Electron microscopy has been instrumental in the study of autophagy. Here, we will report on the range of advanced techniques in electron microscopy which have been utilised to elucidate the origin, expansion and fusion of the phagophore with the lysosome with particular focus on electron tomography, volume EM, immuno EM and cryofixation. Data from this research has revealed an intriguing look into the biogenesis of the phagophore as well as information relating to its expansion and elongation. We have also idenified the phagophores capacity to form membrane contact sites with surrounding organelles as well as visualise the mechanism the phagophore uses to migrate towards the lysosome for docking.