This article presents a dataset of raw microscopic images of the prefrontal cortex from wistar rat tissues, after an induced stroke, stained with NeuN antibody. The raw images were captured using a microscope equipped with a digital camera. The dataset is useful for testing techniques for the improvement, registration, and stitching to generate a high-resolution image with a full reconstruction of tissues. Besides, this dataset can be used to assess the neuronal brain after an ischemic event. The dataset contains 1370 microscope images with 20x magnification and 36 (Hierarchical Data Format version 5) hdf5 files with homography matrices between every pair of sequential images per tissue rows.