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Through-focus scanning optical microscopy (TSOM) is a model-based optical metrology method that involves the scanning of a target through the focus of an optical microscope. Unlike a conventional optical microscope that directly extracts the diffraction-limited optical information from a single in-focus image, the TSOM method extracts nanometer scale sensitive information by matching the target TSOM data/image to reference TSOM data/images that are either experimentally or computationally collected. Therefore, the sensitivity and accuracy of the TSOM method