Tissue proteins without antibodies: MorphoProt lets RNA pick the H&E scale, beating SPRINT on held-out tonsil, spleen and liver
Spatial transcriptomics often measures RNA without matching protein, and RNA abundance does not fully reflect protein abundance. MorphoProt uses each spot's RNA expression as a query over five H&E fields of view, then aggregates physical and transcriptomic neighborhoods through gated pathways before jointly decoding the protein panel. On held-out sections of human tonsil, mouse spleen and human liver it reached mean protein-wise Spearman correlations of 0.652, 0.604 and 0.372, above RNA-only, graph-based, HIPI and SPRINT comparisons in all three tissues.