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

Abstract

Some embodiments relate to a computer system for determining a structural image of a sample. The computer system is configured to receive and process raw measured data produced by a scanning microscope and being indicative of at least one scan dataset (I)acquired in a scan session and corresponding to a sequence of N measurements on a sample located in proximity to a focal plane of the scanning microscope. Each measurement includes data provided by M detection channels associated with M-segment detector (M≥3). The computer system includes a data analyzer capable of processing 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 single scan dataset.