Open data repository of journal article "Deep learning-based automated lesion segmentation on mouse stroke magnetic resonance images" by Jeehye An et al. At time of publication of this dataset, the manuscript is still under revision. This dataset contains mouse T2 weighted MRI data, and manually and automated segmented ischemic stroke lesion masks for developing and evaluating a deep learning-based automated lesion segmentation. All files are in NIFTI format.