the illuminating assembly , move the stage to a subsequent field of view. - control the imaging assembly to illuminate the sample (S) with the imaging light source such that the camera acquires at least one image of a field of view of the sample (S), - process the at least one image automatically in real-time based on a predefined criterion so as to determine targeted points in the at least one image and so as to obtain a coordinate information of the targeted points, - control the pattern illumination device and the illuminating light source of the illuminating assembly to illuminate the field of view with a pattern corresponding only to the targeted points of the sample (S) according to the coordinate information of the targeted points, and - after all the targeted points having been illuminated by the illuminating assembly , move the stage to a subsequent field of view. <EOS>