The top figure shows that the Iba-1 stain density, which we define as the fraction of the area occupied by segmented stain, showed a degree of microgliosis consistent with the disease progression from 2 to 3 to 4 months post-injection. The stain density was initially higher in the ipsilateral side and anterior brain regions, such as the piriform cortex, with more posterior regions, such as entorhinal cortex, and the contralateral hemisphere being affected later in the disease progression. However, a fraction of mice in most PFF-inoculated groups showed levels comparable to mice from the PBS-control groups. In addition, many changes did not show statistical differences. For example, no significant difference was detected in the entorhinal cortex on the contralateral side up to 3 months post-injection.

The middle figure shows the density of cells classified as activated by our model. The metric showed a much clearer distinction between the PFF and the PBS groups. A similar progression in terms of regions and ages was observed, but now generally all mice from the disease groups had several fold higher activated cell density. All comparisons had higher levels of significance. In particular, several new pairwise comparisons became statistically significant.

This difference could also be observed visually as can be seen in the bottom figure. Comparing mice in the median of their respective groups showed the appearance of activated cells (shown by red boxes) in the cortex on the contralateral side at 2 months post-inoculation, even though the density of cells (shown as the blue and red boxes) and Iba1 stain was similar.