A method 300 of breast image reconstruction includes positioning a breast on an imaging system support plate 150, compressing the breast with a flexible paddle 500, obtaining 305 imaging data, estimating a breast thickness profile by at least one one of placing markers on the breast, performing an image-based analysis of the obtained data, using an auxiliary system, and performing a model-based computation. The three dimensional reconstruction 320 including using a thickness profile of the breast surface in at least one of an iterative reconstruction, a filtered back-projection reconstruction, and a joint reconstruction performed using information obtained from an ultrasound scan. A non-transitory medium having executable instructions to cause a processor to perform the method is also disclosed.
