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We present a formalism for self-calibrating tomography of arbitrary dimensional systems. Self-calibrating quantum state tomography was first introduced in the context of qubits, and allows the reconstruction of the density matrix of an unknown quantum state despite incomplete knowledge of the unitary operations used to change the measurement basis. We show how this can be generalized to qudits, i.e. d-level systems, and provide a specific example for a V-type three-level atomic system whose transition dipole moments are not known. We show that it is always possible to retrieve the unknown state and process parameters, except for a set of zero measure in the state-parameter space.

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