Visualising the Charge and Cooper Pair Density Waves in Cuprates This thesis reports on the use of scanning tunnelling microscopy to elucidate the atomic scale electronic structure of a charge density wave revealing that it has a d symmetry form factor hitherto unobserved in nature. It then details the development of an entirely new class of scanned probe: the scanning Josephson tunnelling microscope. This scans the Josephson junction formed between a cuprate superconducting microscope tip and the surface of a cuprate sample thereby imaging the superfluid density of the sample with nanometer resolution. This novel method is used to establish the existence of a spatially modulated superconducting condensate something postulated theoretically over half a century ago but never previously observed. Unconventional Superconductivity and Density Wave Order in Cuprates Spectroscopic Imaging STM (SI STM) Sub Lattice Segregated SI STM in Cuprates Atomic scale Electronic Structure of the Cuprate d symmetry Form Factor Charge Density Wave The Scanned Josephson Tunnelling Microscope Pair Density Waves in Cuprates Detection of a Cooper Pair Density Wave in Bi2Sr2CaCu2O8+δ Summary and Future Directions.