A method and apparatus for imaging a specimen using a scanning-type microscope, by irradiating a specimen with a beam of radiation using a scanning motion, and detecting a flux of radiation emanating from the specimen in response to the irradiation, in the first sampling session {S1} of a set {Sn}, gathering data from a first collection of sparsely distributed sampling points {P1} of set {Pn}. A mathematical registration correction is made to compensate for drift mismatches between different members of the set {Pn}, and an image of the specimen is assembled using the set {Pn} as input to an integrative mathematical reconstruction procedure.