Aggregates of alpha-synuclein (-syn) and tau propagate through template-induced misfolding in the brains of Parkinson\'s (PD) and Alzheimer\'s disease (AD) patients. Prion-like seeding is crucial in disease initiation and progression and represents a major target for drug-modifying therapies. The detection of aggregated -syn and tau seeding activity with seeding amplification assays (SAAs) have remarkable diagnostic and research potential. However, current SAAs rely on bulk tissue homogenates or fluids, losing critical spatial and cellular resolution. Here, we report our novel in situ seeding immunodetection (isSID) assay that enables the visualization of -syn and tau seeding activities with unprecedented morphological detail in intact biological samples. Using the isSID assay, we confirm seeding activity in the pathological aggregates of PD and AD, among others, while uncovering neuron-driven -syn seeding events that precede the onset of clinical symptoms in PD. Our findings provide new fundamental insights into the pathogenesis underlying neurodegeneration and establish an invaluable tool for studying protein aggregation dynamics, with potential applications in biomarker discovery, diagnostics and drug testing.