System and method for extraction of structural data of a sample from scan data

A computer system for determining a structural image of a sample, the computer system being configured for data communication with a measured data provider to receive raw measured data produced by a scanning microscope, the raw measured data being indicative of at least one scan dataset acquired in a scan session, the scan dataset (IM)N corresponding to a sequence of N measurements on the sample located in proximity to a focal plane of the scanning microscope, each measurement including data provided by M detection channels associated with M-segment detector (M≥3), the computer system comprising a data analyzer configured and operable to process said at least one scan dataset to compensate image shifts induced by off-axis detection channels for sample features at defocus plane to thereby obtain data indicative of parallax corrected scan image of the sample which enables separation between phase and depth information and extraction of a depth contrast image of the sample from the at least one scan dataset.