of previous methods is due to the challenges associated with managing and registering the histopathology and Magnetic Resonance (MR) images, the lack of open source release of existing methods, and the time constraints associated with running these methods.

Specifically, the registration of histopathology images and prostate MRI has the following challenges. Histologic processing of the resected tissue causes artifacts, e.g., deformations, shrinkage, and tissue ripping. Some of these artifacts (e.g., deformation and shrinking) can be corrected through registration, while others (e.g. tissue ripping) are challenging to correct and may result in discarding slices when such artifacts are major. Furthermore, our method and many others [@kalavagunta_registration_2015; @reynolds_development_2015; @wu_system_2019] assume slice-to-slice correspondence between histopathology and MRI images, which can be improved through the use of customized 3D printed molds based on pre-operative MRI [@turkbey_multiparametric_2011]. However, this approach requires a change in clinical protocol that is not present in the vast majority of institutions performing radical prostatectomy. Finally, the acquired data is different between the histopathology images and MRI. Histopathology images provide a discontinuous serial stack of 4$\mu m$ high-resolution colored images with a pixel size of 0.0005 mm separated by roughly 4 mm spaces, while MRI has a typical resolution of 0.4$\times$0.4$\times$4 