Nanobody-based ONE imaging dataset for automated Parkinson's disease analysis based on cerebrospinal fluid samples

ONE microscopy relies on specific epitope recognition, to determine the presence of specific proteins within samples. It has sufficient resolution to then reveal the structural features of the respective protein assemblies. To test this, we sought to address a pathology-relevant imaging challenge, focusing on Parkinson disease PD, a neurodegenerative disease characterized by the accumulation of aggregates composed of several proteins, of which α-synuclein (ASYN) is the most prominent. In the cell, ASYN can exist as a monomer or can assemble into species of different sizes, including soluble oligomers and fibrils. Importantly, ASYN-containing aggregates are present in the cerebrospinal fluid (CSF) and serum of both persons with PD and controls. Thus, simply identifying aggregates is not useful for diagnostics; being able to reveal the toxic ones, those present specifically in persons with PD, would be much more valuable. We analyzed ASYN assemblies in the fluid samples of persons with PD versus controls, labeling ASYN using a previously published nanobody (as in our previous work, Shaib et al., Nat Biotech, 2025, https://www.nature.com/articles/s41587-024-02431-9). Different types of ASYN assemblies could be detected, with different frequencies in different patients. The attached data represent anonymized analyses of fluid samples, from 8 patients. Their identities and phenotypes are masked, to ensure that a long-term double-blind analysis will be performed correctly. Images were captured using a Leica STED and confocal microscope, in ONE microscopy, as described in the publication named above. Each folder contains data from one patient, including an automatically-derived file, termed “all_particles.tif”. The images are then separated into different categories of morphology, which are saved in different folders, including: Annular: circular objects, of variable diameter Large: structures that are beyond the oligomer size, and approach fibril size Multi-single: structures composed of multiple oligomer-like objects Oligo: simple oligomeric structures, with variable shape Small oligo: small objects, corresponding to dimers or tetramers of ASYN Other: all other types of arrangements, typically larger in size than oligomers, but smaller than fibrils The number of files in each folder indicates the frequency of the different types of oligomers for the respective patients. These data are currently being used to optimize a discrimination procedure for PD.