Cone beam volume CT breast imaging is performed with a gantry frame on which a cone-beam radiation source and a digital area detector are mounted. The patient rests on an ergonomically designed table with a hole or two holes to allow one breast or two breasts to extend through the table such that the gantry frame surrounds that breast. The breast hole is surrounded by a bowl so that the entire breast can be exposed to the cone beam. Spectral and compensation filters are used to improve the characteristics of the beam. A materials library is used to provide x-ray linear attenuation coefficients for various breast tissues and lesions.