The invention relates to a method and apparatus for configuring an imaging system to compensate for fixed pattern noise, variations in pixel values captured from an image sensor that vary according to a fixed pattern. In a method for configuring an imaging system for compensating an additive term component of fixed pattern noise, a pixel array is exposed to a scene of known radiance and an average white value is determined for each pixel of an array. Each average white value is compared to a predetermined reference value to determine a correction value for each pixel. In a method for configuring an imaging system for compensating both an additive and multiplicative component of fixed pattern noise, a pixel array is exposed to a first scene having a first known radiance, and frames of the scene are captured, and then the array is exposed to a second scene having a second known radiance and frames of the second scene are captured. After first and second average white values are determined for each pixel additive and multiplicative term correction values for each pixel are then determined by solving for a system of equations relating the first and second average white values and first and second scene radiances. Correction values can be utilized to correct pixel values of a frame of image data, and a decoding algorithm for attempting to decode a frame of image data including corrected pixel values can be activated.