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; 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 with the imaging light source such that the camera acquires at least one image of a field of view of the sample, - 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 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; 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 with the imaging light source such that the camera acquires at least one image of a field of view of the sample, - 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 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 with the imaging light source such that the camera acquires at least one image of a field of view of the sample, - 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 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.