The present invention provides a method for estimating crystal efficiency in a PET detector that takes axial compression into account. It does so via an iterative methodology in which a μ-map is first generated and then is used to obtain a solution for the equation L ⁡ ( ɛ i ) = ∑ n ∈ N ⁢ ⁢ y n ⁢ log ⁢ ∑ i , j ∈ span ⁢ ⁢ g ij ⁢ ɛ i ⁢ ɛ j ⁢ x ij - ∑ i , j ∈ span ⁢ ⁢ g ij ⁢ ɛ i ⁢ ɛ j ⁢ x ij , wherein gij is a geometric factor for LOR(i,j), εi and εj are the efficiencies for crystal i and crystal j, and xij is the line integral of the source distribution along LOR(i,j). Once efficiencies are determined, they are used to calibrate the PET detector.