Correcting pattern noise projection images includes acquiring a set of projection images with an optical tomography system including a processor, where each of the set of projection images is acquired at a different angle of view. A threshold is applied to each projection image produce a set of threshold images. Each threshold image may optionally be dilated to produce a set of dilated images that are summed to form an ensemble image. Each of the dilated images is processed to produce a set of binary images. The set of binary images are summed to form an ensemble mask. The ensemble image is divided by the ensemble mask to yield a background pattern noise image. Each projection image is multiplied by a scaling factor and divided by the background pattern noise to produce a quotient image that is filtered to produce a noise corrected projection image.