We report the direct transmission electron microscopy observation of spin structure transformations in nanoscale Permalloy zigzag wires due to Joule heating during the injection of current pulses. This heating is sufficient to overcome the energy barriers separating the different metastable domain wall spin structures. Due to the large energy barriers these are stable and observable at room temperature by off-axis electron holography and Fresnel imaging. The interaction between different domain walls is probed and the main pinning mechanism is determined to be the edge roughness. In addition to transformations, we also report on thermally assisted domain wall hopping between two pinning sites and structural changes that occur when the samples are subjected to even higher current pulses. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)