Functional imaging allows the quantification of biochemical or biophysiological changes in-vivo through the visualization of the spatial distribution and temporal changes of administrated radiopharmaceuticals. Instrumentation advances such as PET-CT (positron emission tomography - computed tomography) and PET-MR (positron emission tomography - magnetic resonance), improvements in image processing and reconstruction, the development of target and disease-specific radiotracers and improved kinetic modelling techniques, have substantially enhanced our ability to measure functional changes in normal and diseased states. Various combinations of these advances and refinements are now used in routine clinical practice for patient care. In this paper we review recent literature on software developments and applications in image restoration, motion correction, kinetic analysis, and image processing in the field of functional imaging.