Reconstruction of the joint state of a two-mode Bose-Einstein condensate

We propose a scheme to reconstruct the state of a two-mode Bose-Einstein condensate, with a given total number of atoms, using an atom interferometer that requires beam splitter, phase shift and non-ideal atom counting operations. The density matrix in the number-state basis can be computed directly from the probabilities of different counts for various phase shifts between the original modes, unless the beamsplitter is exactly balanced. Simulated noisy data from a two-mode coherent state is produced and the state is reconstructed, for 49 atoms. The error can be estimated from the singular values of the transformation matrix between state and probability data.