An imaging system capable of black level calibration includes an imaging pixel array, at least one black reference pixel, and peripheral circuitry. The imaging pixel array includes a plurality of active pixels each coupled to capture image data. The black reference pixel is coupled to generate a black reference signal for calibrating the image data. Light transmitting layers are disposed on a first side of a pixel array die including the imaging system and cover at least the imaging pixel array and the black reference pixel. A light shielding layer is disposed on the first side of the pixel array die and covers a portion of the light transmitting layers and the black reference pixel without covering the imaging pixel array.