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The quantification and characterization of aggregated α-²õ²â²Ô³Ü³¦±ô±ð¾±²Ô in clinical samples offer immense potential toward diagnosing, treating, and better understanding neurodegenerative synucleinopathies. Here, we developed digital seed amplification assays to detect single α-²õ²â²Ô³Ü³¦±ô±ð¾±²Ô aggregates by partitioning the reaction into microcompartments. Using pre-formed α-²õ²â²Ô³Ü³¦±ô±ð¾±²Ô fibrils as reaction seeds, we measured aggregate concentrations as low as 4 pg/mL. To improve our sensitivity, we captured aggregates on antibody-coated magnetic beads before running the amplification reaction. By first characterizing the pre-formed fibrils with transmission electron microscopy and size exclusion chromatography, we determined the specific aggregates targeted by each assay platform. Using brain tissue and cerebrospinal fluid samples collected from patients with Parkinson's Disease and multiple system atrophy, we demonstrated that the assay can detect endogenous pathological α-²õ²â²Ô³Ü³¦±ô±ð¾±²Ô aggregates. Furthermore, as another application for these assays, we studied the inhibition of α-²õ²â²Ô³Ü³¦±ô±ð¾±²Ô aggregation in the presence of small-molecule inhibitors and used a custom image analysis pipeline to quantify changes in aggregate growth and filament morphology.