Hc pl apo cs2 100 1.40 oil

Brain tissue slides acquired from patients with Alzheimer’s disease in different stages of severity, were stained with Thioflavin, DAPI and anti-PML antibodies (as described before). The slides were imaged using the Leica TCS SP8 confocal microscope system with a 100× oil objective (HC PL APO CS2 100×/1.40 Oil) and tile scans (10 × 10 tiles) containing amyloidogenic plaques were recorded. Additionally, several plaque-free regions were captured as control (n = 9 from 3 individuals). PML bodies and cell nuclei were identified and counted using the CellProfiler™ Software. In the tile scans, rectangular areas around the plaques were defined as ‘plaque near’ (n = 31 from 8 individuals) and the surrounding area as ‘plaque distant’ (n = 28 from 7 individuals), not including cells close to the edge of the tile scans. The acquired data from CellProfiler™ were exported to Excel, sorted in those two groups and compared regarding the amount of PML bodies inside the cells and the percentage of cells containing those aggregates.

A commercial Leica STED system (HC PL APO CS2 ×100/1.40 OIL) and a Leica confocal microscopy (HC PL APO CS2 ×63/1.40 OIL) were used to acquire the confocal/STED training and testing datasets (Extended Data Fig. 9).