Image analysis

All immunohistochemistry images were obtained a Leica DMI6000 motorized inverted microscope. For CD3 and Iba1 quantification, 12 fields of view from 3 sections per mouse were imaged across the cortex. The number of CD3⁺ and Iba1⁺ cells were counted manually. The percent area of Iba1⁺ cells in the cortex was calculated using thresholding with FIJI software⁶⁸. Microglial morphology was analyzed as described previously⁵⁹. Using this method we report ramification as two measures: number of endpoints per cell and summed process length per cell. Image analysis was carried out on the entire field of view. Identification of ZsGreen-expressing neurons was done by imaging and stitching the entire cortex from the 3 most medial sections per mouse and manually counting for ZsGreen⁺ cells. Cyst quantification was done as previously described³¹. In brief, brain sections (12 sections per mouse spanning across a hemisphere) were evaluated on an epifluorescent microscope (EVOS) and the number of Dolichos⁺, mCherry⁺ cysts were counted manually. One type III–infected mouse was excluded as an outlier. Statistical significance is not changed upon the inclusion of the outlier.