Figure 1.

Experimental paradigm. The stroke model (A), used for the development of the automated algorithm, was first analyzed manually (B), to evaluate the impact of the infarct on microglia morphology (C). (A) The scheme depicts the regions of interest for confocal imaging in the peri-infarct area and the homotypic area in the contralateral cortex 3 days after stroke. Images show representative maximum intensity projections of image stacks at both positions from Iba1-stained brain sections. (B) The schemes illustrate graphically the calculation base for the circularity index (left) and Shoenen ramification index (right) for the manual analysis. (C) Swarm plots show individual cells in the peri-infarct area (peri) and in the contralateral hemisphere (contra) for the manually analyzed circularity index (left) and Shoenen ramification index (right). Seventy-five to seventy-nine cells per region of n = 4 mice, colors correspond to individual mice.