Neurotoxic deposits of the proteins TDP-43 and FUS play a direct key role in the pathology of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Our working hypothesis is that aggregates composed of TDP-43 and/or FUS can act as biomarkers for ALS and FTD. Hence, the number, morphologies and distributions of such aggregates may inform on the stage of advancement of the disease. With the Target ALS project we aim at applying a new methodology based on the combination of aptamer design and super-resolution microscopy to characterize individual TDP-43/FUS deposits in tissues, guts and bio-fluids of patients. Such approach will clarify which aggregate species can act as biomarkers, with the ultimate intention of generating a potential diagnostic tool, a biomarker for progression, and a platform upon which therapeutic interventions targeting protein aggregation can be tested.