Abstract

Reconstructing 3D molecular volumes from sparsely sampled 2D tissue sections is limited by per-section marker dropout and tissue loss. We present 3D-Omics-Flow, a generative pipeline that jointly repairs damaged sections and interpolates between them at single-cell resolution. Across datasets spanning health and disease, 3D-Omics-Flow expands 3D spatial proteomics to practical sampling regimes, enabling atlas construction and downstream analysis from imperfect 2D section stacks.