Nuclear medicine imaging modalities assist commonly in surgical guidance given their functional nature. However, when used in the operating room they present limitations. Pre-operative tomographic 3D imaging can only serve as a vague guidance intra-operatively, due to movement, deformation and changes in anatomy since the time of imaging, while standard intra-operative nuclear measurements are limited to 1D or (in some cases) 2D images with no depth information. To resolve this problem we propose the synchronized acquisition of position, orientation and readings of gamma probes intra-operatively to reconstruct a 3D activity volume. In contrast to conventional emission tomography, here, in a first proof-of-concept, the reconstruction succeeds without requiring symmetry in the positions and angles of acquisition, which allows greater flexibility. We present our results in phantom experiments for sentinel node lymph node localization. The results indicate that 3D intra-operative nuclear images can be generated in such a setup up to an accuracy equivalent to conventional SPECT systems. This technology has the potential to advance standard procedures towards intra-operative 3D nuclear imaging and offers a novel approach for robust and precise localization of functional information to facilitate less invasive, image-guided surgery.