The atom probe microscope provides a flexible platform for high resolution mass spectrometry, field desorption microscopy, field ion microscopy and atom probe tomography. Significantly, by combining various information from these modalities, it has recently become possible to discern local crystallographic information. This innovation changes the way that we use the instrument—from a tool that was primarily for microanalysis to one that serves as an holistic microscope. This lecture will present recent developments undertaken primarily at the University of Sydney in atom probe microscopy. The post-experimental data workflow is reviewed in detail. Frontiers in mass spectrometry, the tomographic reconstruction, analysis and visualisation will be discussed. On the basis of these developments, it is proposed that an exciting era of integration is opening up, where computational techniques such as density functional theory approaches, and atomic-resolution microscopy can solve problems that were previously difficult or impossible by one approach alone.