  Tomography is an indispensable part of quantum computation as it enables
diagnosis of a quantum process through state reconstruction. Existing
tomographic protocols are based on determining expectation values of various
Pauli operators which typically require single-qubit rotations. However, in
realistic systems, qubits often develop some form of unavoidable stray coupling
making it difficult to manipulate one qubit independent of its partners.
Consequently, standard protocols applied to those systems result in unfaithful
reproduction of the true quantum state. We have developed a protocol, called
coupling compensated tomography, that can correct for errors due to parasitic
couplings completely in software and accurately determine the quantum state. We
demonstrate the performance of our scheme on a system of two transmon qubits
with always-on $\textit{ZZ}$ coupling. Our technique is a generic tomography
tool that can be applied to large systems with different types of stray
inter-qubit couplings and facilitates the use of arbitrary tomography pulses
and even non-orthogonal axes of rotation.
