Laser Speckle Contrast Imaging (LSCI) has become a widely used technique to image cerebral blood flow in vivo. However, the quantitative accuracy of blood flow changes measured through the thin skull has not been investigated thoroughly. We recently developed a new Multi Exposure Speckle Imaging (MESI) technique to image blood flow while accounting for the effect of scattering from static tissue elements. In this paper we present the first in vivo demonstration of the MESI technique. The MESI technique was used to image the blood flow changes in a mouse cortex following photothrombotic occlusion of the middle cerebral artery. The Multi Exposure Speckle Imaging technique was found to accurately estimate flow changes due to ischemia in mice brains in vivo. These estimates of these flow changes were found to be unaffected by scattering from thinned skull.