1. A method of breast image reconstruction, the method comprising: positioning a breast on a support plate of an imaging system; compressing the breast with a flexible paddle; obtaining imaging data of the breast; estimating a breast thickness profile by at least 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; and performing a three dimensional reconstruction of the breast, the reconstruction including mitigation of effects associated with compression by the flexible compression paddle.