This dataset contains partial data underlying figure 2 (first 2 rows), 3 and 5 in "Deep Learning-Assisted Co-registration of Full-Spectral Autofluorescence Lifetime Microscopic Images with H&E-Stained Histology Images". The rest of the data in figure 1, 2 (last 3 rows), 4, 6, and 7 are available at https://doi.org/10.7488/ds/3099. The code to post-processing those raw data is also available at https://doi.org/10.7488/ds/3099. The software associated with the paper is available at https://github.com/qiangwang57/coreg_flim_histology.