1. An image pickup system for performing noise reduction processing on signals from an image pickup element, comprising: first noise estimating means for estimating a first amount of noise related to a target pixel in the signals for which the noise reduction processing is performed, from a signal level of the target pixel, by using an estimation reference for estimating a given first amount of noise related to a given pixel in an arbitrary signal based on inputs of a signal level of the given pixel and information given independently of the signal level of the given pixel; extraction means for extracting similar pixels that resemble the target pixel from a neighborhood of the target pixel based on the target pixel and the first amount of noise; second noise estimating means for estimating a second amount of noise from the target pixel and the similar pixels; and noise reduction means for reducing noise of the target pixel based on the second amount of noise.