Fig. 1.

Quantification of lesion size and location for the two stroke protocols aiming for small (blue) and large (red) infarct, respectively, in the somatosensory and motor cortex. a, d Individual stroke masks based on T2WI were averaged across all mice and plotted as incidence maps and overlay with the Allen Mouse Brain Reference Atlas (ARA). Image sections selected to show the maximal extent of ischemic injury at day 1 and 7 after photothrombosis resulting in small (a) and large (d) strokes. b, e A multi-step registration of the ARA with the T2WI achieved a detailed atlas-based lesion analysis was achieved by a multi-step registration of the ARA with the T2WI. Less brain distortion due to the space occupying effect of the lesion (red area) was visible in small (c) compared with large strokes (f). c, f A landmark-based registration was used to register selected ARA plates with stitched whole mouse brain section histology (GFAP, red; DAPI, blue; scale bar 1 mm) shown here as an overlay with atlas labels for the small (c) and large (f) strokes groups. g Lesion mapping from in vivo and ex vivo imaging summarized as heat maps for small (blue) and large (red) strokes, where the color code indicates the percentage of mice in which a specific brain atlas label was inside the stroke mask at days 1/7 (MRI) and 28* (histology), selected regions only, for the full list see Supplementary Material Fig. 1a. h Calculation of percent infarct per selected brain region corpus callosum (cc), primary somatosensory unassigned (un)/upper limb (ul)/lower limb (ll), and primary and secondary motor area (MOs and MOp). i Quantitative lesion size analysis based on the T2-weighted MRI (left y-axis) and GFAP histology (right y-axis), respectively. j Calculation of percent infarct per selected brain region based on histology for GFAP. Significant differences between the groups at the same time points (*) and at different time points (^#) are shown as */^#p ≤ 0.05, **/^##p ≤ 0.01, and ***/^###p ≤ 0.001, respectively