Multi-parametric MRI is an indispensable tool for prostate cancer (CaP) management and spatial alignment of in vivo MRI to histopathology is critical for its development. In addition, ex vivo MRI has distinct advantages for investigating ultrahigh-resolution MRI and quantitative MRI of CaP. In this work, we propose a new system for spatial alignment of in vivo MRI, ex vivo MRI, and whole-mount histopathology slides. Results from a pilot study of CaP patients demonstrate successful integration with the clinical workflow and good spatial alignment of the image sets. This new system may enable novel research of CaP biomarkers and predictive models.