Breast cancer affects 1 in 7 women in Australia, and the risk of death from metastatic (stage 4) disease remains high. In recent years, chemotherapy and new targeted therapies have improved the overall survival of breast cancer patients. However, these treatments do not completely eliminate the risk of disease progression, and metastatic disease and cancer relapse remain difficult to treat. Understanding the interactions between heterogeneous lesions and the blood vessels that facilitate their spread, will enable better characterisation of these metastasis-initiating cells. New methodologies and technologies are required to facilitate such discoveries and are rapidly developing in the fields of microscopy and cancer. Here, we show a novel protocol for 3-dimensional whole organ imaging in a murine model of metastatic breast cancer. Lightsheet microscopy was used to capture large volumetric images, reducing the loss of information observed in single plane 2-dimensional images. We used lentiviral gene ontology (LeGO) vectors, an optical barcoding method, to locate individual clones within heterogenous metastases. In combination with vessel casting, a perfusion-based method that enables vasculature imaging without arduous antibody staining protocols, we reveal the relationship of aggressive breast cancer clones and the blood vasculature in the murine lungs and brain.