Today one of the main open challenges in cancer treatment is the presence and growth of drug-tolerant persister cells. Innovative studies across multiple scientific fields, such as medicine, biology and biomedical engineering, are being conducted to deepen our understanding of these cells. This thesis presents a contribution to the development of a dual-modality imaging system within the context of the REAP European project, which aims to utilize multiple contrast-enhanced optical techniques to detect and characterize rare cancer cells in therapy-resistant breast cancer models using genetically engineered organoid-based murine mammary tumors. Specifically, this work focuses on the design and implementation of the software architecture required to acquire images using photoacoustic microscopy (PAM) and optical coherence microscopy (OCM) modalities with micrometric resolution.