Bladder cancers comprise a heterogeneous spectrum of tumors including those with squamous differentiation such as pure squamous cell carcinoma (SCC). SCC evolves from a dynamic phase transition of microscopically recognizable non-invasive precursor lesions towards invasive cancers. However, precise oncogenic pathways remained elusive and prognostic markers helping to stratify precursor lesions are still missing. Based on molecular studies (genome wide genetic, epigenetic and transcriptomic data) reflecting the whole steps of SCC development, we now aim to decipher the 3D arrangement of transformed cells. This analysis using synchrotron technology would represent the missing piece that will allow us to generally understand the 3D architecture of transformed urinary bladder tissues and to implement these histological features into our pipeline of an integrative analysis considering the molecular available data which to reconstruct a holistic depiction of SCC development.