Neurodegenerative diseases, including Alzheimer's and Parkinson's diseases, are characterised by the progressive, irreversible loss of neuronal tissue accompanied by protein aggregation in the brain. Although identified as a leading pathology, the role of protein aggregates in the pathogenesis remains elusive. They are a highly heterogeneous population spanning from the fibrous forms visible in histology to the nanoscopic oligomers, both characterised by various structural conformations. Many of these distinct proteoforms have been created \textit{in vitro} allowing detailed biochemical studies. However, there are gaps between our in vitro understandings of aggregates and their in vivo behaviours. The slow progression of the diseases, low concentration of proteins and involvement of cellular machinery are in contrast with the idealised test tube conditions.

In this work, super-resolution fluorescence imaging is firstly applied for the study of alpha-synuclein, the protein associated with Parkinson's disease. A new method is described combining single-molecule localisation microscopy and an alpha-synuclein aggregate specific aptamer to characterise surface immobilised aggregates. This method is validated on an in vitro alpha-synuclein aggregation time course, before being applied to the imaging of supernatants from a familial Parkinson's disease induced pluripotent stem cell model. The method determines the number density and size distribution of alpha-synuclein oligomers that are below the diffraction limit. Single-molecule localisation microscopy is also applied to characterise alpha-synuclein molecules in mouse brain tissue sections. The last chapter of this work studies the distribution of histological tau tangles in post mortem brain sections which are associated with Alzheimer's disease and several tauopathies. By using a digital pathology approach, cellular segmentation and pathological quantification are conducted with efficiency and reproducibility, allowing single-cell analysis into the distribution pattern of tau aggregates in the brain. Both the single-molecule and single-cell approaches aim to address the heterogeneity associated with aggregated proteins and provide tools for identifying the key molecular or cellular event in the pathogenesis.