Lessons from 3D Reconstruction of Cancer

Imaging biological samples in three dimensions across scales is essential for capturing the complex spatial relationships that govern cancer initiation, invasion, and therapeutic response. As biological inquiry shifts from isolated molecular measurements toward spatially contextualized, multiomic profiling, new strategies have emerged to reconstruct tissue architecture at the whole-organ scale and subcellular resolution. These advances offer more anatomically faithful representations of tissue organization and open doors to integrating morphology with deep multiomic profiling in spatially resolved formats. As a result, we are improving our understanding of inter- and intratumoral heterogeneity and the key role of rare events and minority cell populations in tumor progression. The primary techniques used for 3D imaging of tumors include intact tissue imaging for targeted visualization of biological processes and serial sectioning for integration of diverse, multiomic platforms. In this review, we survey the major technologies used to image tumors in three dimensions, highlighting key methodologies, trade-offs, and recent innovations that make these approaches increasingly central to modern cancer research.