Spatial transcriptomics technology is increasingly being applied because it enables the measurement of spatial gene expression in an intact tissue along with imaging morphology of the same tissue. However, current analysis methods for spatial transcriptomics data do not use image pixel information, thus missing the quantitative links between gene expression and tissue morphology.We developed a user-friendly deep learning software, SpaCell, to integrate millions of pixel intensity values with thousands of gene expression measurements from spatially-barcoded spots in a tissue. We show the integration approach outperforms the use of gene-count data alone or imaging data alone to build deep learning models to identify cell types or predict labels of tissue images with high resolution and accuracy.The SpaCell package is open source under a MIT license and it is available at https://github.com/BiomedicalMachineLearning/SpaCell.Supplementary data are available at Bioinformatics online.