In this data report we make available to the community a highly variable longitudinal MRI mouse brain data set of ischemic lesion after transient middle cerebral artery occlusion (tMCAo). Together with the provided semi-automated and automated segmentations, these data can be used to further improve the method proposed by Mulder et al. (2017) and also to serve as a benchmark for comparison between different approaches to segment ischemic lesions in MRI mouse brain data. It can also be used to develop and validate algorithms that further classify the stroke area into core and penumbra.