Different tumor micro-environments or habitats are discernible by MRI. In order study these; a co-registration framework was developed using 3D-printed tumor-molds created from in-vivo MRI images of five mice with implanted breast cancer tumors. The results of automated 3D-alignment of MRI images and histology slices are promising and encourage further experiments using the presented workflow. Tumor habitats clustering from multi-parametric MRI images showed encouraging results with similarities to the hypoxic pattern observed by immunohistochemistry. This work will help understanding MRI habitats to monitor cancer evolution as a means to aid treatment decisions in the future.