A method and apparatus for diagnosing and/or calibrating underperforming pixels in detectors in a small pixelated photon counting CT system utilizes a series of tests on image data acquired in-situ as part of a series of calibration scans in the CT system. Tests are performed on the acquired data to determine the existence of underperforming pixels within the detectors such that the information acquired by those pixels can be replaced by alternate data from surrounding pixels (e.g. by interpolation). The underperforming pixels are stored in “bad” pixel tables and may be specific to a type of image (e.g., spectral or counting) and a specific protocol.