Systems and methods for attenuation compensation in nuclear medicine imaging based on emission data are provided. One method includes acquiring emission data at a plurality of energy windows for a person having administered thereto a radiopharmaceutical comprising at least one radioactive isotope. The method also includes performing a preliminary reconstruction of the acquired emission data to create one or more preliminary images of a peak energy window and a scatter energy window and determining a body outline of the person from at least one of the reconstructed preliminary image of the peak energy window or of the scatter energy window. The method further includes identifying a heart contour and segmenting at least the left lung. The method additionally includes defining an attenuation map based on the body outline and segmented left lung and reconstructing an image of a region of interest of the person using an iterative joint estimation reconstruction.